A Bibliography of Molecular Computation and Splicing Systems

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• 97a - PSB97
  , editor. Pacific Symposium on Biocomputing. -, 1997, http://WWW-SMI.Stanford.EDU/people/altman/psb97/index.html.
• 97b - SNAC
  SNAC school on natural computation --- working material, August 1997.
• 99 - BioSP3
  , editor. Second Workshop on Bio-Inspired Solutions to Parallel Processing Problems (BioSP3). -, April 12--16 1999. Caribe Hilton, San Juan, Puerto Rico, USA.
• ACD00 - UMC2K
  I. Antoniou, C.S. Calude, and M.J. Dinneen, editors. Unconventional Models of Computation, UMC'2K, Solvay Institutes, Brussels, 13 - 16 December 2000. Center for Discrete Mathematics and Theoretical Computer Science the International Solvay Institute for Physics and Chemistry and the Vrije Universiteit Brussel Theoretical Physics Division, 2000, ISBN 1-85233-415-0.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• ACD04 - ACDvT
  J. J. Arulanandham, C. S. Calude, and M. J. Dinneen. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Balance Machines: Computing = Balancing, pages 36--48. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• AD97 - AmosDunn97
  M. Amos and P. E. Dunne. DNA simulation of boolean circuits. Technical Report CTAG-97009, Department of Computer Science, University of Liverpool, UK, December 1997, http://www.csc.liv.ac.uk/~ctag/archive/t/CTAG-97009.ps.gz.
  Abstract: In this paper we describe a simulation of Boolean circuits using standard bio-molecular techniques. Previously proposed simulations have been shown to run in time proportional to the size of the circuit. The simulation we present here runs in time proportional to the depth of the circuit. We describe the abstract model and its laboratory implementation, before concluding with a brief analysis.
• ADG98
  M. Amos, P. E. Dunne, and A. Gibbons. Efficient time and volume DNA simulation of CREW PRAM algorithms. Technical Report CTAG-98006, Department of Computer Science, University of Liverpool, UK, May 1998, http://www.csc.liv.ac.uk/~ctag/archive/t/CTAG-98006.ps.gz.
  Abstract: We present, in this paper, a detailed translation from algorithms implemented on a standard model of parallel computation - the CREW PRAM - to DNA-based methods. Our translation is efficient in the following sense: if A is a PRAM algorithm using P(n) processors, S(n) space and taking T(n) time then the total volume of DNA used is O(P(n)T(n)S(n)logS(n)); furthermore, the total computation time of the DNA algorithm is bounded by O(T(n)logS(n)). As a consequence our methods give a direct translation from any NC algorithm to an effective DNA algorithm.
• ADHK97 - DM97
  R. Altaman, K. Dunker, L. Hunter, and T. Klein, editors. On some operations suggested by genome evolution, 1997.
  Pacific Symposium on Biocomputing 1997, Hawaii
• ADHK98 - PSB98
  R. Altman, A. Dunker, L. Hunter, and T. Klein, editors. Proceedings of Pacific Symposium on Biocomputing, 3, Kapalua, Maui, January 1998, Hawaii, USA. World Scientific Publishing Company, 1998.
• Adl94
  L. M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021--1024, November 11, 1994, http://www.usc.edu/dept/molecular-science/fp-sci94.ps.
  Abstract: The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.
• Adl95a - Adl95
  L. M. Adleman. On constructing a molecular computer. In R. J. Lipton [DBC], pages 1--22, http://citeseer.nj.nec.com/rd/0%2C148223%2C1%2C0.25%2CDownload/http://citeseer.nj.nec.com/compress/0/papers/cs/1063/http:zSzzSzaid.wu-wien.ac.atzSz frischzSzpaperszSzadleman-construct.ps.gz/adleman95constructing.ps .
  Abstract: It has recently been suggested that under some circumstances computers based on molecular interactions may be a viable alternative to computers based on electronics. Here, some practical aspects of constructing a molecular computer are considered.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• Adl95b - Adl95B
  L. M. Adleman. On the potential of molecular computing - reply. Science, 268(5210):483--484, 1995.
• Adl98
  Leonard M. Adleman. Computing with DNA. Scientific American, 279(2):54--61, August 1998.
  The manipulation of DNA to solve mathematical problems is redefining what is meant by ``computation''.
• ADS+02 - ADeo02
  M. Andronescu, D. Dees, L. Slaybaugh, Y Zhao, A. Condon, B. Cohen, and S. Skiena. Algorithms for testing that DNA word designs avoid unwanted secondary structure. In Hagiya and Ohuchi [PP8], pages 182--195.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• ADS+03 - Andeo03
  M. Andronescu, D. Dees, L. Slaybaugh, Y. Zhao, A. Condon, B. Cohen, and S. Skiena. Algorithms for testing that sets of DNA words concatenate without secondary structure. Natural Computing, 2(4):391--415, 2003.
• aGAMK - BMK01
  Z. R. Boyiadjian ans G. A. Manukyan and A. T. Karapetian. A model of the complexes ethidium bromide with single-stranded poly(dA) and poly(dT). Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• AGDar - AGD
  M. Amos, A. Gibbons, and P. E. Dunne. The complexity and viability of DNA computations. In Bio-Computing and Emergent Computation, Fixme[year], http://www.csc.liv.ac.uk/~ctag/archive/t/CTAG-97001.ps.
  Abstract: In this paper we examine complexity issues in DNA computation. We believe that these issues are paramount in the search for so-called "killer applications", that is, applications of DNA computation that would establish the superiority of this paradigm over others in particular domains. An assured future for DNA computation can only be established through the discovery of such applications. We demonstrate that current measures of complexity fall short of reality. Consequently, we define a more realistic model, a so-called strong model of computation which provides better estimates of the resources required by DNA algorithms. We also compare the complexities of published algorithms within this new model and the weaker, extant model which is commonly (often implicitly) assumed.
• AGH96a - AGH96
  M. Amos, A. Gibbons, and D. Hodgson. Error-resistant implementation of DNA computation. In Landweber and Baum [2AWDBC], http://www.csc.liv.ac.uk/~martyn/princeton.ps. Previously: Research Report CS-RR-298, Department of Computer Science, University of Warwick, Coventry CV4 7AL, England, January 1996.
  Description: This paper introduces a new model of computation that employs the tools of molecular biology whose implementation is far more error-resistant than extant proposals. We describe an abstraction of the model which lends itself to natural algorithmic description, particularly for problems in the complexity class NP. In addition we describe a number of linear-time algorithms within our model, particularly for NP-complete problems. We describe an in vitro realization of the model and conclude with a discussion of future work.
  A [Lipton95A]-like model designed for error-resistance. ``The main advantage of our model is that it doesn't repeatedly use the notoriously error-prone separation by DNA hybridization method to extract strands containing a certain subsequence.'' Instead, strands complementary to the undesired sequences are added, causing them to form dsDNA that can be cut with restriction enzymes with nearly 100 effectiveness.
• AGH96b - AGH96-2
  Martyn Amos, Alan Gibbons, and David Hodgson. A new model of DNA computing. In 12th British Colloquium on Theoretical Computer Science, University of Kent, UK, April1--4, 1996.
• AHSar - Arita97
  Masanori Arita, Masami Hagiya, and Akira Suyama. Joining and rotating data with molecules. In IEEE International Conference on Evolutionary Computation, pages 243--248, Fixme[year], ftp://nicosia.is.s.u-tokyo.ac.jp/pub/staff/arita/icec97.ps.gz, http://ylab-gw.cs.uec.ac.jp/../Papers/MCP/abst.ps.gz.
  Abstract: DNA-based computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported in experiments. We suggest a data encoding in the form of (tag data tag)⁺, and report our experimental results of performing concatenation and rotation of DNA. Our results also show the possibility of join and other operations in relational database with molecules.
• Alf98
  G. Alford. An explicit construction of a universal extended H system. In Calude et al. [UMC98], pages 108--117.
  Abstract: Lately there has been much interest concerning H systems, a generative mechanism based on the splicing operation, itself a language-theoretical equivalent of DNA recombination. Paun et al. have shown that regular extended H systems are theoretically universal but one has not yet been explicitly constructed. In this paper we describe how to explicitly construct universal extended H systems.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Ame95a - AmenComputer
  John-Thones Amenyo. BIOCOMPUTERS: Architecture, engineering and technology, ftp://ftp.ans.net/pub/misc/biocomputer.txt. Fixme: [Status?], January 1995.
• Ame95b - AmenFlow
  John-Thones Amenyo. What is a computer?, ftp://ftp.ans.net/pub/misc/biocompflow.txt. Fixme: [Status?], 1995.
• Ame96a - Amenyo96
  J.-T. Amenyo. Mesoscopic computer engineering: Automating DNA-based molecular computing via traditional practices of parallel computer architecture design. In Landweber and Baum [2AWDBC], ftp://ftp.ans.net/pub/misc/jta/DNAComparch.ps.gz.
  Abstract: How does one go about automating the steps of DNA computing, or what amounts to the same thing, the practical engineering of hands-free, general-purpose DNA computers? The intent of this paper is to indicate how familiar computer design principles for electronic computers can be exploited to build practical computers at the mesoscopic scales of macromolecules and bio-polymers. DNA computing is the most realistic harbinger of such molecular computers. Pragmatically, it is expected that DNA computer architectures will be used routinely and not just for solving theoretically hard computational problems. The ideas discussed here are akin to the design of a practical programming language for a virtual computer. The paper shows that all proposed DNA computing algorithms can be run on parallel computer architectures configured from trellis/lattice banks, filter banks and switching banks. Thus, DNA computation can be re-interpreted as dataflow (or signal flow) networks and subject to conventional treatment.
• Ame96b - AmenyoReport96
  John-Thones Amenyo. Workshop report: Personal impressions about the 2nd Annual Workshop on DNA Computing, June 21, 1996, ftp://ftp.ans.net/pub/misc/jta/DNAComp2rept.txt.
• Ame97 - AmenyoReport97
  John-Thones Amenyo. Workshop report: Personal impressions about the 3rd Annual Workshop on DNA Computing, November 5, 1997, ftp://ftp.ans.net/pub/misc/jta/DNAComp3rept.txt.
• Amo96 - Amos96
  Martyn Amos. DNA computing - harnessing the double helix. Nanotechnology Magazine Pre-press Monthly, September 1996, http://www.csc.liv.ac.uk/~martyn/nano.html.
• Amo97 - Amos97
  Martyn Amos. DNA Computation. PhD thesis, Department of Computer Science, University of Warwick, UK, September 1997, http://www.csc.liv.ac.uk/~ctag/archive/th/amos-thesis.ps.gz. Abstract at http://www.csc.liv.ac.uk/~ctag/archive/th/amos-thesis.ab.html.
• Amo01 - Amos01
  M. Amos. Theoretical and experimental DNA computation, volume -, pages 614--630. World Scientific, 2001.
• AMV00a - AMV00-1
  A. Atanasiu and C. Martín-Vide. P systems with context-free languages. unpublished, 2000.
• AMV00b - AMV00
  A. Atanasiu and C. Martín-Vide. Recursive calculus with membranes. unpublished, 2000.
• AMVP04 - AVPvT
  A. Alhazov, C. Martín-Vide, and L. Pan. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Solving Graph Problems by P Systems with Restricted Elementary Active Membranes, pages 1--22. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Ari - Arita03
  M. Arita. DNA sequence design using multiple templates. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• Ari04 - AvT
  M. Arita. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Writing Information into DNA, pages 23--35. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• ARRW96 - Adl96
  L. M. Adleman, P. W. K. Rothemund, S. Roweis, and E. Winfree. On applying molecular computation to the data encryption standard. In Landweber and Baum [2AWDBC], ftp://hope.caltech.edu/pub/pwkr/DIMACS/des.ps.
  Abstract: Recently, Boneh, Dunworth, and Lipton described the potential use of molecular computation in attacking the United States Data Encryption Standard (DES). Here, we provide a description of such an attack using the sticker model of molecular computation. Our analysis suggests that such an attack might be mounted on a table-top machine, using approximately a gram of DNA and might succeed even in the presence of a large number of errors.
• Ata96 - Atan96
  A. Atanasiu. On the free crossovering operation. Ann. Univ. Buc., Matem.-Inform., 45:3--8, 1996.
• Ata99 - At99
  A. Atanasiu. About a class of P systems. manuscript, 1999.
• Ata00
  A. Atanasiu. Arithmetic with membranes. In Calude et al. [WMP2000], pages 1--17.
  Abstract: P systems are computing models, where certain objects can evolve in parallel into an hierarchical structure. Recent results show that this model is a promising framework for solving NP complete problems in polynomial time.
  The present paper considers the possibility to perform operations with integer numbers in a P system. All four arithmetical operations are implemented in a way which seems to have a lower complexity that when implementing in usual computer architecture.
  TR140, CDMTCS, Univ. Auckland
• AU71
  A. V. Aho and J. D. Ullman. The theory of parsing, translation and compiling. Prentice Hall, Englewood Cliffs, N.J., 1, 1971.
• AU73
  A. V. Aho and J. D. Ullman. The theory of parsing, translation and compiling. Prentice Hall, Englewood Cliffs, N.J., 2, 1973.
• AWH+98 - AWHOG98
  M. Amos, S. Wilson, D. A. Hodgson, G. Owenson, and A. Gibbons. Practical implementation of DNA computations. In Calude et al. [UMC98], pages 1--18.
  Abstract: Several theoretical models of DNA computation have been proposed since Adleman's original experiment, but there has been a shortage of empirical results in the literature. In this paper we describe preliminary investigations into the laboratory implementation of one existing model, the parallel filtering model. We describe the lessons to be drawn form such experiments, and show how techniques such as PCR and affinity purification may be replaced by more error-resistant alternatives. We also describe one possible solution to the problem of solution read-out.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• AYT+99 - YoshiEA98
  Y. Aoi, T. Yoshinobu, K. Tanizawa, K. Kinoshita, and H. Iwasaki. Ligation errors in DNA computing. In Kari et al. [P4], pages 181--187.
  Abstract: DNA computing is a novel method of computing proposed by Adleman (1994), in which the data is encoded in the sequence of oligonucleotides. Massively parallelism reactions between oligonucleotides are expected to make it possible to solve huge problems. In this study, reliability of the ligation process employed in the DNA computing is tested by estimating the error rate at which wrong oligonucleotides are ligated. Ligation of wrong oligonucleotides would result in a wrong answer in the DNA computing. The dependence of the error rate on the number of mismatches between oligonucleotides and on the combination of bases is investigated.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• BACG - BACG01
  A. V. Baranda, F. Arroyo, J. Castellanos, and R. Gonzalo. Towards an electronic implementation of membrane computing: a formal description of non-deterministic evolution in transition p-system. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• BACG01 - BCeo01
  A. Baranda, F. Arroyo, J. Castellanos, and R. Gonzalo. Towards an electronic implementation of membrane computing: a formal description of nondeterministic evolution in transition P systems. submitted, 2001.
• BAPE+03 - BAeo03
  Yaakov Benenson, Rivka Adar, Tamar Paz-Elizur, Zvi Livneh, and Ehud Shapiro. Dna molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA, 2003, http://www.pnas.org/cgi/content/abstract/0535624100v1. Published on line before print.
  Abstract: The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule/input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software/input hybrid. In the previous automaton, software/input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x 1012 automata per µl performing 6.6 x 1010 transitions per second per µl with transition fidelity of 99.9%, dissipating about 5 x 10-9 W/µl as heat at ambient temperature.
• Bau - BaumOrgano
  Eric B. Baum. Computing with DNA. Talk Given at the Organo Electronic Materials Conference, http://www.neci.nj.nec.com/homepages/eric/talk.ps.
• Bau95a - Baum
  E. A. Baum. A DNA associative memory potentially larger than the brain. In R. J. Lipton [DBC], pages 23--28.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• Bau95b - Baum95
  E. B. Baum. Building an associative memory vastly larger than the brain. Science, 268:583--585, April 28, 1995. Also in [Baum].
  Abstract: The techniques of [Adl94] and [Lipton94] may be usable to construct an associative (= content-addressable) memory with a capacity that exceeds that of the human brain. Given a part of the content, this part can be used in extracting those molecules that match it. The ``cue'' can be used e.g.\ with magnetic bead extraction.
• Bau96a - Baum96-2
  Eric B. Baum. DNA sequences useful for computation, http://www.neci.nj.nec.com/homepages/eric/seq.ps. -, June 1996.
  Abstract: Recent proposals for DNA based computing [Adl94], [Lipton95A], [Baum95] encode Boolean vector component values with sequences of DNA. It has previously been assumed that sufficient length random subsequences could be used to encode component values. However use of such subsequences will inadvertently result in long complementary subsequences. Complementary subsequences of sufficient length would stick to each other and cause mistakes or delays in computation. We suggest some constraints on DNA subsequences to be used in encodings, and describe maximal sets of subsequences satisfying these constraints.
  [Adl94][Lipton94] work with codes based on random subsequences of DNA as codewords. In strings in these codes, there may be long complementary subsequences that can result in undesired annealing. Furthermore, the codewords might even self-anneal. In this paper, the problem of finding a code that does not suffer from these problems is formalized and solved. A similar code is termed unequivocable in [Beav95C].
• Bau96b - Baum96-3
  Eric B. Baum. Will future computers be made of DNA? Windows Magazine, June 1996, http://www.neci.nj.nec.com/homepages/eric/window.ps.
• BB96 - BaumBoneh96
  E. B. Baum and D. Boneh. Running dynamic programming algorithms on a DNA computer. In Landweber and Baum [2AWDBC], http://www.neci.nj.nec.com/homepages/eric/dpr.ps.
  Abstract: In this paper we show that DNA computers are especially useful for running algorithms which are based on dynamic programming. This class of algorithms takes advantage of the large memory capacity of a DNA computer. We present algorithms for solving certain instances of the knapsack problem using a dynamic programming approach. Unlike other algorithms [Adl94], [Lipton95A] for DNA computers, which are brute force, dynamic programming is the same algorithm one would use to solve (smaller) problems on a conventional computer.
• BB99
  B. Bloom and C. Bancroft. Liposome-mediated biomolecular computation. In Winfree and Gifford [P5], pages 39--48, http://inka.mssm.edu/cb.
  Abstract: Biological vesicles are composed of a phospholipid membrane bilayer, which has folded on itself to form a spherical structure with an aqueous cavity. We propose that synthetic vesicles, termed liposomes, composed of specific species of phospholipids might provide a useful architecture for the execution of some existing algorithms for DNA based computation. In this model, the liposomes would serve simultaneously as water-filled chambers containing specific DNA reactants; and as valves to permit, via controlled fusion, interaction of only the DNA molecules and possibly enzymes appropriate for a particular stage of computation.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• BBF+ - BBeo00
  E. Best, H. Burchard, H. Fleischhack, A. Hackmann, S. Kuhnapfel, E. Kretschmann, and A. Rakow. Simulation of DNA computing. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• BCAG - BCAG00
  A. V. Baranda, J. Castellanos, F. Arroyo, and R. Gonzalo. Data structures for implementing P systems in silico. In Calude et al. [WMP2000], pages 21--34.
• BCAL01 - BCAeo01
  A. Baranda, J. Castellanos, F. Arroyo, and C. Luengo. Bio-language for computing with membranes. In J. Kelemen and P. Sasik, editors, Proc. ECAL 2001, Praga, LNAI, pages 176--185. Springer Verlag, Berlin, Heidelberg, New York, 2001.
• BCD+03 - Bieo03
  H. Bi, J. Chen, R. Deaton, M. Garzon, H. Rubin, and D. H. Wood. In vitro selection of non-crosshybridizing oligonucleotides for computation. Natural Computing, 2(4):417--426, 2003.
• BCGT96 - BachEA96
  Eric Bach, Anne Condon, Elton Glaser, and Celena Tanguay. DNA Models and Algorithms for NP-complete Problems, pages 290--299. IEEE Computer Society Press, 1996, http://www.cs.wisc.edu:80/%7Econdon/papers/bcgt.ps. Proceedings of the 11th Conference on Computational Complexity.
  Abstract: A goal of research on DNA computing is to solve problems that are beyond the capabilities of the fastest silicon-base supercomputers. Adleman and Lipton present exhaustive search algorithms for 3SAT and 3-Coloring, which can only be run on small instances and hence are not practical. In this paper, we show how improved algorithms can be developed for the 3-Coloring and Independent Set problems. Our algorithms use only the DNA operations proposed by Adleman and Lipton, but combine them in more powerful ways, and use polynomial preprocessing on a standard computer to tailor them to the specific instance to be solved. The main contribution of this paper is a more general model of DNA algorithms than that proposed by Lipton. We show that DNA computation for NP-complete problems can do more than just exhaustive search. Further research in this direction will help determine whether or not DNA computing is viable for NP-hard problems. A second contribution is the first analysis of errors that arise in generating the solution space for DNA computation.
• BCJ+02 - BCeo02
  R. S. Braich, N. Chelyapov, C. Johnson, P. W. K. Rothemund, and L. Adleman. Solution to a 20-variable 3-SAT problem on a DNA computer. Science, 296(5567):499--502, 2002.
• BCM+ - BCMeo01
  A. Baranda, J. Castellanos, R. Molina, F. Arroyo, and L. F. Mingo. Data structures for implementing transition P systems in silico. In Calude et al. [WMP2000], pages 21--34.
  TR140, CDMTCD, Univ. Auckland
• BCM+00 - BCM00
  A. Baranda, J. Castellans, R. Molina, F. Arroyo, and L. F. Mingo. Data structures for implementing transition P system in silico. In Calude et al. [WMP2000], pages 21--34.
  Too long abstract
• BDL95 - BDL96
  D. Boneh, C. Dunworth, and R. J. Lipton. Breaking DES using a molecular computer. In R. J. Lipton [DBC], pages 37--66.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• BDLS96a - BonehEA96
  D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall. Making DNA computers error resistant. In Landweber and Baum [2AWDBC].
  Abstract: We describe methods for making volume decreasing algorithms more resistant to certain types of errors. Such error recovery techniques are crucial if DNA computers ever become practical. Our first approach relies on applying PCR at various stages of the computation. We analyze its performance and show that it increases the survival-probability of various strands to acceptable proportions. Our second approach relies on changing the method by which information is encoded on DNA strands. This encoding is likely to reduce false negative errors during the bead separation procedure.
  Introduces two methods to deal with common sources of errors:
  • PCR after each selection step is shown to increase good strands' survival probability (for volume-decreasing algorithms such as Adleman's or Lipton's).
  • Double encoding improves the probability that correct strands are extracted.
  Note that [KaplanEA96][Smith] suggest PCR may be a major source of errors itself!
• BDLS96b - biocircuit
  D. Boneh, C. Dunworth, R. J. Lipton, and J. Sgall. On the computational power of DNA. Discrete Applied Mathematics, 71(1-3):79--94, 1996. Also Technical Report, TR-499-95, Princeton University, october 1995. ftp://ftp.cs.princeton.edu/pub/people/dabo/biocircuit.ps.Z, ftp://ftp.cs.princeton.edu/reports/1995/499.ps.Z.
  Abstract: We show how DNA-based computers can be used to solve the satisfiability problem for boolean circuits. Furthermore, we show how DNA computers can solve optimization problems directly with problems. Our methods also enable random sampling of satisfying assignments.
• Bea94 - Beav94
  D. Beaver. Factoring: The DNA solution. In J. Pieprzyk and R. Safavi-Naini, editors, Advances in Cryptology - Asiacrypt '94 Proceedings 4th International Conference on the Theory and Applications of Cryptology, volume 917 of Lecture Notes in Computer Science, pages 419--423, Wollongong, Australia, November--December 1994. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-59339-X, http://www.transarc.com/afs/transarc.com/public/beaver/html/research/alternative/molecute/publications/b94asia.ps.
  Summary How to factor and compute NP functions using DNA, using a novel procedure for site-directed mutagenesis.
  Abstract: We consider molecular models for computing and derive a DNA-based mechanism for solving intractable problems through massive parallelism. In principle, such methods might reduce the effort needed to solve otherwise difficult tasks, such as factoring large numbers. We investigate the application of such techniques to cryptography.
  Extended abstract. The full version is [Beav95A]
• Bea95a - Beav95A
  D. Beaver. Computing with DNA. Journal of Computational Biology, 2(1):1--8, 1995.
  Summary How to factor and compute NP functions using DNA, using a novel procedure for site-directed mutagenesis.
  Abstract: We consider molecular models for computing and derive a DNA-based mechanism for solving intractable problems through massive parallelism. In principle, such methods might reduce the effort needed to solve otherwise difficult tasks, such as factoring large numbers, a computationally-intensive task whose intractability forms the basis for much of modern cryptography.
• Bea95b - Beav95B
  D. Beaver. Molecular computing. Technical Report TR95-001, Penn State University, January 31 1995.
  Summary How to build and operate a Turing machine consisting of a single DNA molecule. How to compute NP and PSPACE functions using massively parallelized molecular computations. (Refinements, such as a more efficient encoding, or simplified experimental techniques, are not included.)
  Abstract: We design a molecular Turing machine and determine the complexity of the problems solvable by molecular computers. In [Adl94], a combinatorial molecular experiment to solve the NP-complete problem of Hamiltonian Path was proposed and implemented. Using our design, we show that such molecular computers can in fact compute PSPACE, under the generous assumptions implicit in [Adl94]. Under stronger and somewhat more practical restrictions, which [Adl94] fails to satisfy, we show that molecular computers are limited to solving problems in P.
• Bea95c - Beav95D
  D. Beaver. A universal molecular computer. In R. J. Lipton [DBC], pages 29--36.
  Summary How to build and operate a Turing machine consisting of a single DNA molecule. How to compute NP and PSPACE functions using massively parallelized molecular computations. (Refinements, such as a more efficient encoding, or simplified experimental techniques, are not included.)
  Abstract: We design a molecular Turing machine and determine the complexity of the problems solvable by molecular computers. Interest in ``nanocomputation'' has been sparked by Adleman's recent experiment demonstrating the possibility that molecular computers might solve intractable problems, such as Hamiltonian Path, using large-scale parallelism achievable only through molecular-scale miniaturization. We propose a method for site-directed mutagenesis (namely, a molecular ``editing'' reaction) and use it to build a universal computer, stepping beyond Adleman's special-purpose, one-time problem solver. Using the generous assumptions on parallelism implicit in Adleman's methods, we show that molecular computers can in fact compute PSPACE. Under stronger and more realistic restrictions, we show that molecular computers --- both ours and Adleman's --- are limited to solving problems in BPP.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• Bea96 - Beav95C
  D. Beaver. Universality and complexity of molecular computation. Unpublished, 1996.
  Abstract: Adleman recently designed and executed an experiment to solve instances of the Hamiltonian Path problem using DNA molecules ([Adl94]). Two questions naturally arise, both of which we answer in this paper: First, is universal computation possible? Second, does NP characterize the limit of such computation? We design a (nondeterministic) Turing machine based on interactions of small DNA molecules, supporting general-purpose computation rather than just special-purpose oracle queries. Our construction supports massively parallel, synchronized operations of heterogeneous, communicating, nondeterministic Turing machines, using fairly conventional techniques from molecular biology. In the loosely restricted model implicit in Adleman's solution to Hamiltonian Path, we show that molecular computation is capable not merely of NP but of PSPACE. More generally, our results show how to utilize the parallelism of molecular computation to conduct any S(n)-space-bounded computation in O(S(n)) laboratory steps using molecules of size O(S(n)).
• Ben93 - Benne93
  R. Benne, editor. RNA-Editing : The Alteration of Protein Coding Sequences of RNA. Ellis Horwood, 1993.
• Ber96 - Bertone96
  Paul Bertone. Combinatorial solution of search problems via biomolecular computation in vivo, http://www.umassd.edu/public/people/pbertone/research/Biocomp_Rev_2-27.ps.Z,. Draft, February 1996.
  Description: A model is developed for recombinant DNA-based computation realized via genetic engineering of a living component. It is shown that solutions to arbitrarily large combinatorial formulas may be generated in constant time. We further show the solution of NP-hard optimization problems to be straightforward using this method. Some foundations of hard computational problems are briefly introduced, followed by an overview of previous in vitro biomolecular computing strategies and the design of the new algorithm.
• Ber03 - Berman03
  H. Berman. How the protein data bank and nucleic acid database enable structural bioinformatics. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 1, 2003.
• Bes00
  D. Besozzi. P systems with gemmation. Master Thesis, Univ. Insubria, Como, Italy, 2000.
• BF97
  R. Beigel and B. Fu. Molecular computing, bounded nondeterminism, and efficient recursion. In Proceedings of the 24th International Colloquium on Automata, Languages, and Programming, number 1256 in Lecture Notes in Computer Science, pages 816--826, 1997, http://www.eecs.lehigh.edu/~beigel/papers/bf-dnaalgorithms-tr.PS.gz. Also in Algorithmica, 25 (2-3), 222-238 (1999).
  Abstract: The maximum number of strands used is an important measure of a molecular algorithm's complexity. This measure is also called the space used by the algorithm. We show that every NP problem that can be solved with b(n) bits of nondeterminism can be solved by molecular computation in a polynomial number of steps, with four test tubes, in space 2 b(n) . In addition, we identify a large class of recursive algorithms that can be implemented using bounded non determinism. This yields improved molecular algorithms for important problems like 3-SAT, independent set, and 3-colorability.
• BF98
  Richard Beigel and Bin Fu. Solving intractable problems with DNA computing. http://www.eecs.lehigh.edu/~beigel/papers/bf-dnasurvey-complexity98.PS.gz, 1998.
  Abstract: We survey the theoretical use of DNA computing to solve intractable problems. We also discuss the relationship between problems in DNA computing and questions in complexity theory.
• BFMZ03 - BFMZ00
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. DNA and circular splicing. In Condon and Rozenberg [P6], pages 117--129.
  Abstract: Circular splicing has been very recently introduced to model a specific recombinant behavior of circular DNA, carrying on the investigation initiated with linear splicing. In this paper we restrict ourselves to the relationship between circular regular languages and circular splicing languages. We provide partial results toward a characterization of the class of circular regular languages generated by finite circular splicing systems. Using automata theory and combinatorial techniques on words, we show that a subclass of star languages (i.e. languages X* closed under conjugacy relation and with X a regular language) are circular splicing languages. In particular, star languages with X being a finite set or X* being a free monoid belong to this subclass.
• BFMZ01a - BFMZ01-3
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. Developments on circular splicing, September 2001. scheduled talk at WORDS01, Palermo, Italy.
  Abstract: In this paper we carry on the investigation initiated in [BFMZ00], [BFMZ01-2], [BFMZ01-1], where some results are given about the computational power of finite (Paun) circular splicing systems, with no additional hypothesis. More precisely, we focus our interest on which kind of regular circular languages are generated by circular splicing with both finite I and R. We prove that we can decide whether a regular language on one-letter alphabet is generated by a finite Paun circular splicing system. We presents a circular regular language which is neither Paun nor Pixton generated, proving that the class of circular regular splicing languages is a proper subset of the class of all circular regular languages. Finally, we introduce a class of circular regular languages which are generated by circular Pixton splicing.
• BFMZ01b - BFMZ01-1
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. Linear and circular splicing. Presented at Words99 (Rouen, France), 2001.
• BFMZ01c - BFMZ01
  P. Bonizzoni, C. Ferretti, G. Mauri, and R. Zizza. Separating some splicing models. Information Processing Letters, 79(6):255--259, 2001.
  Abstract: In this paper we show that the three main definitions of the splicing operation known in the literature, i.e. Head's, Paun's and Pixton's definitions, give rise to different subclasses of regular languages, when a finite set of rules is iterated on a finite set of axioms. More precisely, we show that the family of regular languages generated by finite splicing as defined in the early paper by Head, is strictly included in the family defined later by Paun, which is in turn strictly included in the splicing family defined by Pixton. We describe instance languages in the difference sets, and we prove how they cannot be generated by the smaller families.
• BFMZ02a - BFMZ02
  D. Besozzi, C. Ferretti, G. Mauri, and C. Zandron. Parallel rewriting P systems with deadlock. In Hagiya and Ohuchi [PP8], pages 302--314.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• BFMZ02b - BFMZ02-1
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. Decision problems for linear and circular splicing systems. In M. Ito and M. Toyama, editors, DLT 2002, LNCS 2450, pages 78--92, 2002.
  Abstract: In a formal language framework, we consider linear and circular splicing systems. We deal with the problem of deciding whether a regular language L is generated by a finite Paun (linear or circular) splicing system. Using the syntactic monoid of L, we give a class of languages which are generated by linear splicing. We characterize those circular unary languages L' which are generated by a finite Paun circular splicing system. We prove that we can decide whether a regular language L' belongs to this class. We give a description of a minimal finite Paun circular splicing system generating L'
• BFMZ02c - BFMZ02-2
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. On the power of linear and circular splicing, 2002. Submitted.
  Abstract: Looking for a characterization of the proper subclass of regular languages which are generated by Paun linear systems, we consider the still open problem of deciding whether a regular language belongs to this class of languages. We show via automata properties that we can decide whether or not a regular language on a one-letter alphabet is generated by finite (Paun) circular splicing systems. The characterization of such languages have been previously done and is generalized here to some languages on alphabets of any cardinality. Nevertheless, we exhibit a circular regular language that cannot be generated by any finite circular splicing system.
• BFMZ03a - BFMZ01-2
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. Circular splicing and regularity. accepted for publication in Theoretical Informatics and Applications, 2003.
  Abstract: Circular splicing has been very recently introduced to model a specific recombinant behaviour of circular DNA, continuing the investigation initiated with linear splicing. In this paper we restrict ourselves to the relationship between circular regular languages and languages generated by finite circular splicing systems and provide some results toward a characterization of the intersection between these two classes. We consider a class of languages X<sup>*</sup>, called here star languages, which are closed under conjugacy relation and with X being a regular language. Using automata theory and combinatorial techniques on words, we show that for a subclass of star languages the corresponding circular languages are (Paun) circular splicing languages. For example, star languages belong to this subclass when X<sup>*</sup> is a free monoid or X is a finite set. We also give a characterization of Paun circular splicing language over a one-letter alphabet. Cyclic and weak cyclic languages, which will be introduced in this paper, show that this result does not hold when we increase the size of alphabets, even if we restrict ourselves to regular languages.
• BFMZ03b - BFeo03
  P. Bonizzoni, C. De Felice, G. Mauri, and R. Zizza. Regular languages generated by reflexive finite splicing systems. In Z. Esik and Z. Fulop, editors, Developments in Language Theory, DLT, pages 134--145, 2003. Szeged, Hungary, July 7-11, LNCS 2710.
  Abstract: In this paper we will face the problem of characterizing the class of regular languages generated by finite splicing systems. We will solve this problem for the special class of the reflexive finite splicing systems, introduced in [Head97] and for each of the three definitions of splicing given by Head, Paun and Pixton. As a byproduct, we give a characterization of the regular languages generated by finite Head splicing systems. As in already known results, the notion of constant, given by Schutzenberger, intervenes.
• BGH04 - BGHvT
  F. Bernardinia, M. Gheorghe, and M. Holcombe. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Eilenberg P Systems with Symbol-Objects, pages 49--60. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Bis98 - Biswas98
  S. Biswas. A note on DNA representation of binary strings. In Paun [CBMtitle], pages 153--157.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• BJR+00 - BJeo00
  R. S. Braich, C. Johnson, P. W. K. Rothemund, D. Hwang, N. Chelyapov, and L. M. Adleman. Solution of a satisfiability problem on a gel-based DNA computer. In Condon and Rozenberg [P6], pages 27--42.
  Abstract: We have succeeded in solving an instance of a 6-variable 11-clause 3-SAT problem on gel-based DNA computer. operations were performed using probes covalently bound to polyacrylamide gel. During the entire computation, NA was retained within a single gel and moved via electrophoresis. The method used appear to be readily automat able and should be suitable for problems of a significant larger size.
• BK04 - BKvT
  M. Sakthi Balan and K. Krithivasan. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Realizing Switching Functions Using Peptide-Antibody Interactions, pages 353--360. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• BKR99
  T. B\"ack, J. N. Kok, and G. Rozenberg. Evolution as computation, chapter Evolutionary computation as a paradigm for DNA-based computing, pages 15--40. In Landweber and Winfree [LW99], 1999.
• BKW02
  S. Basu, D. Karig, and R. Weiss. Engineering signals processing in cells: Towards molecular concentration band detection. In Hagiya and Ohuchi [PP8], pages 61--72.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• BKW03
  S. Basu, D. Karig, and R. Weiss. Engineering signal processing in cells: Towards molecular concentration band detection. Natural Computing, 2(4):463--478, 2003.
• BL95 - biobatch
  Dan Boneh and Richard J. Lipton. Batching DNA computations, ftp://ftp.cs.princeton.edu/pub/people/dabo/biobatch.ps.Z. -, 1995.
  Description: In this short note we point out that in some cases batching computations on a molecular computer is very cheap. This is especially useful for breaking cryptosystems and can be useful for other applications as well.
• BL96 - bioseq
  D. Boneh and R. J. Lipton. A divide and conquer approach to sequencing. In Landweber and Baum [2AWDBC], ftp://ftp.cs.princeton.edu/pub/people/dabo/bioseq.ps.Z.
  Description: We suggest an approach to sequencing based on a ``divide and conquer method''. This approach eliminates the need for solving a hard NP-complete problem which arises when using traditional sequencing techniques. At the present time this algorithm has not been tried out in the lab. However, computer simulations using parts of the human genome provide some encouraging data.
• BLMM
  P. Bottoni, A. Labella, V. Manca, and V. Mitrana. Superpositions based on watson-crick complementarity. Theory of Computing Systems.
  submitted to Information and Computation
• BLMVP00 - BLMeo00
  P. Bottoni, A. Labella, C. Martín-Vide, and G. Paun. Rewriting P systems with conditional communication. unpublished, 2000.
• Blu96 - Blumb97
  A. J. Blumberg. Parallel computation on a DNA substrate. In Landweber and Baum [2AWDBC].
  The preliminary proceedings contain [Adl96], [Amenyo96], [AGH96], [bioseq]. [BaumBoneh96], [BonehEA96], [DMGFS96], [GuaranieriBancroft96], [JonaskaKarl96], [KaplanEA96], [KurtzEA96], [LeeteEA96], [LiuEA96], [Mir96], [Oliver96], [Paun96], [RoweisEA96], [SeemanEA96], [WilliamsWood96], [Winf96], [Blumb97]. Program committee: E. B. Baum, D. Boneh, P. Kaplan, R. Lipton, J. Reif and N. C. Seeman.
• Blu97 - Blumberg97
  A. J. Blumberg. Parallel computation on a DNA substrate. In Rubin and Wood [P3], pages 275--289.
  Abstract: Much work in DNA computing has focused on solution of problems under a passive computational paradigm; all possible solutions are generated and incorrect solutions are filtered away. In this paper it is argued that such a model of computing is inadequate and a methodology for performing various forms of active computation is presented. Within this framework, I describe how to perform the parallel evaluation of continuous functions, how to compute boolean circuits, and I present a direct simulation of a Connection Machine (a massively parallel SIMD computer). There is also a brief presentation of an implementation of a genetic algorithm. Although the algorithms are presented in an error-free regime, I discuss a strategies for ensuring that these algorithms could actually be carried out experimentally.
• BM02
  R. Barua and J. Misra. Binary arithmetic for DNA computers. Poster paper at the 8th International Workshop on DNA-Based Computers, Sapporo, Japan, 10-13 June, 2002.
• BMFZ00
  P. Bonizzoni, G. Mauri, C. Ferretti, and R. Zizza. Separating some splicing models. In International Workshop Grammar Systems 2000 (R. Freund, A. Kelemenova), Bad Ischl, Austria, July 2000, pages 55--60, 2000.
  Abstract: This work shows that the family of languages generated by splicing as defined in the early paper by T. Head is strictly included in the family defined by later definitions by Head , G. Paun, and others. It also proves the strict inclusion of this latter family in the splicing family defined by D. Pixton when proving the regularity of splicing languages. We describe instance languages in the difference sets, and prove how they cannot be generated by the smaller families.
• BMVPR00 - BMPR00
  P. Bottoni, C. Martín-Vide, G. Paun, and G. Rozenberg. Membrane systems with promoters/inhibitors. unpublished, 2000.
• BMZ03
  D. Besozzi, G. Mauri, and C. Zandron. Deadlock decidability in partial parallel P systems. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 52--56, 2003.
• BNPJSC02 - BPS02
  D. Balbontin-Noval, M.J. Perez-Jimenez, and F. Sancho-Caparrini. A mzscheme implementation of transition p systems. Lecture Notes in Computer Science, 2597, 2002. To appear.
  Abstract: The main goal of this paper is to present the design of a program on MzScheme that allows us to simulate the behavior of transition P systems. For that, a library of procedures have been developed that work in two stages. In the first one, parsing/compiling stage, the input P system is checked, and if it is well defined, it is represented by means of an internal grammar. In a second stage, simulation, the computation tree associated to the P system is generated until a prefixed level.
• BP - BoehmPaun
  Corrado Bohm and G. Paun. Cooperating distributed splicing systems. Hand-out workshop on Molecular Computing, August 17-24 1997, Mangalia, Romania.
  Abstract: Inspired by the way of 'computing' in combinatory logic by sequencing operators (combinators) from a given finite set, we introduce a kind of distributed language generating device which consists of a given set of splicing systems (sets of splicing rules plus sets of axioms). We call them cooperating distributed H systems. By applying iteratively the component systems (starting from a given initial string), in a sequence which runs nondeterministically, in such a way that a step is considered correctly finished only of no more splicing is possible, we obtain a language. Somewhat surprisingly if we take into account the loose control on the operations we carry out, a characterization of recursively enumerable languages is obtained, by mechanisms as above with only three components.
• BPEA+01 - BPAeo01
  Y. Benenson, T. Paz-Elizur, R. Adar, E. Keinan, Z. Livneh, and E. Shapiro. Programmable and autonomous computing machine made of biomolecules. Nature, 414(1):430--434, November 22, 2001, http://www.nature.com/nature/links/011122/011122-2.html.
  Abstract: A Turing machine, as defined in the mid-1930s by Alan Turing, is a hypothetical device capable of storing information and responding to computational questions. The concept has inspired a number of designs of molecular DNA computers, but few have been able to operate autonomously. A programmable 'finite automaton' has now been developed using a restriction nuclease and ligase as 'hardware', and software consisting of transition rules encoded by DNA. 'Programming' in this computer amounts to choosing the DNA strands that encode the required computational transitions. Once these have been mixed with input DNA strands, the automaton produces a detectable output molecule that defines the automaton's final state.
• BPL98
  Mark H. Butler, Ray C. Paton, and Paul H. Leng. Unconventional approaches for biologically inspired computing. In Calude et al. [UMC98].
  Abstract: This paper presents a framework for considering the relationship between biological computation and unconventional computation. The paper first considers several standard views of computation. Next it outlines what motivates our interest in unconventional computation and how our view of computation can be extended. Biomolecular and biological computation are compared and contrasted, with particular attention to recent work on smart proteins, fuzzy enzymes and computational tissues. Finally a generic decomposition of unconventional computing systems is discussed along with the properties of their parts.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Bre99 - Br99
  R. Brent. Evolution as computation, chapter Using artificial reagents to dissect cellular genetic networks, pages 210--215. In Landweber and Winfree [LW99], 1999.
• BT00 - CBT00
  Claudia Borchard-Tuch. Herausforderung: Biocomputer oder Zuruck zur Natur. Georg Olms Verlag AG, 2000. In German.
  The book gives a wide overview on all what biocomputing is. The contents reach from DNA to Adleman's experiment, from H-systems to sticker systems. Biocomputing by DNA is opposed to biocomputing by bacteriorhodopsin, and biocomputing is embedded in other nanocomputing systems, especially mechanical nanocomputers and quantum computers. The book shows that the construction of a universal DNA compute r is possible - at least theoretically: the constructions of Boolean circuits, Turing machines and H -systems by DNA molecules are shown. In this context DNA Pascal, the programming language for DNA computers, is described.
• BZMS01 - BZeo00
  D. Besozzi, C. Zandron, G. Mauri, and N. Sabadini. P systems with gemmation of mobile membranes. In Proc. ICTS, volume 2202 of Lecture Notes in Computer Science, pages 136--153, Oct. 2001. Turin, Italy.
• Cam95 - Campbel95
  D.M. Campbell. [review of] Adleman, molecular computation of solutions to combinatorial problems. Computing Reviews, 36(8):435, August 1995.
• Car - Car00
  Shawn Carlson. PCR at home, http://www.sciam.com/2000/0700issue/0700amsci.html. -.
  Abstract: Scientific American's "Amateur Scientist" column this month tells how to amplify and isolate DNA chains in your kitchen, using the tried-and-true Polymerase Chain Reaction technique. Use it for massively parallel computing experiments; to ID friends, pets, and favorite houseplants; or to help eliminate epidemics. But what'll happen when enterprising teenagers start playing with plasmids and recombinant DNA?
• CBW - TBW02
  C. L. Taylor Clelland, C. Bancroft, and D. H. Wood. Universal biochip readout of directed hamiltonian path problems. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• CCC+96 - CaiEA96
  Weiping Cai, Anne E. Condon, Robert M. Corn, Elton Glaser, Zhengdong Fei, Tony Frutos, Zhen Guo, Max G. Lagally, Qinghua Liu, Lloyd M. Smith, and Andrew Thiel. The power of surface-based DNA computation, July 1 1996, ftp://corninfo2.chem.wisc.edu/Papers/powerDNA.ps. Preprint.
  Abstract: A new model of DNA computation that is based on surface chemistry is studied. Such computations involve the manipulation of DNA strands that are immobilized on a surface, rather than in solution as in the work of Adleman. Surface-based chemistry has been a critical technology in many recent advances in biochemistry and offers several advantages over solution-based chemistry, including simplified handling of samples and elimination of loss of strands, which reduce error in the computation. The main contribution of this paper is in showing that surface-based DNA chemistry efficiently supports general circuit computation on many inputs in parallel. To do this, an abstract model of computation that allows parallel manipulation of binary inputs is described. It is then shown that this model can be implemented using fairly standard chemistry, in which inputs are encoded as DNA strands and the strands are repeatedly modified in parallel on a surface using the chemical processes of hybridization, exonuclease degradation, polymerase extension or ligation. Thirdly, it is shown that the model supports efficient circuit simulation in the following sense: exactly those inputs that satisfy a circuit can be isolated, and the number of parallel operations needed to do this is proportional to the size of the circuit. Finally, results are presented on the power of the model when another resource of DNA computation is limited, namely strand length.
  Presents an abstract model of the surfaced-based approach to DNA computation presented in [LiuEA96] and describes its power and limitations.
• CCD98 - UMC98
  C.S. Calude, J. Casti, and M.J. Dinneen, editors. Unconventional Models of Computation. Springer Verlag, Berlin, Heidelberg, New York, 1998, ISBN 981-3083-69-7.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• CCT01 - Cio01-1
  G. Ciobanu, V. Ciubotariu, and B. Tanasa. A computational model of membrane transportation. submitted, 2001.
• CDMO - CDMO01
  V. V. Chasov, A. A. Deev, I. S. Masulis, and O. N. Ozoline. Periodical patterns in the structural organization of bacterial promoters. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• CDP00 - WMP2000
  C. S. Calude, M. J. Dinneen, and G. Paun, editors. Pre-proceedings of Workshop on Multiset Processing, Curtea de Arges, Romania, August 2000, TR 140, CDMTCS, University of Auckland, New Zealand, 2000.
  The pre proceedings contain [Ata00], [BCM00], [CV00], [F00], [K00], [Kr00], [M00], [GP00-1], [R00], [SH00], [ST00], [ZFM00-1], [BCAG00], [KMP00], [Fr00-1], [Manca00-2], [Stefan00], [BCMeo01].
• CDW03
  J. Chen, R. Deaton, and Y.-Z. Wang. A DNA-based memory with in vitro learning and associative recall. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 127--136, 2003.
• Cet98
  R. Ceterchi. Modeling DNA recombinant behavior with fixed-point equations. In Paun [CBMtitle], pages 340--352.
  Abstract: We introduce the concept of selective CP-function (cut-and-paste function) in order to provide an unified framework for the formal treatment of a great variety of behaviors involving cut and paste operations on strings. We show that the splicing operation can be modeled with fixed-point equations, thus adding a new and powerful tool, of a purely algebraic nature, to the existing generative device.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• CFLL99 - CukrEA98
  A. R. Cukrasa, D. Faulhammer, R. J. Lipton, and L. F. Landweber. Chess games: A model for RNA based computation. In Kari et al. [P4], pages 35--45.
  Abstract: Here we develop the theory of RNA computing and a method for solving the "knight problem" as an instance of a satisfiability (SAT) problem. Using only biological molecules and enzymes as tools, we developed an algorithm for solving the knight problem (3 x 3 chess board) using a 10-bit combinatorial pool and sequential RNase H digestions. The result of preliminary experiments presented here reveal that the protocol recovers far more correct solutions than expected at random, but the persistence of errors still presents the greatest challenge.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• Cio98 - Ciob98
  G. Ciobanu. A molecular abstract machine. In Paun [CBMtitle], pages 61--79.
  Abstract: This paper describes a "molecular" abstract approach to the DNA computing, looking for theoretical developments related to a suitable abstract machine for this idea of computing using molecules, and to the computational power of the molecular machine - which has at least the same power as the Turing Machine. In order to define the abstract machine and to prove its computational power, we use notions and results of current communicating systems (CCS) theory, \pi-calculus, and encodings of \lambda-calculus into \pi-calculus.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Cio00a - Cio00-1
  G. Ciobanu. Formal description of the molecular processes. Recent topics in mathematical and computational linguistic, pages 82--96, 2000. Academy Publishing House, Bucharest.
• Cio00b - Cio00-2
  G. Ciobanu. Molecular structures. Words, Sequences, Languages: Where Computer Science, Biology and Linguistics Come Across, pages 299--317, 2000.
• Cio02 - Cio02-1
  G. Ciobanu. Molecular interaction. J. of Theoretical Computer Science, 2002.
• CK97
  Venkatesan T. Chakaravarthy and Kamala Krithivasan. A note on extended H systems with permitting/forbidding context of radius one. Bulletin of the EATCS, 62:208--213, June 1997.
• CKS04 - CKSvT
  K. Culik, J. Karhum\"aki, and P. Salmela. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Fixed Point Approach to Commutation of Languages, pages 119--131. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• CM01
  J. Castellanos and V. Mitrana. Words, Semigroups, and Transductions, chapter Some remarks on hairpin and loop language, pages 47--59. World Scientific, Singapore, 2001.
• CMVMS01 - CMMS01
  J. Castellanos, C. Martíin-Vide, V. Mitrana, and J. Sempere. Solving NP-complete problems with networks of evolutionary processors. In Proc. of the 6th International Work-Conference on Artificial and Natural Neiral Networks, IWANN 2001, pages 621--628. Springer Verlag, Berlin, Heidelberg, New York, 2001. LNCS 2048.
• CMVS04 - CVSvT
  R. Ceterchi, C. Martín-Vide, and K.G. Subramanian. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter On Some Classes of Splicing Languages, pages 84--105. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Con85
  Michael Conrad. On designing principles for a molecular computer. Comm. of the ACM, 28:464--480, 1985.
• Con88
  Michael Conrad. The price of programmability. The universal Turing Machine: a half-century survey, pages 285--307, 1988.
• Con90 - Conrad90
  Michael Conrad. Molecular computing. In Marshall C. Yovits, editor, Advances in Computers, volume 31, pages 235--324. Academic Press, New York, 1990.
• Con92a - Conrad92
  Michael Conrad. Guest editor's introduction: Molecular computer paradigms. Computer, 25(11):6--9, November 1992.
• Con92b - Con92
  Michael Conrad. Quantum molecular computing: The self-assembly model. International Journal of Quantum Chemistry: Quantum Biology Symposium, 19:125--143, 1992.
  Abstract: The principle of macromolecular self-assembly is used to construct a model of computing that exploits quantum effects to achieve enhanced real-time capabilities. Signals impinging on a device (or biological cell) trigger the appearance of macromolecules that self-assemble into a mosaic. Adaptor enzymes recognize features of the mosaic and link these to the output of the device. In this way, a symbolic pattern recognition problem is converted to a free-energy minimization process. A Hartree-type self-consistent-field formalism is developed for treating the self-assembly process. The formalism demonstrates that the parallelism inherent in the quantum mechanical wave function (the superposition of electronic states) can speed up the exploration of the potential surface, thereby increasing computational search power over what can be achieved with conventional models of computation.
• Con99 - Conrad98
  M. Conrad. Molecular and evolutionary computation: the tug of war between context freedom and context sensitivity. In Kari et al. [P4], pages 99--110.
  Abstract: Proteins and nucleic acids constitute a vast potential reservoir of pattern recognizers that operate on the basis of shape complementarity. It is possible to construct models of computing in which these shape-based interactions contribute directly to recognition of signal patterns at the device (or cell) level. The input-output transform is molded by variation-selection evolution. Such models provide clueas as to the organizational features that enable biomolecular matter to acquire nonevolutionary modes of problem solving through the evolutionary process. The requisite organizations are characterized by a high dimensionality that allows them to simultaneously exhibit aspects of context-sensitivity and context-independence.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• CP00
  C. Calude and G. Paun. Computing with cells and atoms, page Chapter 3. Taylor and Francis, London, 2000. Computing with membranes.
• CP01 - CP00-1
  G. Ciobanu and D. Paraschiv. P-system software simulator. Fundamenta Informaticae, 49, 2001.
• CPRP00 - PCRP00
  J. Castellanos, G. Paun, and A. Rodriguez-Paton. P systems with worm objects. In IEEE 7th. International Conference on String Processing and Information Retrieval, SPIRE 2000, La Coruna, Spain, pages 64--74, 2000. Also in CDMTCS TR 123, University of Auckland, 2000 (www.cs.auckland.ac.nz/CDMTCS).
• CR00a - CR00
  K. Chen and V. Ramachandran. A space-efficient randomized DNA algorithm for k-SAT. In Condon and Rozenberg [P6], pages 199--208, http://cs-www.cs.yale.edu/homes/vijayr/papers/dna_k-sat.ps.
  Abstract: We present a randomized DNA algorithm for k-SAT based on the classical algorithm of Paturi et al. [PPZ97]. For an n-variable, m-clause instance of k-SAT (m>n), our algorithm finds a satisfying assignment, assuming one exists, with probability 1-e^-\alpha, in worst-case time O(k²mn) and space O(2^(1-i/k)n+log \alpha). This makes it the most space-efficient DNA k-SAT algorithm for k>3 and k < n/ log \alpha (i.e. the clause size is small compared to the number of variables). In addition, our algorithm is the first DNA algorithm to adapt techniques from the field of randomized classical algorithms.
• CR00b - P6
  A. Condon and G. Rozenberg, editors. DNA Computing: 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 13-17, 2000, Revised Papers, volume 2054 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, New York, 2000.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• CR03 - PP9
  J. Chen and J. Reif, editors. Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003. Madison, Wisconsin, 2003.
  The volume contains [Berman03], [LLeo03], [LKeo03], [FLeo03], [LJeo03], [KSeo03], [WBeo03], [LPeo03], [MRV03], [BMZ03], [SKeo03], [JM03], [SCeo03], [GHB03], [UH03-1], [UH03-2], [YFeo03], [YHeo03], [CRW03], [SLeo03-1], [RPW03], [Istrail03], [SJS03], [CDW03], [GBN03], [TKeo03], [LL03], [NL03], [SH03-1], [NS03], [KZW03], [SH03-2], [LS03], [KYeo03].
  Poster papers presented at the conference [Zingel03], [ZZeo03], [Arita03], [UT03], [KKeo03], [SLeo03-2], [LZP03], [WY03], [RHB03], [Profir03], [YLBeo03], [ZS03], [CW03], [LLC03], [SS03].
• CRW03
  M. Cook, P. W. K. Rothemund, and E. Winfree. Self-assembly circuit patterns. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 99--110, 2003.
• CS02a - CS02-1
  A. Carbone and N. C. Seeman. Circuits and programmable self-assembling DNA structures, http://www.ihes.fr/~carbone/topic8.html. PNAS, to appear, 2002.
  Abstract: Self-assembly is beginning to be seen as a practical vehicle for computation. We investigate how basic ideas on tiling can be applied to the assembly and evaluation of circuits. We suggest that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as the program or circuit that leads to the computation of a particular Boolean expression. This layer templates the assembly of tiles whose associations then lead to the actual evaluation involving the input data. We describe DNA motifs that can be used for this purpose; we show how the template layer can be programmed, much the way that a general-purpose computer can run programs for a variety of applications. The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers.
• CS02b - CS02
  A. Carbone and N. C. Seeman. A route to fractal DNA-assembly. Natural Computing, 1(4):469--480, 2002.
• CS02c - CS02-2
  A. Carbone and N. C. Seeman. A route to fractal DNA-assembly, http://www.ihes.fr/~carbone/topic8.html. to appear in Natural Computing, 2002.
  Abstract: Crystallization is periodic self-assembly on the molecular scale. Individual DNA components have been used several times to achieve self-assembled crystalline arrangements in two dimensions. The design of a fractal system is a much more difficult goal to achieve with molecular components. We present DNA components whose cohesive portions are compatible with a fractal assembly. These components are DNA parallelograms that have been used previously to produce two dimensional arrays. To obtain a fractal arrangement, however, we find it necessary to combine these parallelograms with glue-like constructs. The assembly of the individual parallelograms and a series of glues and protecting groups appear to ensure the fractal growth of the system in two dimensions. Synthetic protocols are suggested for the implementation of this approach to fractal assembly.
• CS03 - CS03-1
  A. Carbone and N. C. Seeman. Coding and geometrical shapes in nanostructures: A fractal DNA-assembly. Natural Computing, 2(2):133--151, 2003.
• CS04 - CSvT
  A. Carbone and N. C. Seeman. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Molecular Tiling and DNA Self-assembly, pages 61--83. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• CT01a - CT02-3
  G. Ciobanu and B. Tanasa. Gene expression by software mechanisms. Fundamenta Informaticae, 49, 2001.
• CT01b - CT02-2
  G. Ciobanu and B. Tanasa. An operating system view of the molecular processes. Chinese Journal of Computers, 2001.
  Special Volume on Molecular Computing
• CV91
  J. Collado-Vides. The search for theory of gene regulation is formally justified by showing the inadequacy of context-free grammars. CABIOS, 7:321--326, 1991.
• CVFKP96a - CsuhajEA96B
  E. Csuhaj-Varjú, R. Freund, L. Kari, and G. Paun. DNA computing based on splicing: universality results. In Biocomputing: Proceedings of the 1996 Pacific Symposium, 1996, http://www.cgl.ucsf.edu/psb/psb96/proceedings/cshhaj-varju.ps. Also: Technical report 185-2/FR-2/95, TU Wien, Institute for Computer Languages, Wien, Austria, 1995, http://www.csd.uwo.ca/~lila/four.ps.
  Abstract: The paper extends some of the most recently obtained results on the computational universality of extended H systems (with regular sets of rules respectively with finite sets of rules used with simple additional mechanisms) and shows the possibility to obtain universal systems based on these extended H systems, i.e. the theoretical possibility to design programmable universal DNA computers based on the splicing operation. The additional mechanisms considered here are: multisets (counting the numbers of copies of each available string), checking the presence/absence of certain symbols in the spliced strings, and organizing the work of the system in a distributed way (like in a parallel communicating grammar system). In the case of multisets we also consider the way of simulating a Turing machine (computing a partial recursive function) by an equivalent H system (computing the same function), in the other cases we consider the interpretation of algorithms as language generating devices, hence the aim is to reach the power of Chomsky type-0 grammars, the standard model for representing algorithms equivalent with Turing machines taken as language generators.
• CVFKP96b - CFKP96
  E. Csuhaj-Varju, R. Freund, L. Kari, and G. Paun. DNA computing based on splicing: universality results. Proceedings First Annual Pacific Symposium on Biocomputing, Hawaii, pages 179--190, 1996.
• CVKP96 - CsuhajEA96A
  E. Csuhaj-Varjú, L. Kari, and G. Paun. Test tube distributed systems based on splicing. Computers and AI, 15(2--3):211--232, 1996, http://www.csd.uwo.ca/~lila/dnapcgs.ps.
  Abstract: We define a symbol processing mechanism with the components (test tubes) working as splicing schemes in the sense of T. Head and communicating by redistributing the contents of tubes (in a similar way to the separate operation of Lipton-Adleman). (These systems are similar to the distributed generative mechanisms called Parallel Communicating Grammar Systems.) Systems with finite initial contents of tubes and finite sets of splicing rules associated to each component are computationally complete, they characterize the family of recursively enumerable languages. The existence of universal test tube distributed systems is obtained on this basis, hence the theoretical proof of the possibility to design universal programmable computers with the structure of such a system.
• CVM00
  E. Csuhaj-Varju and V. Mitrana. Evolutionary systems: A language generating device inspired by evolving communities of cells. Acta Informatica, 11(36):913--926, 2000.
• CvN99 - CN99
  J. P. Crutchfield and E. van Nimwegen. Evolution as computation, chapter The evolutionary unfolding of complexity, pages 67--94. In Landweber and Winfree [LW99], 1999.
• CVS04 - VSvT
  E. Csuhaj-Varju and A. Salomaa. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter The Power of Networks of Watson-Crick D0L Systems, pages 106--118. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• CVV00 - CV00
  E. Csuhaj-Varju and G. Vaszil. Objects in test tube systems. In Calude et al. [WMP2000], pages 68--77.
  Abstract: We introduce the notion of a test tube with objects, a distributed parallel computing device operating with multiset of symbols, motivated by characteristic of biochemical processing. We prove that these constructs are suitable tools for computing, any recursively enumerable set can be identified by a TTO system. We also rise some open questions arising from the unconventional nature of this computational tool.
• CW97 - ChenWood97
  J. Chen and D. H. Wood. A new DNA separation technique with low error rate. In Rubin and Wood [P3], pages 43--56.
  Abstract: A new method for separation of DNA according to its substrings is developed and demonstrated. Our method is for circular single strands of DNA. These strands are assumed to be designed to minimize unwanted hybridization (sticking). The new method is enzyme-based and notable for its simplicity, and suitability for scaling up to computations involving kilogram quantities of DNA. Errors are below the level of detectability in gels that exhibit the desired, separated strands. This purity is a significant improvement over the usual "affinity purification" separation method. Additional more sensitive instrumentation will be required to precisely measure the error rate of the new method.
• CW99
  K. Chen and E. Winfree. Error correction in DNA computing: Misclassification and strand loss. In Winfree and Gifford [P5], pages 49--63.
  Abstract: We present a method of transforming an extract-based DNA computation that is error-prone into one that is relatively error-free. These improvements in error rates are achieved without the supposition of any improvements in the reliability of the underlying laboratory techniques. We assume that only two types of errors are possible: a DNA strand may be incorrectly processed or it may be lost entirely. We show how to deal with each of these errors individually and then analyze the trade off when both must be optimized simultaneously.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• CWL+ - CW03
  Y. Chen, L. Wang, M. Lu, M. Shortreed, T. Knight, and N. M. Smith. A new DESTROY-UNMARKED operation in multiple word DNA computing on surfaces. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• CZ97
  Michael Conrad and Klaus-Peter Zauner. Design for a DNA conformational processor. In Rubin and Wood [P3], pages 290--295.
  Abstract: We describe a conceptual model of DNA-based computing that utilizes the conformational dynamics of pattern classification. Input signals are coded into unmethylated and methylated oligonucleotides. Hybridization is used to arrange these input oligonucleotides on a backbone strand that contains complementary sequences. Different input signal patterns are thus re-represented as DNA duplexes with distinctly different conformational dynamics, in particular different equilibria of B and Z DNA that can be read out using circular dichroism. The system could be trained to carry out desired pattern recognition functions (input-output mappings) through evolutionary procedures.
• CZ00
  M. Conrad and K.-P. Zauner. Molecular computing with artificial neurons. Commun. KISS, 18(8):78--89, 2000, http://www.cs.wayne.edu/~kjz/KPZ/PublicationsOnline/ComKISSV18N8P78/ComKISSV18N8P78.html.
  Abstract: Today's computers are built up from a minimal set of standard pattern recognition operations. Logic gates, such as NAND, are common examples. Biomolecular materials offer an alternative approach, both in terms of variety and context sensitivity. Enzymes, the basic switching elements in biological cells, are notable for their ability to discriminate specific molecules in a complex background and to do so in a manner that is sensitive to particular milieu features and indifferent to others. The enzyme, in effect, is a powerful context sensitive pattern recognizer. We describe a tabletop pattern processor that in a rough way can be analogized to a neuron whose input-output behavior is controlled by enzymatic dynamics.
• DA96 - MacD96
  Mac Dónaill and Dónall A. On the scalability of molecular computational solutions to NP problems. The Journal of Universal Computer Science, 2(2):87--95, February 1996, http://www.iicm.edu/jucs_2_2/on_the_scalability_of/ps/paper.ps.gz.
  Abstract: A molecular computational procedure in which manipulation of DNA strands may be harnessed to solve a classical problem in NP --- the directed Hamiltonian path problem --- was recently proposed [Adl94][Gifford94]. The procedure is in effect a massively parallel chemical analog computer and has a computational capacity corresponding to approximately 10⁵ CPU years on a typical 10 MFLOP workstation. In this paper limitations on the potential scalability of molecular computation are considered. A simple analysis of the time complexity function shows that the potential of molecular systems to increase the size of generally solvable problems in NP is fundamentally limited to 10². Over the chemically measurable picomolar to molar concentration range the greatest practical increase in problem size is limited to 10¹.
  Reiterates the argument of [Hartmanis95][Hartmanis95-2] that Molecular Computation brings nothing new to the theory of computational complexity: it cannot break the exponential barrier.
• DAG98
  P. E. Dunne, M. Amos, and A. Gibbons. Boolean transitive closure in DNA. In Paun [CBMtitle], pages 127--137, http://www.csc.liv.ac.uk/~ctag/archive/t/CTAG-98004.ps.gz.
  Abstract: Existing models of DNA computation have been shown to be Turing-complete, but their practical significance is unclear. If DNA computation is to be competitive in the future we require a method of translating abstract algorithms into a sequence of physical operations on strands of DNA. In this paper we describe one such translation, that of transitive closure. We argue that this method demonstrates the feasibility of constructing a general framework for the translation of P-RAM algorithms into DNA.
• Das96 - Dassen96
  J.H.M. Dassen. Molecular computation and splicing systems. Msc thesis, Leiden University, August 1996.
  Abstract: This thesis provides an overview of the related subjects of Molecular Computation and Splicing Systems. Molecular Computation is computation using (biological) macromolecules like DNA as information carriers. These macromolecules are manipulated using biological operators, such as enzymes, and operations commonly used in bio-technology and genetic manipulation, such as filtering operations. It has received much attention following Adleman's seminal article [Adl94]. Splicing Systems are models in Formal Language Theory that use the splicing operator instead of concatenation. The splicing operator is an operator on two strings that is an abstraction of the effect of restriction enzymes on strands of double-stranded DNA combined with ligation. It was introduced in [Head87]. Several models are discussed, including models that are capable of universal computation. Biochemical background is provided in an appendix. Extensive references are provided.
• Das98 - Dassen97
  J.H.M. Dassen. DNA computing: Promises, problems and perspective. IEEE Potentials, 16(5):27--28, December 1997--January 1998 1997-1998.
• DCB+02 - DCeo02
  R. Deaton, J. Chen, H. Bi, M. Garzon, H. Rubin, and D. H. Wood. A PCR-based protocol for in vitro selection of non-crosshybridizing oligonucleotides. In Hagiya and Ohuchi [PP8], pages 196--204.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• DCBR - DCBR02
  R. Deaton, J. Chen, H. Bi, and J. A. Rose. A software tool for generating non-crosshybridizating libraries of DNA oligonucleotides. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• DEO00
  S. Diaz, J. L. Esteban, and M. Ogihara. A DNA-based random walk method for solving k-SAT. In Condon and Rozenberg [P6], pages 209--219.
  Abstract: This paper presents an implementation of a concurrent version of Schoning's algorithm for k-SAT in [Sch99]. It is shown that the algorithm can be implemented with space complexity O((2-2/k)ⁿ) and time complexity O(kmn + n³), where n is the number of variables and m the number of clauses. Besides, borrowing ideas from the above mentioned implementation, it is presented an implementation of resolution, a widely studied and used proof system, mainly in the fields of Proof Complexity and Automated Theorem Proving.
• DG89 - DenninghoffGatterdam89
  K.L. Denninghoff and R. W. Gatterdam. On the undecidability of splicing systems. International Journal of Computer Mathematics, 27:133--145, 1989.
  Abstract: The notion of splicing system has been used to abstract the process of DNA digestion by restriction enzymes and subsequent relegation. A splicing system language is the formal language of all DNA strings producible by such a process. The membership problem is to devise an algorithm (if possible) to answer the question of whether or not a given DNA string belongs to a splicing system language given by initial strings and enzymes. In this paper the concept of a sequential splicing system is introduced. A sequential splicing system differs from a splicing system in that the latter allows arbitrarily many copes of any string in the initial set whereas the sequential splicing system may restrict the initial number of copies of some strings. The main result is that there exist sequential splicing systems with recursively unsolvable membership problem. The technique of the proof is to embed Turing machine computations in the languages.
  Introduces multisets into splicing systems, and shows such splicing systems to be universal.
• DG98
  R. Deaton and M. Garzon. Thermodynamic constraints on DNA-cased computing. In Paun [CBMtitle], pages 138--152.
  Abstract: Computing with biological macromolecules, such as DNA, is fundamentally a physical/chemical process. The DNA chemistry introduces a level of complexity that makes reliable, efficient, and scalable computations a challenge. All the chemical and thermodynamic factors have to be analyzed and controlled in order for the molecular algorithm to produce the intended result. For instance, a computational based on DNA requires that the problem instance be encoded in single strands of DNA and that these strands reacts as planned, that molecular biology protocols, such as PCR or affinity separation, correctly extract the result, and the sufficient flexibility remains so that worthwhile computations can be done. In this paper, various thermodynamic and chemical constraints on DNA computing are enumerated. A similar measure, based on Gibb's free energy of formation, is defined to judge the goodness of DNA encodings. Finally, the DNA computation problem for implementing molecular algorithms is defined, and it is likely that it is as difficult as the combinatorial optimization problems they are intended to solve.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• DG99 - DP99
  J. Dassow and Paun G. On the power of membrane computing. J. Univ. Computer Sci., 5(2):33--49, 1999, http://www.iicm.edu/jucs.
• DG01
  R. Deaton and M. Garzon. Fuzzy logic with biomolecules, volume 5(1), pages 2--9. Springer Verlag, Berlin, Heidelberg, New York, 2001, http://link.springer.de/link/service/journals/00500/tocs/t1005001.htm.
• DGM+96 - Deaton96
  R. Deaton, Max H. Garzon, R. C. Murphy, Donald R. Franceschetti, and S.E. Stevens, Jr. Genetic search of reliable encodings for DNA based computation. In Fixme[booktitle], 1996, http://www.msci.memphis.edu:80/~garzonm/gp-96.ps.
• DHS97
  M. Deputat, G. Hajduczok, and E. Schmitt. On error-correcting structures derived from DNA. In Rubin and Wood [P3], pages 223--229.
  Abstract: A structure based on Mutually Orthogonal Latin squares of order 4 is shown to be error correcting. This structure is unique in that encoding is not based in the information sequence. A theoretical error-correcting automaton is developed, using MOLS (Mutually Orthogonal Latin Structures) as inputs, and next state information. A possible correlation between MOLS and the four base, triplet codon structure of DNA is made.
• DHvV00 - DHV00
  R. Dassen, H. J. Hoogeboom, and N. van Vugt. A characterization of non-iterated splicing with regular rules, pages 319--327. Kluwer Academic, 2000. Where Mathematics, Computer Science, Linguistic and Biology Meet.
  Abstract: The family S(LIN, REG) of languages obtained by (noniterated) spliced linear languages using regular rules does not coincide with one of the Chomsky families. We give a characterization of this family, and show that we can replace the regular rule set by a finite one.
• DLN97 - BCEC97
  Bjorn Olsson Dan Lundh and Ajit Narayanan, editors. Bio-Computing and Emergent Computation. World Scientific, 1997, ISBN 981-02-3262-4. BCEC97 - BioComputing and Emergent Computation, University of Skovde, Sweden, September 1--2, 1997. http://www.ida.his.se/ida/~bcec.
• dlT02 - Torre02
  P. de la Torre. How efficiently can room at the bottom be traded away for speed at the top? In Hagiya and Ohuchi [PP8], pages 95--111.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• dlT03 - Torre0r32
  P. de la Torre. How efficiently can room at the bottom be traded away for speed at the top? Natural Computing, 2(4):349--389, 2003.
• DM96a - DM97-1
  J. Dassow and V. Mitrana. Evolution grammars: a grammatical model for genome evolution. In Bioinformatics. Proceedings of German Conference on Bioinformatics GBC'96, 1996. also in Lecture Notes in Computer Science, 1278, Springer-Verlag, 1997, 199-209.
• DM96b - DassowMitrana96
  J. Dassow and V. Mitrana. Splicing grammar systems. Computers and AI, 15(2--3):109--122, 1996.
  Abstract: The aim of this paper is to bring together two new and powerful tools: on the one hand, the splicing operation as a basic operation on DNA sequences and, on the other hand, the parallelism and communication features in grammar systems. As expected, the result of the above combination is a very powerful mechanism, leading to a new characterization of recursively enumerable languages.
• DM98
  J. Dassow and V. Mitrana. Self cross-over systems. In Paun [CBMtitle], pages 283--294.
  Abstract: We consider the following way of generating a language, by using the cross-over operation: start with a finite set of strings and a given set of cross-over rules which are applicable only to the identical strings. By applying a cross-over rule to two copies of an initial string we get two new strings. Iteratively, we get a language. Some properties (closure, decidability, etc.) of these languages are investigated.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• DMG+96 - DMGFS96
  R. Deaton, R.C. Murphy, M. Garzon, D.R. Franceschetti, and S.E. Stevens, Jr. Good encodings for DNA-based solutions to combinatorial problems. In Landweber and Baum [2AWDBC], http://www.ee.memphis.edu/~rdeaton/pubs/dna_codes.ps, http://www.msci.memphis.edu/~garzonm/mcggood.ps.
  Abstract: Adleman has solved the Hamiltonian path problem by encoding the vertices and edges of the graph in oligonucleotides of DNA, hybridizing the oligonucleotides to produce potential answers, and extracting any DNA which corresponds to the Hamiltonian path. Depending on the conditions under which the DNA reactions occur, two oligonucleotides can hybridize without exact matching between their base pairs. This possibility was verified by experiment. For DNA-based solutions to combinatorial problems to become a viable and practical technology, the possibility of false positives must be eliminated. The primary mechanism for the production of false positives is hybridization stringency that depends on the reaction conditions, of which the most important is temperature. Evidence is provided that encoding the vertices and edges of the graph in DNA oligonucleotides that are a minimum distance apart results in reliable encodings that virtually eliminate the risk of false positives. A genetic algorithm was shown to be useful to search the space of possible codewords. The Hamming bound is shown to be an upper bound on the number of reliable encodings. Laboratory results confirmed that the choice of good encodings is very dependent on the reaction conditions.
• DMR+97 - Deaton97
  R. Deaton, R. C. Murphy, J. A. Rose, M. H. Garzon, D. R. Franceschetti, and S. E. Stevens, Jr. A DNA based implementation of an evolutionary search for good encodings for DNA computation. In IEEE International Conference on Evolutionary Computation, pages 267--271, 1997. Indiana University Purdue University, Indianapolis, Illinois, USA.
• DMS97
  J. Dassow, V. Mitrana, and A. Salomaa. Context-free evolutionary grammars and the structural language of nucleic acids. BioSystems, 4:169--177, 1997.
• DMS01
  J. Dassow, V. Mitrana, and A. Salomaa. Operations and grammars suggested by the genome evolution, (fundamental study). Theoretical Computer Science, 270(1-2), 2001.
• DP98
  J. Dassow and G. Paun. Remarks on operations suggested by mutations in genomes. Fundamenta Informaticae, 36:183--200, 1998.
• DP01 - DPa99
  J. Dassow and G. Paun. Concentration controlled P systems. Acta Cibernetica, 15(1), 2001.
• DPTY00
  J. Dassow, G. Paun, G. Thierrin, and S. Yu. Tree-systems of morphism. manuscript, 2000.
• DQSA97 - KOTL97
  Kaplan Peter D., Ouyang Q., Thaler David S., and Libchaber Albert. Parallel overlap extension for construction of computational DNA libraries. J. Theor. Biol., 188:333--341, 1997, http://www.idealibrary.com/links/citation/0022-5193/188/333.
  Abstract: Algorithms for computing with DNA currently require the construction of pools of molecules in which each distinct molecule represents a different starting point for the calculation. We have begun building such pools using the technique of parallel overlap assembly that is already used for the generation of diversity in biologically useful combinatorial search techniques such as gene shuffling. Unlike these applications, a pool in a molecular computer must be complete, containing all possible strands, and ordered, having minimal contamination from incorrectly assembled DNA . We present an experiment in which parallel overlap assembly is used to construct a computational pool and an experiment in which this pool is used to solve the NP- complete maximal-clique problem.
  Also from http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/referer, Copyright 1997 Academic Press
• DR - DR00
  R. Deaton and J. A. Rose. Simulations of statistical mechanical estimates of hybridization error. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• DST - DST01
  N. G. David, K. G. Subramanian, and D. G. Thomas. A note on graph splicing languages. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• EHP+03 - EHeo01-1
  A. Ehrenfeucht, T. Hariu, I. Petre, D. M. Prescott, and G. Rozenberg. Formal systems for gene assembly in ciliates. Theoretical Computer Science, 292:199--219, 2003.
• EHPR01
  A. Ehrenfeucht, T. Harju, I. P., and G. Rozenberg. Patterns of micronuclear genes in ciliates. In Jonoska and Seeman [P7], pages 279--289.
  Abstract: The process of gene assembly in ciliates is one of the most complex examples of DNA processing known in any organism, and it is fascinating from the computational point of view - it is a primitive example of DNA computing in vivo. In this paper we continue to investigate the three molecular operations (ld, hi, and dlad) that were postulated to carry out the gene assembly proves in the intramolecular fashion. In particular, we focus on the understanding of the IES/MDS patterns of micronuclear genes, which is one of the important goals of research on gene assembly in ciliates. We succeed in characterizing for each subset S of the three molecular operations those patterns that can be assembled using operations in S. These results enhance our understanding of structure of micronuclear genes (and of the nature of molecular operations). They allow one to establish both similarity and complexity measures for micronuclear genes.
• EHPR02
  A. Ehrenfeucht, T. Harju, I. Petre, and G. Rozenberg. Characterizing the micronuclear gene patterns in ciliates. Theory of Computing Systems, 35:501--519, 2002.
• EHRvV99 - EHRV99
  A. Ehrenfeucht, H. J. Hoogeboom, G. Rozenberg, and N. van Vugt. Forbidding and enforcing. In Winfree and Gifford [P5], pages 195--206.
  Abstract: DNA molecules and various operations on them can be conveniently expressed as strings and operations on strings. Hence, many models of DNA computation have been formulated within formal language theory. We propose a novel kind of model, which is based on two types of boundary conditions: forbidding and enforcing. Forbidding conditions say that a `conflicting' group of components may not be present in a system, enforcing conditions say that if a certain group of molecules is present in the system, then some other molecules will eventually be present in the system. Such forbidding-enforcing systems are `tolerant' in describing results of (molecular) computations: one system describes the whole family of outcomes all of which obey the forbidding and enforcing constraints of the system, specifying a possibly infinite family of languages. This should be contrasted with standard formal language theory (grammars and automata) where a grammar specifies one language of all words that can be generated. We illustrate the use of forbidding-enforcing systems for the description of the structure of DNA molecules, the description of splicing systems, and the description of the satisfiability problem. Next to standard issues such as normal forms, we investigate two central issues: finiteness and the structure of computation.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• End99 - En99
  D. Endy. Evolution as computation, chapter Towards a predictive biology: the example of bacteriophage T7, pages 201--209. In Landweber and Winfree [LW99], 1999.
• Eng97
  T. L. Eng. Linear DNA self-assembly with hairpins generates the equivalent of linear context-free grammars. In Rubin and Wood [P3], pages 296--301.
  Abstract: Self-assembly of oligonucleotides in various DNA hybridization models has been shown to be capable of generating sequences equivalent to regular languages and context-free languages. In this paper, we show that the model which generates regular languages can be used to generate linear context-free languages if hairpins are allowed.
• Eng99 - Eng98
  T. L. Eng. On solving 3CNF-satisfiability with an in vivo algorithm. In Kari et al. [P4], pages 135--141.
  Abstract: Several in vitro DNA algorithms have been proposed in the literature for solving various combinatorial search problems. The next logical step is the critical examination of whether or not such computation can be performed within the cellular environment We consider the possibility of solving 3-Conjunctive-Normal-From Satisfiability with one possible in vivo algorithm. The exact biological details still remain to be defined and seem beyond the capabilities of current technologies, but perhaps, this will serve as a springboard for further theoretical inquiries into in vivo approaches.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• EPPR01a - EPeo01-2
  A. Ehrenfeucht, I. Petre, D. M. Prescott, and G. Rozenberg. String and graph reduction systems for gene assembly in ciliates. to appear in Math. Struct. in Comput. Sci., 2001.
• EPPR01b - EPeo01-1
  A. Ehrenfeucht, I. Petre, D. M. Prescott, and G. Rozenberg. Where Do Mathematics, Computer Science, Linguistic and Biology Meet, chapter Universal and simple operations for gene assembly in ciliates, pages 329--342. Kluwer, Dordrecht, 2001. C. Martín-Vide and V. Mitrana (eds).
• EPPR01c - EPeo01-3
  A. Ehrenfeucht, I. Petre, D. M. Prescott, and G. Rozenberg. Words, Semigroups, and Transductions, chapter Circularity and other invariants of gene assembly in ciliates, pages 81--97. World Scientific, Singapore, 2001.
• EPR99 - EPR01
  A. Ehrenfeucht, D. M. Prescott, and G. Rozenberg. Evolution as computation, chapter Computational aspects of gene (un)scrambling in ciliates, pages 216--256. In Landweber and Winfree [LW99], 1999.
• ERB97
  A. D. Ellington, M. P. Robertson, and J. Bull. In vitro evolution - ribozymes in wonderland. Science, 276:546--547, April 1997.
• ES97
  T. L. Eng and B. M. Serridge. A surface-based DNA algorithm for minimal set cover. In Rubin and Wood [P3], pages 74--82.
  Abstract: We present an algorithm that solves the Minimal Set Cover problem within the framework of a surface-based model of computation. Affixing DNA strands to a solid surface reduces the possibility of error resulting from the loss of DNA strands in solution. An algorithm solving the Minimal Set Cover problem has previously been proposed using the sticker model of DNA computation [RoweisEA96]. We show that, by taking advantage of the flexibility afforded by the surface-based model, we can design an encoding that eliminates the need for the separation steps required by the sticker model, thereby reducing both the likelihood of error and the number of "biological manipulation steps" required by the algorithm. To our knowledge, the algorithm we present is the first published DNA computing algorithm to make use of surface-based techniques.
• FB97a - FB97
  B. Fu and R. Beigel. On molecular approximation algorithms for NP optimization problems. In Rubin and Wood [P3], pages 93--101, http://www.eecs.lehigh.edu/~beigel/papers/fb-dnaapprox-dimacs.PS.gz.
  Abstract: We develop a general technique for constructing molecular-based approximation algorithms for NP optimization problems. Our algorithms exhibit a useful volume-accuracy trade off. In particular we solve the Covering problem of Hochbaum and Maass using polynomial time and \cal O(\ell²(\log\ell)n² ( arrayc n(n-1) \ell²/2 array)) volume with error ratio (1 + 1/ \ell)². We also present the first candidate for a problem that can be solved more efficiently with the Amplify operation than without.
• FB97b - FB97-2
  Bin Fu and Richard Beigel. A comparison of resource-bounded molecular computation models. In Proceedings of the 5th Israeli Symposium on Theory of Computing and Systems, pages 6--11, 1997, http://www.eecs.lehigh.edu/~beigel/papers/fb-dnamodels-tr.PS.gz. Also in Algorithmica, 24(2); 87-95 (1999).
  Abstract: The number of molecular strands used by a molecular algorithm is an important measure of the algorithm's complexity. This measure is also called the space used by the algorithm. We prove that three important polynomial- time models of molecular computation with bounded space are equivalent to models of polynomial-time Turing machine computation with bounded nondeterminism. Without any assumption, we show that the Split operation does not increase the power of polynomial-time molecular computation. Assuming a plausible separation between Turing machine complexity classes, the Amplify operation does increase the power of polynomial-time molecular computation.
• FB99 - FuBei98
  B. Fu and R. Beigel. Length bounded molecular computing. In Kari et al. [P4], pages 155--163, http://www.eecs.lehigh.edu/~beigel/papers/fb-lengthbounded-dimacs.PS.gz.
  Abstract: Length of DNA strands is an important resource in DNA computing. We show how to decrease strand lengths in known molecular algorithms for some NP-complete problems, such as like 3-SAT and Independent Set, without substantially increasing their running time or volume.
• FBR - FBR00
  U. Feldkamp, W. Banzhaf, and H. Rauhe. A DNA sequence compiler. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• FBZ99 - FBZ98
  B. Fu, R. Beigel, and F. X. Zhou. An \tilde o(2ⁿ) volume molecular algorithm for hamiltonian path. In Kari et al. [P4], pages 217--226, http://www.eecs.lehigh.edu/~beigel/papers/fb-dnaham-dimacs.PS.gz.
  Abstract: We design volume-efficient molecular algorithms for all problems in \#P, using only reasonable biological operations. In particular, we give a polynomial-time O(2ⁿn² \log² n)-volume algorithm to compute the number of Hamiltonian paths in an n-node graph. This improves Adleman's celebrated n!-volume algorithm for finding a single Hamiltonian path.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• FC+00 - FCLL
  D. Faulhammer, A. R. Cukras, , R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. In Proc. Nat. Acad. Sci. USA, volume 97, pages 13690--13695, 2000.
• FCLL99
  D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. When the knight falls: On constructing an RNA computer. In Winfree and Gifford [P5], pages 1--7.
  Abstract: Recently, we introduced and developed RNA based computing as a general approach for the solution of `satisfiability' (SAT) problems [CukrEA98]. As an example, we chose to solve a 9-bit instance of the ``Knight Problem,'' which asks generally how many knights and what configurations can one place on an n x n chess board such that no knight is attacking any other knight on the board. By introducing a destructive algorithm of sequential ribonuclease (RNase) digestions to manipulate strands of a 10-bit binary RNA library (representing all positions on a 3 x 3 chessboard), we recovered a set of 42 out of 43 molecules that describe solutions to this problem [FCLL]. Here, we present experimental data on several controls and highlight our solutions to possible pitfalls encountered on the way to a successful algorithm.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• FCVW97 - Freund97
  Rudolf Freund, Erzsébet Csuhaj-Varjú, and Franz Wachtler. Test tube systems with cutting/recombination operations. In fixme[booktitle], 1997, http://www-smi.stanford.edu/people/altman/psb97/freund.pdf.
  Abstract: We introduce test tube systems based on operations that are closely related to the splicing operation, i.e. we consider the operations of cutting a string at a specific site into two pieces with marking them at the cut ends and of recombining two strings with specifically marked endings. Whereas in the splicing of two strings these strings are cut at specific sites and the cut pieces are recombined immediately in a crosswise way, in CR(cutting/recombination)-schemes cutting can happen independently from recombining the cut pieces. Test tube systems based on these operations of cutting and recombination turn out to have maximal generative power even if only very restricted types of input filters for the test tubes are used for the redistribution of the contents of the test tubes after a period of cuttings and recombinations in the test tubes.
• FD - bmcss
  Pierluigi Frisco and J.H.M. Dassen. A bibliography of molecular computation and splicing systems. HTML: http://www.wi.LeidenUniv.nl/~pier/dna.html, BibTeX source: http://www.wi.LeidenUniv.nl/~pier/dna.bib. This bibliography is hooked into http://liinwww.ira.uka.de/bibliography/index.html, The Collection of Computer Science Bibliographies.
  Description A hyperbibliography on the subject of Molecular Computation and the related theoretical model of Splicing Systems. Molecular Computation is computation using (biological) macromolecules like DNA as information carriers, that are manipulated using biological operators, such as enzymes, and operations commonly used in bio-technology and genetic manipulation, such as filtering operations and the polymerase chain reaction. It has received much attention following Adleman's seminal article [Adl94]. Splicing Systems are models in Formal Language Theory that use the splicing operator instead of concatenation. The splicing operator is an operator on two strings that is an abstraction of the effect of restriction enzymes on strands of double-stranded DNA combined with ligation. It was introduced in [Head87].
• Fer98 - Ferretti98
  C. Ferretti. Report on the OWDNAC, week II. http://www.dsi.unimi.it/~ferretti/rep.htm, September 1998.
• FF96 - Freund96
  Rudolf Freund and Franziska Freund. Test tube systems or how to bake a DNA cake. Acta Cybernetica, 12(4):445--459, 1996.
  Abstract: We introduce various general models for test tube systems which not only are a theoretical basis for the different test tube systems used for practical applications (confer to [Adl94][Adl95][biocircuit][Lipton94]), but also cover different theoretical models to be found in literature, e.g. the test tube systems based on the operations of cutting and recombination introduced in [9] Rudolf Freund, E. Csuhaj-Varjú, F. Wachtler, Test tube systems with cutting/recombination operations, Proceedings PSB'97, 1997. In test tube systems specific operations are applied to the objects in their components (test tubes) in a distributed and parallel manner; the results of these computations are redistributed according to specific input and/or output filters. We investigate relations between the different models of test tube systems introduced in this paper and show how the results presented in [CsuhajEA96A] and [9] fit into our general framework. Moreover, we investigate the computational power of test tube systems with context-free productions and regular filters.
• FF97
  Dirk Faulhammer and Michael Famulok. In vitro selection and characterization of DNA enzymes. In Rubin and Wood [P3].
• FF00a - FrFr00
  R. Freund and F. Freund. Molecular computing with generalized homogeneous P-systems. In Condon and Rozenberg [P6], pages 130--144.
  Abstract: Recently P-systems were introduced by G. Paun as a new model for computations based on membrane structures. The basic variants of P-systems shown to have universal computational power only took account of the multiplicities of atomic objects, some other variants considered rewriting rules on strings. Using the membranes as a kind of filter for specific objects when transferring them into an inner compartment or out into the surrounding compartment turned out to be a very powerful mechanism in combination with suitable rules to be applied within the membranes in the model of generalized P-systems, GP-systems for short. GP-systems were shown to allow for the simulation of graph controlled grammars of arbitrary type based on productions working on single objects; moreover, various variants of GP-systems using splicing or cutting and recombination of strings were shown to have universal computational power, too. In this paper, we consider GP-systems with homogeneous membrane structures, GhP-systems for short, using splicing or cutting and recombination of string objects with specific markers at the ends of the strings that can be interpreted as electrical charges. The sum of these electrical charges determines the permeability of the membranes to the string objects, and we allow only objects with the absolute value of the difference of electrical charges being equal to 1 to pass a membrane in both directions. We show that such GhP-systems have universal computational power; for GhP-systems using splicing and a bounded number of markers the obtained results are optimal with respect to the underlying membrane structure. Moreover, a very restricted variant of such GhP-systems characterizes the (strictly) minimal linear languages.
• FF00b - ReFF00
  R. Freund and F. Freund. Test tube systems: when two tubes are enough. In Rozenberg and Thomas [DLT99].
  Abstract: We consider various models of test tube systems using the splicing operation or the operations of cutting and recombination. With respect to specific regular filters guarding the communication of objects between the tubes, test tubes systems with only two tubes turns out to have the computational power of arbitrary grammars. Instead of using filters, we can also control the communication between the tubes by only taking those objects having undergone a specific number of operations; such cooperating distributed test tube systems with only two tubes and communicating only those objects having undergone exactly three operations (splicing or cutting/recombination, respectively) turn out to have universal computational power, too.
• FFM98 - FMF98
  C. Ferretti, P. Frisco, and G. Mauri. Simulating Turing machines by extended mH systems. In Paun [CBMtitle], pages 221--238, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: In this article we describe a method of translation from a deterministic Turing machine to an extended mH splicing system. The accuracy of this translation is proved by a theorem which shows that the only string present in single copy is a coding of a configuration of the simulated Turing machine. A simpler translation from a universal Turing machine with three tapes to an extended mH system is given too.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• FFO97
  R. Freund, F. Freund, and M. Oswald. Universal H systems using multisets. manuscript, 1997.
• FFO04 - FFOvT
  F. Freund, R. Freund, and M. Oswald. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Splicing Test Tube Systems and Their Relation to Splicing Membrane Systems, pages 139--151. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• FFar - Freund97-2
  Rudolf Freund and Franziska Freund. Test tube systems with controlled applications of rules. In IEEE International Conference on Evolutionary Computation, pages 237--242, Fixme[year].
• FHS02 - FHS01
  P. Frisco, H. J. Hoogeboom, and P. Sant. A direct construction of a universal P system. Fundamenta Informaticae, 49(1-3):103--122, 2002.
  Abstract: We present a direct universal P system based on splicing. Our approach differs from those shown in previous papers as the P system we construct takes as input an encoding of another P system. Previous results were based on the simulation of universal type-0 grammars or Turing machines. We think that the approach we use can be applied to other variants of P systems.
• Fix01 - scb2001
  Fixme, editor. Soft computing with biomolecules, volume 5,1 of Soft computing. Springer Verlag, Berlin, Heidelberg, New York, 2001. ISSN 1432-7643 (printed version), ISSN 1433-7479 (electronic version).
  The book contains: [GC01], [DG01], [MTeo01], [WCeo01] and [NYH01].
• FJ02
  P. Frisco and S. Ji. Conformons-P systems. In Hagiya and Ohuchi [PP8], pages 291--301.
  Abstract: The combination of a theoretical model of the living cell and membrane computing suggests a new variant of a computational model based on membrane-enclosed compartments defined and presented in this paper for the first time. This variant is based on simple and basic concepts: conformons, a combination of information and energy; locality of the interactions of conformons, permitted by the presence of membrane-enclosed compartments; communication via conformons between membrane-enclosed compartments. The computational power of this new system is sketched. Possible other variants of this model and links with Petri nets are outlined.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• FK96 - FerrettiKobayashi96
  C. Ferretti and S. Kobayashi. DNA splicing systems and Post systems. In Biocomputing: Proceedings of the 1996 Pacific Symposium, pages 288--299, 1996, http://www.cgl.ucsf.edu/psb/psb96/proceedings/ferretti.ps.
  Abstract: This paper concerns the formal study on the generative powers of extended splicing (H) systems. First, using a classical result by Post which characterizes the recursively enumerable languages in terms of his Post Normal systems, we establish several new characterizations of extended H systems which not only allow us to have very simple alternative proof methods for the previous results mentioned above, but also give a new insight into the relationships between families of extended H systems. We show a kind of normal form for extended H systems exactly characterizing the class of regular languages. We also show a new representation result for the family of context-free languages in terms of extended H systems.
• FKP99 - Freund
  R. Freund, L. Kari, and G. Paun. DNA computation based on splicing: The existence of universal computers. Theory of Computing Systems, 32:69--112, 1999, http://www.csd.uwo.ca/~lila/jacm.ps.
  Abstract: Splicing systems are generative mechanism based on the splicing operation introduced by T. Head as a model of DNA recombination. We prove that the generative power of finite extended splicing systems equals that of Turing machines, provided we consider multisets or provided a control mechanism is added. We also show that there exist universal splicing systems with the properties above, i.e. there exists a universal splicing system with fixed components which can simulate the behaviour of any given splicing system, when an encoding of the particular splicing system is added to its set of axioms. In this way the possibility of designing programmable DNA computers based on the splicing operations is proved.
• FLL99 - FaulhEA98
  D. Faulhammer, R. J. Lipton, and L. F. Landweber. Counting DNA: Estimating the complexity of a test tube of DNA. In Kari et al. [P4], pages 193--196.
  Abstract: We consider the problem of estimation of the 'complexity' of a test tube of DNA. The complexity of a test tube is the number of a different kinds of strands of DNA in the test tube. It is easy to estimate the number of total strands in a test tube, especially if the strands are all the same length. Estimation of the complexity is much less clear. We propose a simple kind of DNA computation that can estimate the complexity.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• FLL+03 - FLeo03
  S. Fang, H. Lee, M. Li, R. M. Crooks, and R. Corn. Synthesis and characterization of DNA-dendrimer building blocks for the creation of DNA-based nanostructures. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 4--8, 2003.
• FM98 - FreMi98
  R. Freund and V. Mihalache. Molecular computations on circular and linear strings. In Calude et al. [UMC98], pages 210--217.
  Abstract: We consider (extended) splicing systems (H-systems), cutting and pasting systems (CP-systems), and cutting and recombination systems (CR-systems) working on linear and circular strings. As it was proved previously, extended H-systems, CP-systems and CR-systems with a finite set of rules can only generate regular languages when starting with a finite or even regular set of axioms; on the other hand provided with a finite set of axioms and a finite set of rules together with some sort of control mechanism (e.g. test tubes, multisets, permitting or forbidden context, programmed sequences, etc.) extended H-systems, CP-systems and CR-systems can generate any recursively enumerable language of linear strings, and the same results hold true for circular strings and mixtures of linear and circular strings, too. In this paper we give an overview on these results and, moreover, we show that extended H-systems, CP-systems, and CR-systems with a finite set of axioms and a finite set of rules working on a mixture of linear and circular strings can already generate any recursively enumerable language as soon as in these systems we distinguish between rules working on linear strings and rules working on circular strings.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• FM04 - FMvT
  C. Ferretti and G. Mauri. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Remarks on Relativisations and DNA Encodings, pages 132--138. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• FMKY00 - FMKY97
  C. Ferretti, G. Mauri, S. Kobayashi, and T. Yokomori. On the universality of Post and splicing systems. Theoretical Computer Science, 231(2):171--180, 2000.
• FMVM02 - FMM
  R. Freund, C. Martíin-Vide, and V. Mitrana. On some operations suggested by gene assembly in ciliates. New Generation Computing, 2002.
• FMVP00
  R. Freund, C. Martín-Vide, and G. Paun. Computing with membranes: three more collapsing hierarchies. unpublished, 2000.
• FP00
  R. Freund and G. Paun. On a hierarchy of rewriting P systems. manuscript, 2000.
• FPRS97a - FPRS97
  R. Freund, G. Paun, G. Rozenberg, and A. Salomaa. Watson-crick finite automata. In Rubin and Wood [P3], pages 305--317.
  Abstract: We introduce a new type of automata, working on data structures called Watson-Crick tapes. Such a tape is a double stranded sequence of symbols related by a complementarity relation (of the sort present in DNA). A Watson-Crick automaton can separately scan each of the two strands, in a correlated manner, and can have a finite number of states controlling the moves. Moreover, the automaton either moves on both strands in the same direction, or it moves in opposite directions on the strands. Considering different alternatives leads to several types of automata. In many cases, when augmented with squeezing mechanisms like weak codings or deterministic sequential transducers, they characterize the recursively enumerable languages. Techniques and results related to the characterization of recursively enumerable languages by equality sets and twin-shuffle languages are used.
• FPRS97b - FPRoS97
  R. Freund, G. Paun, G. Rozenberg, and A. Salomaa. Watson-crick automata. Techn. Report 97-13, Dept. of computer science, Leiden Univ., 1997.
• FPRS98
  R. Freund, G. Paun, G. Rozenberg, and A. Salomaa. Bidirectional sticker systems. In Altman et al. [PSB98], pages 535--546.
• Fra97 - Fraenkel97
  A. S. Fraenkel. Protein folding, spin glass and computational complexity. In Rubin and Wood [P3], pages 175--191.
  Abstract: A reduction from "Ground State of Spin Glass" in physics to the minimum-energy model of protein folding is made, which shows that the latter is NP-complete (high-complexity). The method also enables to show that even if the backbone of the protein is fixed, the folding of the side-chains is NP-complete. In a separate second part, the possibility of synthesizing proteins to solve arbitrary instances of the spin glass problem is speculated upon.
• Fre - Fr00-1
  R. Freund. Sequential P systems. In Calude et al. [WMP2000].
  Also Theorietag 2000, Workshop on New Computing Paradigms, (R. Freund ed), TU University Vienna, 2000, 177-183 and Romanian J. of Information Science and Technology 4, 1-2 (2001), 77-88
• Fre95 - Freund95
  Rudolf Freund. Splicing systems on graphs. In Proceedings Intelligence in Neural and Biological Systems, pages 189--195. IEEE, IEEE Press, May 1995.
• Fre98
  R. Freund. Bidirectional sticker systems and representation of RE languages by copy languages. In Paun [CBMtitle], pages 182--199.
  Abstract: We prove how any recursively enumerable language L \subseteq T<sup>*</sup> can be represented as h_T(h_1(L_0)\cap h_2(L_0)), i.e., as the projection of the intersection of two morphic images of a specific language L_0, e.g., L_0 can be chosen as the copy language cp(V<sup>+</sup>) = \ww \mid w \in V<sup>+</sup>\ or the reversed copy language rcp(V<sup>+</sup>) = \ww<sup>R</sup> \mid w \in V<sup>+</sup>\ for some alphabet V. Moreover, we point out how these results arise from bidirectional sticker systems, a model of DNA computing introduced recently.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Fre99a - Fr99
  S. J. Freeland. Evolution as computation, chapter Is ours the best of all possible codes?, pages 125--139. In Landweber and Winfree [LW99], 1999.
• Fre99b - Fre99
  R. Freund. Generalized P systems. Proc. of FCT'99 conf., pages 281--292, 1999. LNCS.
  Iasi, Romania
• Fre99c - RFr99
  R. Freund. Generalized P systems with splicing and cutting/recombination. Proc. of FCT'99 conf., 1999. Also in Grammars, 2, 3 (1999), 189-199.
  Iasi, Romania
• Fri00a - Fri00
  P. Frisco. Diophantine equations and splicing: a new demonstration of the generative capability of H systems. In Condon and Rozenberg [P6], pages 43--52, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: Systems based on the splicing operation are computationally complete. Usually demonstrations of this are based on simulations of type-0 grammars. We propose a different way to reach this result by solving Diophantine equations using extended H system with permitting context. Completeness then follows from Matiyasevich's theorem stating that the class of Diophantine sets is identical to the class of recursive enumerable sets. Solutions to a Diophantine equation are found in parallel. The numbers are coded in base one.
• Fri00b - Fri00-1
  P. Frisco. Parallel arithmetic with splicing. Romanian Journal of Information Science and Technology, 3(2):113--128, 2000, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: Computing by splicing is one of the main branches of DNA Computing. We address here the problem of computing the basic arithmetical operations in a parallel way by using splicing systems. Addition, subtraction, multiplication, and integer division between natural numbers are considered. The operations are performed in two steps: the generation of strings and a filtering phase. Both these steps are implemented by H systems or extended H systems with permitting contexts. The numbers are coded in base one.
• Fri01a - F01
  P. Frisco. A direct construction of a universal extended H system. In Margenstern and Rogozhin [MCU01], pages 226--239, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: A direct universal extended H system receives as input the coding of an extended H system with double splicing and simulates it. It is the first time that a direct construction is described: universal results obtained until now were based on the simulation of universal type-0 grammars or Turing machines.
• Fri01b - F00
  P. Frisco. On two variants of splicing super-cell systems. Romanian Journal of Information Science and Technology, 4(1-2):89--100, 2001, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: New computability models, called super-cell systems or P systems, based on the evolution of objects in a membrane structure, were recently introduced. The seminal paper of G. Paun describes three ways to look at them: transition, rewriting and splicing super-cell systems having different properties.
  Here we investigate two variants of splicing super-cell systems improving results concerning their generative capability. This is obtained with a variant of the "rotate-and-simulate" technique classical in H systems area.
• Fri03 - F03
  P. Frisco. Direct constructions of universal extended H systems. Theoretical Computer Science, 296(2):269--293, March 2003.
  Abstract: A direct universal extended H system receives as input the coding of an extended H system with a particular control mechanism and simulates it. We present a direct construction for five kinds of control for the extended H systems under consideration. It is the first time that a direct construction is described: universal results obtained until now were based on the simulation of universal type-0 grammars or Turing machine.
• FS99
  Hans-Werner Fink and Christian Schoenenberg. Electrical conduction through DNA molecules. Nature, 398(6726):407--410, April 1, 1999, http://www.nature.com/server-java/Propub/nature/398407A0.frameset?context=toc.
  Abstract:The question of whether DNA is able to transport electrons has attracted much interest, particularly as this ability may play a role as a repair mechanism after radiation damage to the DNA helix. Experiments addressing DNA conductivity have involved a large number of DNA strands doped with intercalated donor and acceptor molecules, and the conductivity has been assessed from electron transfer rates as a function of the distance between the donor and acceptor sites. But the experimental results remain contradictory, as do theoretical predictions. Here we report direct measurements of electrical current as a function of the potential applied across a few DNA molecules associated into single ropes at least 600 nm long, which indicate efficient conduction through the ropes. We find that the resistivity values derived from these measurements are comparable to those of conducting polymers, and indicate that DNA transports electrical current as efficiently as a good semiconductor. This property, and the fact that DNA molecules of specific composition ranging in length from just a few nucleotides to chains several tens of micrometers long can be routinely prepared, makes DNA ideally suited for the construction of mesoscopic electronic devices.
• FSR01
  U. Feldkamp, S. Saghafi, and H. Rauhe. DNAsequencegenerator - a program for the construction of DNA sequences. In Jonoska and Seeman [P7], pages 23--32.
  Abstract: In DNA computing and DNA nanotechnology the design of proper DNA sequences turned out to be an elementary problem. We here present a software program for the construction of sets ("polls") of DNA sequences. The program can create DNA sequences to meet logical and physical parameters such as uniqueness, melting temperature and GC ratio as required by user. It can create sequences in novo, complete sequences with graphs and allows import and recycling of sequences that are still in use. The program always creates sequences that are - in terms of uniqueness, GC ratio and melting temperature - "compatible" to those already in the pool, no matter whether those were added manually or created or completed by the program itself. The software comes with a GUI and a sequence wizard. In vivo tests of the program's output were done by generating a set of oligomers designed for self-assembly. The software is available for download under http://LS11-www.cs.uni-dortmund.de/molcomp/Downloads/downloads.html.
• FTC+97 - FTCSC97
  A. G. Frutos, A. J. Thiel, A. E. Condon, L. M. Smith, and R. M. Corn. DNA computing at surfaces : 4 base mismatch word design. In Rubin and Wood [P3], page 238.
• FW96
  Rudolf Freund and F. Wachtler. Universal systems with operations related to splicing. Computer and AI, 15(4):273--293, 1996.
• FZ01
  P. Frisco and C. Zandron. On variants of communicating distributed H systems. Fundamenta Informaticae, 48(1):9--20, October 2001, http://www.wi.leidenuniv.nl/home/pier.
  Abstract: A recent result shows that a variant of communicating distributed H system with two components can generate recursive enumerable languages. In this variant the filters are a finite union of sets whose number depends upon the simulated system. We prove here that it is possible to obtain the same result using filters testing the presence of couples of symbols. The number of the couples does not depend upon the simulated systems. Moreover we investigate variants of communicating distributed H systems with limitations in the redistribution process.
• GAH97 - Gibbons97
  Alan Gibbons, Martyn Amos, and David Hodgson. DNA computing. Current Opinion in Biotechnology, 8:103--106, 1997.
• GAHar - Gibbons96
  Alan Gibbons, Martyn Amos, and David Hodgson. Models of DNA computation. In Fixme[booktitle], pages 18--36, Fixme[year].
• Gat89
  R. W. Gatterdam. Splicing systems and regularity. Inter. J. Comput. Math., 31:63--67, 1989.
• Gat92 - Gatterdam92
  R. W. Gatterdam. Algorithms for splicing systems. SIAM Journal on Computing, 21(3):507--520, June 1992.
• Gat94 - Gatterdam94
  R. W. Gatterdam. DNA and twist-free splicing systems. In M. Ito and H. Jurgensen, editors, Words, Languages and Combinatorics, volume 2, pages 170--178. World Scientific, Singapore, 1994, ISBN 9810206453.
• GB96 - GuaranieriBancroft96
  F. Guarnieri and C. Bancroft. Use of a horizontal chain reaction for DNA-based addition. In Landweber and Baum [2AWDBC].
• GBG+98 - GBGMP98
  Tino Gramss, Stefan Bornholdt, Michael Gross, Melanie Mitchell, and T. Pellizzari. Non-Standard Computation: Molecular Computation, Cellular Automata, Evolutionary Algorithms, Quantum Computers. Wiley-VCH, Weinheim, Berlin, May 1998, ISBN 3-527-29427-9. Foreword by M. Schroeder, Introduction by H. Schuster.
• GBH04 - GBHvT
  M. H. Garzon, K. V. Bobba, and B. P. Hyde. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Digital Information Encoding on DNA, pages 152--166. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• GBN03
  M. H. Garzon, K. Bobba, and A. Neel. Efficiency and reliability of semantic retrieval in DNA-based memories. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 137--149, 2003.
• GC01
  Max H. Garzon and Michael Conrad. Soft computing with biomolecules, volume 5(1), pages 1--1. Springer Verlag, Berlin, Heidelberg, New York, 2001, http://link.springer.de/link/service/journals/00500/tocs/t1005001.htm.
  Editorial
• GDDR - GDDR00
  M. Garzon, E. Drumwright, R. J. Deaton, and D. Renault. Virtual test tubes: a new methodology for computing. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• GDMMPJ02 - GMP02
  C. Graciani-Diaz, F.J. Martin-Mateos, and M.J. Perez-Jimenez. Specification of adleman's restricted model using an automated reasoning system: Verification of lipton's experiment. Lecture Notes in Computer Science, 2509:126--136, 2002.
  Abstract: The aim of this paper is to develop an executable prototype of an unconventional model of computation. Using the PVS verification system (an interactive environment for writing formal specifications and checking formal proofs), we formalize the restricted model, based on DNA, due to L. Adleman. Also, we design a formal molecular program in this model that solves SAT following Lipton's ideas. We prove using PVS the soundness and completeness of this molecular program. This work is intended to give an approach to the opportunities offered by mechanized analysis of unconventional model of computation in general. This approach opens up new possibilities of verifying molecular experiments before implementing them in a laboratory.
• GDN+97 - GDNMFS97
  M. Garzon, R. Deaton, P. Neathery, R.C. Murphy, D.R.Franceschetti, and S.E. Stevens, Jr. On the encoding problem for DNA computing. In Rubin and Wood [P3], pages 230--237, http://www.msci.memphis.edu/~garzonm/dna97code.ps.
  Abstract: The encoding problem for DNA computing consists of mapping the instances of an algorithmic problem in a systematic manner onto specific molecules and chemical protocols so that the resulting products contain the answers to the problem's instances. A good solution of the problem prevents unwanted hybridization errors and enables easy retrieval of the answer(s) in the extraction steps. Establishing the formal complexity of this problem relies heavily on unanswered questions on the relevant biochemistry and the role of reactions conditions. To address the problem, we further develop an error-preventing approach based on a new metric (related to but different from the Hamming metric), more suitable to analyze errors in hybridization in DNA computational experiments. The new metric makes possible the development of error-preventing encodings. General properties of the structure of a DNA cube, the space of all oligos available for encodings, are explored. The best codes are given by maximal cliques at high distance in the DNA cubes, and they are of small size. A greedy algorithm is provided that can compute them for low lengths, but generating them in polynomial time for arbitrary lengths seems to be rather difficult to achieve.
• GDN+ar - Garzon97-2
  Max H. Garzon, R. Deaton, P. Neathery, Donald R. Franceschetti, and R.C. Murphy. A new metric for DNA computing. In Fixme[booktitle], Fixme[year], http://www.msci.memphis.edu/~garzonm/gp97code.ps.
• GDRF99
  Max Garzon, Russell J. Deaton, John A. Rose, and Donald R. Franceschetti. Soft molecular computing. In Winfree and Gifford [P5], pages 91--100.
  Abstract: Molecular computing (MC) utilizes the complex interaction of biomolecules and molecular biology protocols to effect computation. Lab experiments in MC are unreliable, inefficient, unscalable, and expensive compared to conventional computing standards. A critical issue in MC is therefore to test encodings and protocols to minimize errors and mishaps that can thwart experiments when actually run in vitro. The purpose of this paper is to describe Edna, an integrated software platform developed to address this problem. The platform will allow MC practitioners to use digital computers to gain insight on the performance of a protocol before it actually unfolds in the tube. Currently, Edna provides tools to find good encodings for a given set of hybridization conditions, by design or evolution, tools to visualize the quality of these encodings, tools to estimate the complexity of given protocols based on bounded complexity, and tools to estimate the reliability of the protocols. Edna includes graphical interfaces, click-and-drag facilities, and a virtual test tube simulator. Edna is object-oriented and extensible, so that it can easily evolve as the field progresses.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• GEBS91 - SzostakEA91
  Rachel Green, Andrew D. Ellington, David P. Bartel, and Jack W. Szostak. In vitro genetic analysis: Selection and amplification of rare functional nucleic acids. Methods, 2:75--86, 1991.
• Geo97 - Georgescu97
  Gianina Georgescu. On the generative capacity of splicing grammar systems. In G. Paun and A. Salomaa, editors, Lecture Notes in Computer Science, volume 1218, pages 330--345. Springer Verlag, Berlin, Heidelberg, New York, 1997.
  Abstract: The generative capacity of splicing grammar systems is investigated in this paper. It is proved that: 1) any linear language can be generated by a splicing grammar system with two regular components; 2) any context-free language can be generated by a splicing grammar system with three regular components; 3) any recursively enumerable language can be generated by a splicing grammar system with four right linear components. The first two results answer a problem left open in [Paun96-2], the last result improves results in the same paper.
• GFB96
  F. Guarnieri, M. Fliss, and C. Bancroft. Making DNA add. Science, 273(5272):220--223, July 12 1996.
  Abstract: Recent studies have demonstrated the feasibility of using DNA-based experiments to compute solutions to combinatorial problems. However, a prerequisite for designing a computer useful in a wide range of applications is the ability to perform mathematical calculations. The development of a DNA-based algorithm for addition is presented. The DNA representation of two nonnegative binary numbers is presented in a form permitting a chain of primer extension reactions to carry out the addition operation. To demonstrate the feasibility of this algorithm, a simple example was executed biochemically.
• GGM+97 - GGMRDFS97
  Y. Gao, M. Garzon, R.C. Murphy, J.A. Rose, R. Deaton, D. R. Franceschetti, and S.E. Stevens, Jr. DNA implementation of nondeterminism. In Rubin and Wood [P3], pages 204--211.
  Abstract: We explore the capabilities of DNA reactions to implement nondeterministic computations at levels lower than the Hamiltonian Path Problem. We provide a technique for programmable fault-tolerant implementation of nondeterministic finite-state machines that enforces the basic conditions in the subset constructions that permit efficient computation. The implementation can be extended to arbitrary nondeterministic Turing machines of a moderate size in practice since they are basically finite-state machines with a large state set. It also suggests an experiment to provide evidence for the open analogous questions about the trade off between nondeterminism and computational resources.
• GGR+98 - GGRMDFS98
  M. Garzon, Y. Gao, J.A. Rose, R.C. Murphy, R. Deaton, D.R. Franceschetti, and S.E. Stevens, Jr. In-vitro implementation of finite-state machines. In Proc. 2nd Int. Workshop on Implementing Automata WIA'97, number 1436 in Lecture Notes in Computer Science, pages 56--74. Springer Verlag, Berlin, Heidelberg, New York, 1998, http://www.msci.memphis.edu/~garzonm/csys/wia97.ps.
  Abstract: We explore the information processing capabilities and efficiency of DNA computations by giving two different types of implementations of finite-state machines. A ligation-based approach allows input of arbitrary length and can be readily implemented with current biotechnology, but requires sequential input feed and different molecules for different machines. In a second implementation not based on ligation, transitions are represented by reusable molecules, and the input, coded as a molecule, can be introduced at once. We extend the technique for programmable fault-tolerant implementation of nondeterministic finite-state machines by enforcing the basic conditions in the subset constructions that permit efficient computation. All implementations allow optical extraction of the status of the machine.
• GHB03
  M. H. Garzon, B. Hyde, and K. Bobba. Binary models for codeword design and evaluation. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 70--79, 2003.
• Gif94 - Gifford94
  David K. Gifford. On the path to computation with DNA. Science, 266:993--994, November 11, 1994, http://www.hks.net/~cactus/doc/science/molecule_comp_perspect.html.
  An essay on molecular computation in the `perspective' section of Science, in the same issue as [Adl94]. It discusses the promises of molecular computation
  
  • ``DNA ligation can effectively search a large space of potential solutions'', and similar techniques may be developed for molecule design (e.g. for proteins).
  • unheard of information representation density
  • extremely energy-efficient
  and the problems
  
  • not practical enough yet
  ``There may be other computational processes lurking behind seemingly simple biological processes''.
• GJ99 - GarzJon98
  Max Garzon and Natasa Jonoska. The bounded complexity of DNA computing. In Kari et al. [P4], pages 63--72.
  Abstract: This paper proposes a new approach to analyze DNA-based algorithms in molecular computation. Such protocols are characterized abstractly by: encoding, tube operations and extraction. Implementation of these approaches involves encoding in a multiset of molecules that are assembled in a tube having a number of physical attributes. The physico -- chemical state of a tube can be changed by a prescribed number of elementary operations. Based on realistic definition of these elementary operations, we define complexity of a DNA-based algorithm using the physico--chemical property of each operation. We show that new algorithms for Hamiltonian path are about twice as efficient as Adleman's original one and that a recent algorithm for Max--Clique provides a similar increase in efficiency. Consequences of this approach to tube complexity and DNA computing are discussed.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• GLR99
  Ashish Gehani, T. H. LaBean, and John H. Reif. DNA-based cryptography. In Winfree and Gifford [P5], pages 233--249, http://www.cs.duke.edu/~reif/paper/DNAcrypt/crypt.ps, http://www.cs.duke.edu/~reif/paper/DNAcrypt/crypt.pdf.
  Abstract: DNA-based Cryptography Ashish Gehani, T. H. LaBean, and John H. Reif Abstract. Recent research has considered DNA as a medium for ultra-scale computation and for ultra-compact information storage. One potential key application is DNA-based, molecular cryptography systems. We present some procedures for DNA-based cryptography based on one-time-pads that are in principle unbreakable. Practical applications of cryptographic systems based on one-time-pads are limited in conventional electronic media, by the size of the one-time-pad; however DNA provides a much more compact storage media, and an extremely small amount of DNA suffices even for huge one-time-pads. We detail procedures for two DNA one-time-pad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pair-wise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of (appropriately recoded) natural DNA, and also for the encryption of DNA encoding binary data. In the latter case, we also present a novel use of chip-based DNA micro-array technology for 2D data input and output. Finally, we examine a class of DNA steganography systems, which secretly tag the input DNA and then disguise it (without further modifications) within collections of other DNA. We consider potential limitations of these steganography methods, showing that with some assumptions on the information theoretic entropy of the plain text messages, certain DNA steganography systems may not be cryptographically secure, and can be broken. We also discuss various modified DNA steganography systems which appear to have improved security.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• GO01
  M. Garzon and C. Oehmen. Biomolecular computation in virtual test tubes. In Jonoska and Seeman [P7], pages 117--128.
  Abstract: Biomolecular computing (BMC) aims to capture the innumerable advantages that biological molecules have gained in the course of millions of years for computational purposes, in the same way that evolutionary algorithms capture, in silicon, the key properties of natural evolution. While biomolecules have resolved fundamental problems as a parallel computer system that we are just beginning to decipher, BMS still suffer from our inability to harness these properties to bring biomolecular computations to levels of reliability, efficiency and scalability that are now taken from granted with solid-state based computers. We explore an alternative approach to exploiting these properties by building virtual test tubes in electronics that would capture the best of both worlds. We describe a distributed implementation of a virtual tube, EdnaCo, on a cluster of PCs that aims to capture the massive asynchronous parallelism of BMC. We report several experimental results, such as solutions to the Hamiltonian Path problem (HPP) for large families of graphs than has been possible on single processors or has been actually carried out in wet labs. The result show that the paradigm of molecular computing can me implemented much more efficiently (time and cost wise) in silico than the corresponding wet experiments. Consequently, we pinpoint a range of practical problem sizes that would make a critical difference in establishing wet biomolecular solutions superior to electronics.
• GP00 - EGP01
  E. Goode and D. Pixton. Semi-simple splicing systems, pages 343--352. Kluwer Academic, 2000. Where Mathematics, Computer Science, Linguistic and Biology Meet.
  Abstract: The family S(LIN, REG) of languages obtained by (noniterated) spliced linear languages using regular rules does not coincide with one of the Chomsky families. We give a characterization of this family, and show that we can replace the regular rule set by a finite one.
• GP04a - GPvT
  E. Goode and D. Pixton. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Splicing to the Limit in Aspects of Molecular Computing, pages 189--201. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• GP04b - GP04
  E. Goode and D. Pixton. Recognizing splicing languages: syntactic monoids and simultaneous pumping. submitted, 2004.
• GPZ97
  V. Gupta, S. Parthasarathy, and M. J. Zaki. Arithmetic and logic operations with DNA. In Rubin and Wood [P3], pages 212--220, ftp://ftp.cs.rochester.edu/pub/papers/theory/97.DIMACS.Arithmetic_and_logic_operations_with_DNA.ps.gz.
  Abstract: A lot of research in DNA computing has been directed toward solving difficult combinatorial search problems. However, for DNA computing to be applicable on a wider range of problems, support for basic computational operations such as logic operations like AND, OR and NOT and arithmetic operations like addition and subtraction is necessary. Unlike search problems, which can be solved by generating all possible combinations and extracting the correct output, these operations mandate that only a unique output be generated by specific inputs. The question of suitability of DNA for such simple operations has so far largely been unaddressed. In this paper we describe a novel method for using DNA molecules to solve the basic arithmetic and logic operations. We also show that multiple rounds of operations can be performed in a single test tube, utilizing the output of an operation as an input for the next. Furthermore, the operations can be performed in a linear series or a series-parallel fashion and operators can be mixed to form any operation sequence.
• GR99 - GehaReif98
  A. Gehani and J. H. Reif. Microflow bio-molecular computation. In Kari et al. [P4], http://www.cs.duke.edu/~reif/paper/geha/microflow.ps, http://www.cs.duke.edu/~reif/paper/geha/microflow.pdf.
• GRG+97 - Garzon97
  Max H. Garzon, J.A. Rose, Y. Gao, R. Deaton, Donald R. Franceschetti, and R.C. Murphy. DNA implementation of finite-state machines. In Second Conference on Genetic Programming, 1997, http://www.msci.memphis.edu/~garzonm/csys/gp97fsm.ps.
• GTL04 - GBRvT
  A. Gehani and J. Reif T. LaBean. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter DNA-based Cryptography, pages 167--188. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• GWC00
  E. Goode, D. H. Wood, and J. Chen. DNA implementation of a royal road fitness evaluation. In Condon and Rozenberg [P6], pages 247--262.
  Abstract: A model for DNA implementation of Royal Road evolutionary computations is presented. An encoding for a Royal Road problem is presented. Experimental results utilizing 2-d denaturing gradient gel electrophoresis (2-d DGGE) and polyacrylamide gel electrophoresis (PAGE) for separation by fitness in this sample Royal Road problem are shown. Suggestions for possible use of the MutS and MutY proteins as tools for separation by fitness are given. Plans for future experiments and implementation are discussed.
• Hag00 - Hagi00
  M. Hagiya. From molecular computing to molecular programming. In Condon and Rozenberg [P6], pages 89--102.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• HAK+97 - HAKSY97
  M. Hagiya, M. Arita, D. Kiga, K. Sakamoto, and S. Yokoyama. Towards parallel evaluation and learning of boolean \mu-formulas with molecules. In Rubin and Wood [P3], pages 105--114.
  Abstract: A \mu-formula is a Boolean formula in which each variable occurs at most once. The paper treats its molecular representation including its queries using techniques in molecular biology. The novelty is that this method can evaluate a Boolean formula in a single tube within a short time. The preliminary experimental result suggests the possibility of parallel evaluation and learning of general \mu-formulas. This method is essentially a simulation of state transitions and can be used to simulate a decision tree or a state machine.
• Har95a - Hartmanis95-2
  Juris Hartmanis. On the computing paradigm and computational complexity. In Jirí Wiederman and Petr Hájek, editors, Mathematical Foundations of Computer Science 1995. 20th International Symposium, MFCS '95. Proceedings., volume 969 of Lecture Notes in Computer Science, pages 82--92, Prague, Czech Republic, August-September 1995. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-60246-1.
  Abstract: Computational complexity theory is the study of the quantitative laws that govern computing. Since the computing paradigm is universal and pervasive, the quantitative laws of computational complexity apply to all information processing from numerical computations and simulation to logical reasoning and formal theorem proving, as well as processes of rational reasoning. In this view, the search for what is and is not feasibly computable takes on an even deeper significance than just a central problem in theoretical computer science. The search for the limits of what is feasibly computable is the search for the limits of scientific theories and, possibly, rational reasoning.
  An overview of the state of computational complexity theory. Reiterates the argument of [Hartmanis95] that Molecular Computation cannot break the exponential barrier.
• Har95b - Hartmanis95
  Juris Hartmanis. On the weight of computations. Bulletin of the European Association for Theoretical Computer Science, 55:136--138, February 1995.
  Shows that Molecular Computation cannot break the exponential barrier: exponential-complexity algorithms remain infeasible even for fairly small problem instances. Applying the approach of [Adl94] to a 200-node graph would require an amount of DNA weighing more than the Earth. The main argument is reiterated in [Hartmanis95-2].
• HCH02
  C. E. Heitsch, A. E. Condon, and H. H. Hoos. From RNA secondary structure to coding theory: A combinatorial approach. In Hagiya and Ohuchi [PP8], pages 215--228.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• HCN+01 - HCNeo01
  T. Head, X. Chen, M. J. Nichols, M. Yamamura, and S. Gal. Aqueous solutions of algorithmic problems: emphasizing knights on a 3x3. In Jonoska and Seeman [P7], pages 191--201.
  Abstract: A pattern for performing several DNA computations is outlined using the aqueous approach, the essence of which is writing on molecules dissolved in water. Four of the indicated computations have been carried out in wet labs in the aqueous style. As an illustration, gel photos will be exhibited that confirm the correctness of a small SAT computation. Emphasis will be placed on the aqueous approach, now in progress, to the problem of producing the set of all patterns in which knights can be placed on a 3 X 3 chessboard with no knight attacking another. Currently the writing technology used is based on molecular biology. In the future we hope that light can replace biochemistry as the writing procedure.
• Hea87 - Head87
  T. Head. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bulletin of Mathematical Biology, 49(6):737--759, 1987.
  Abstract: A new manner of relating formal language theory to the study of informational macromolecules is initiated. A language is associated with each pair of sets where the first set consists of double-stranded DNA molecules and the second set consists of the recombinational behaviors allowed by specified classes of enzymatic activities. The associated language consists of strings of symbols that represent the primary structures of the DNA molecules that may potentially arise from the original set of DNA molecules under the given enzymatic activities. Attention is focused on the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules. The associated languages are analyzed by means of a new generative formalism called a splicing system. A significant subclass of these languages, which we call the persistent splicing languages, is shown to coincide with a class of regular languages which have been previously studied in other context: the strictly locally testable languages. This study initiates the formal analysis of the generative power of recombinational behaviors in general. The splicing system formalism allows observations to be made concerning the generative power of general recombination and also of sets of enzymatic activities that include general recombination.
• Hea92a - H92
  T. Head. Splicing schemes and DNA. Lindenmayer Systems; Impact on Theoretical Computer Science and Developmental Biology, pages 371--383, 1992.
• Hea92b - Head92
  T. Head. Splicing systems and DNA, volume Fixme[volume], pages 371--383. Fixme[publisher], 1992.
• Hea97a - Head97-4
  T. Head. Right splicing and reversibility. Draft., August 1997.
  Abstract: Elementary examples show that reversible languages need not be splicing languages. The results here have arisen from a persistent attempt to relate reversibility with splicing. A restricted splicing action, called right splicing, is introduced. A new class of regular languages, the DB languages, is also introduced. An algorithm is given for deciding whether an arbitrary regular language is a DB language. The conclusion that every reversible language is a right splicing language is drawn as a Corollary of a much more general Theorem presented here that provides an algorithmic construction of a right splicing representation for each DB language.
• Hea97b - Head97-2
  T. Head. Splicing representations of strictly locally testable language. Also in Journal of Discrete Applied Mathematics, 87, 139-147 (1998)., 1997.
  Abstract: The relationship between the family SH of simple splicing languages, which was recently introduced by A. Mateescu and coauthors, and the family SLT of strictly locally testable languages is clarified by establishing an ascending nest of families S_iH: i \geq 1 of splicing languages that begins with the family of simple splicing languages and has the family SLT as its union. A procedure is given which, for an arbitrary regular language L, determines whether L is in SLT and, when L is in SLT, specifies constructively the smallest family in the nest to which L belongs. Examples are given of sets of restriction enzymes for which the action on DNA molecules is naturally represented by splicing systems of the types discussed.
• Hea97c - Head97
  T. Head. Splicing system and molecular processes. In IEEE International Conference on Evolutionary Computation, 1997.
  Abstract: The splicing system concept and its history are reviewed. A proposed laboratory splicing scheme is discussed. This scheme has suggested that splicing schemes be regarded as specifying not only languages, but also dynamical systems. As an example of a new formal result on splicing languages, a theorem is stated that characterizes those regular languages that are generated by splicing systems which require only one sided context. The theorem provides an algorithm for deciding whether any arbitrary regular language can be so generated.
• Hea97d - H97
  T. Head. Splicing systems and molecular processes. In IEEE International Conference on Evolutionary Computation, pages 202--205, 1997.
• Hea98a - Head97-5
  T. Head. Hamiltonian paths and double stranded DNA. In Paun [CBMtitle], pages 80--92.
  Abstract: It is suggested than computations using DNA molecules as computing units may sometimes be simpler to carry out and less error prone if double stranded DNA molecules are used rather than the single stranded molecules currently being used. A detailed illustration is given of a biomolecular algorithm that uses double stranded DNA for the solution of the directed Hamiltonian path problem.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Hea98b - Head97-3
  T. Head. Splicing languages generated with one sided context. In Paun [CBMtitle], pages 158--181.
  Abstract: The splicing system concept was created in 1987 to allow the convenient representation in formal language theoretic terms of recombinant actions of certain sets of enzymes on double stranded DNA molecules. Characterizations are given here for those regular languages that are generated by splicing systems having splicing rules that test context on only one side. An algorithm is given for deciding whether any arbitrary regular language can be generated by a splicing system in which all splicing rules test context on the same side. Schutzenberger's concept of a constant relative to a language provides the tool for constructing the required splicing rules. To provide a potential biochemical example, the formal generative capacity of the restriction enzyme BpmI in the company of a ligase is discussed. Experimental investigation is suggested.
  Part of [HeadEA97].
• Hea00a - Head99
  T. Head. Circular suggestions for DNA computing. In A. Carbone, M. Gromov, and P. Prusinkiewicz, editors, Pattern formation in biology, vision and dynamics, pages 325--335. World Scientific Publishing Company, 2000.
• Hea00b - Head00
  T. Head. Splicing systems, aqueous computing, and beyond. In Antoniou et al. [UMC2K], pages 68--84.
  Abstract: The origin of the splicing system concept is reviewed and the original motivation for the concept is given. The concept of an aqueous computing architecture is sketched in a manner independent of specific implementations. Wet lab computational made using biomolecular implementations are reported. Hopes for future non-biomolecular realizations are confided.
• Hea01 - Head01
  T. Head. Aqueous simulations of membrane computation. manuscript, 2001.
• HG97
  A. J. Hartemink and D. K. Gifford. Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. In Rubin and Wood [P3], pages 15--25.
  Abstract: Nearly every model of DNA computation proposed to date depends upon sequence-specific hybridization operations. In order to better predict the binding specificity of arbitrary deoxyoligonucleotides, a simulator named BIND is implemented. BIND operates on a single template DNA sequence and a number of shorter primer sequences. For each primer sequence, BIND calculates a theoretical melting temperature at every position of the primer along the template, yielding a measure of binding specificity between each primer and the template. The simulator differs from previous melting temperature programs in that it is intended to be used with oligonucleotides, is designed to handle mismatched base pairs, makes use of the latest thermodynamic parameters, and provides features with DNA computation expressly in mind. This paper describes how BIND is implemented, provides corroborating evidence as to its accuracy, and offers instances of its usefulness to a range of DNA computing applications.
• HGK99 - HGK98
  A. J. Hartemink, D. K. Gifford, and J. Khodor. Automated constraint-based nucleotide sequence selection for DNA computation. In Kari et al. [P4], pages 227--235.
  Abstract: We present techniques for automating the design of computational systems built using DNA, given a set of high-level constraints on the desired behavior and performance of the system. We have developed a program called SCAN that exploits a previously implemented computational melting temperature primitive to search for a ``nucleotide space'' for sequences satisfying a pre-specified set of constraints, including hybridization discrimination, primer 5' end and 3' end stability, secondary structure reduction, and prevention of oligonucleotide dimer formation. The first version of SCAN utilized 24 hours of compute time to search a space of over 7.5 billion unary counter designs and found only 9 designs satisfying all of the pre-specified constraints. One of SCAN's designs has been implemented in the laboratory and has shown a marked performance improvements over the products of previous attempts at manual design. We conclude with some novel ideas for improving the overall speed of the program that offer the promise of an efficient method for selecting optimal nucleotide sequences in an automated fashion.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• HHS01
  T. Hinze, U. Hatnik, and M. Sturm. An object oriented simulation of real occurring molecular biological processes for DNA computing and its experimental verification. In Jonoska and Seeman [P7], pages 1--13.
  Abstract: We present a simulation tool for frequently used DNA operations on the molecular level including side effects based on a probabilistic approach. The specification of the considered operations is directly adapted from detailed observations of molecular biological processes in laboratory studies. Bridging the gap between formal models of DNA computing, we use process description methods from biochemistry and show the closeness of the simulation to the reality.
• HK96 - PSB96
  Lawrence Hunter and Teri Klein, editors. Biocomputing: Proceedings of the 1996 Pacific Symposium. World Scientific Publishing Co., Singapore, January 1996, ISBN 981-02-2578-4.
  See http://www.cgl.ucsf.edu/psb/psb96/proceedings/eproceedings.html. Contains [CsuhajEA96B], [FerrettiKobayashi96] and others.
• HKK01
  S. Hussini, L. Kari, and S. Konstantinidis. Coding properties of DNA languages. In Jonoska and Seeman [P7], pages 57--69.
  Abstract: The computational language of a DNA-cased system consists of all the words (DNA strands) that can appear in any computation step of the system. In this work we define properties of languages which ensure that the words of such languages will not form undesirable bonds when used in DNA computation. We give several characterization of the desired properties and provide methods for obtaining languages with such properties. The decidability of these properties is addressed as well. As an application we consider splicing systems whose computation language is free of certain undesirable bonds and is generated by nearly optimal comma-free codes.
• HLPR - HeadEA97
  T. Head, E. Laun, D. Pixton, and K. J. Reddy. Manuscripts'97 from members of the codes, languages \& DNA group. Consists of Introduction by T. Head, [LR97], [Head97-2] and ...
• HMG99
  Alexander J. Hartemink, Tarjei S. Mikkelsen, and David K. Gifford. Simulating biological reactions: A modular approach. In Winfree and Gifford [P5], pages 111--121.
  Abstract: We develop a general framework for simulating a sequence of biological reactions using small simulation modules. We demonstrate the usefulness of such a framework by implementing a simulator called the cybercycler. The cybercycler contains DNA hybridization, polymerization, ligation, and melting modules linked together to simulate a thermocycling process. This simulator enables us to interpret the behavior of our own programmed mutagenic unary counter in the laboratory. We describe the modules we implemented and then present a comparison of output from the cybercycler with the results of laboratory experiments to evaluate the effectiveness of the cybercycler simulator. We define a concrete specification for transformation modules and for populations of molecules passed between modules. This specification enables the construction of tools for simulating an arbitrarily complex sequence of biological reactions. We provide Java interfaces and classes for building such tools.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• HO02 - PP8
  M. Hagiya and A. Ohuchi, editors. DNA Computing: 8th International Workshop on DNA-Based Computers, DNA8, Sapporo, Japan, June 10-13, 2002. Revised Papers, volume 2568 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, New York, 2002.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• HPG02 - Head02
  T. Head, D. Pixton, and E. Goode. Splicing systems: Regular languages amd below. In Hagiya and Ohuchi [PP8], pages 262--268.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• HPP97 - HPP
  T. Head, G. Paun, and Dennis Pixton. Language theory and molecular genetics. Generative mechanisms suggested by DNA recombination, volume 2, pages 295--360. Springer Verlag, Berlin, Heidelberg, New York, 1997. Handbook of Formal Languages, 3 volumes.
  [HFL]
• HPPar - HPP96
  T. Head, G. Paun, and D. Pixton. Generative Mechanisms Suggested by DNA Recombination, volume 2, page Fixme[pages]. Fixme[publisher], Fixme[year]. Handbook of Formal Languages.
• HPR02
  T. Harju, I. Petre, and G. Rozenberg. The computational nature of gene assembly in ciliates. In Proceedings of ICGT, International Conference on Graph Transformations, pages 430--434, 2002. in LNCS 2505.
• HPR04 - HPRvT
  T. Harju, I. Petre, and G. Rozenberg. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs, pages 202--212. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• HRB+00 - HR00
  T. Head, G. Rozenberg, R. S. Bladergroen, C. K. D. Breek, P. H. M. Lommerse, and H. P. Spaink. Computing with DNA by operating on plasmids. Bio Systems, 57(2):87--93, 2000.
• HSa - HS00
  T. Hinze and M. Sturm. A universal functional approach to DNA computing and its experimental practicability. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• HSb - HS02
  H. Hug and R. Schuler. Implementation of a random walk method for solving 3-SAT on circular DNA molecules. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• HS00 - HS00-1
  T. Hinze and Monika Sturm. Towards an in-vitro Implementation of a Universal Distributed Splicing Model for DNA Computation, pages 185--189. Rudolf Freund, editor, 2000. University of Technology, Vienna, Austria, September 25-27, 2000.
• HS01 - HSc01
  H. Hug and R. Schuler. DNA-based parallel computation of simple arithmetic. In Jonoska and Seeman [P7], pages 321--328.
  Abstract: We propose a model for representing and manipulating binary numbers on a DNA chip which allows parallel execution of simple arithmetic. As an example we describe how addition of large binary numbers can be done by using a DNA chip. The number of steps is independent of the size (bits) of the numbers. However, the time for some biochemical reactions is still large, and increases with the size of the sequences to be assembled.
• HvV98 - HvV
  H. Jan Hoogeboom and N. van Vugt. The power of H-systems: does representation matter? In Paun [CBMtitle], pages 158--181, http://www.wi.leidenuniv.nl/TechRep/1997/tr97-16.ps.gz.
  Splicing rules of the form (u,v,w,x) are usually represented as strings of the form u \# v \ w \# x. The effect of splicing with rules from several families of languages has been determined in the literature. We investigate whether the results about splicing systems obtained in this way are indeed properties of the splicing system and not of the specific string representation of the rules. We study in detail single and iterated splicing systems, by considering the alternative string representation u \# w \ v \# x, and indeed obtain the same classifications as for the standard representation. We briefly discuss some related representations.
  in Proceedings of Workshop on Molecular Computing, August 1997, Mangalia, Romania
• HvV00
  H.J. Hoogeboom and N. van Vugt. Fair sticker languages. Acta Informatica, 37:213--225, 2000, http://www.liacs.nl/TechRep/2000/tr00-01.ps.
  Abstract: Codings of fair sticker languages are characterized as languages accepted by blind one-counter automata.
• HYG99
  T. Head, M. Yamamura, and S. Gal. Aqueous computing: writing on molecules. In Proceedings of the Congress on Evolutionary Computation, pages 1006--1010, 1999.
• IH89 - CulikHarju92
  Karel Culik II and Tero Harju. Dominoes and the regularity of DNA splicing languages. In G. Ausiello, M. Dezani-Ciancaglini, and S. Ronch Della Rocca, editors, Proceedings of the 16th International Colloquium on Automata, Languages and Programming, number 372 in Lecture Notes in Computer Science, pages 222--233, Stresa, Italy, July 1989. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-51371-X.
  Abstract: We introduce semigroups of dominoes as a tool for working with sets of linked strings. In particular, we are interested in splicing semigroups of dominoes. In the special case of alphabetic (symbol-to-symbol linked) dominoes the splicing semigroups are essentially equivalent to the splicing systems introduced by Head to study informational macromolecules, specifically to study the effects of sets of restriction enzymes and ligase that allow DNA molecules to be cleaved an reassociated to produce further molecules. Our main result is that in the case of alphabetic dominoes the splicing semigroup generated from an initial regular set is again regular. This implies positive solution of two open problems stated by Head, namely the regularity of splicing systems and the decidability of their membership problem.
• IH91 - CulikHarju91
  K. Culik II and T. Harju. Splicing semigroups of dominoes and DNA. Discrete Applied Mathematics, 31:261--277, 1991.
• IM96
  L. Ilie and V. Mitrana. Crossing-over on languages. a formal representation of the recombination of genes in a chromosome. In German Conference on Bioinformatics GBC'96, pages 87--93, 1996. Leipzig, Germany.
• IM02 - IM97-1
  L. Ilie and V. Mitrana. Grammars and Automata for String Processing: From Mathematics and Computer Science to Biology and Back, chapter Crossing-over on languages. A formal representation of the chromosome recombination. Taylor and Francis, London, 2002. C. Martíin-Vide and V. Mitrana eds.
• IMVP00a - IMVP00
  M. Ito, C. Martín-Vide, and G. Paun. A characterization of Parikh sets of ET0L languages in terms of P systems. unpublished, 2000.
• IMVP00b - IMP00
  M. Ito, C. Martín-Vide, and G. Paun. A characterization of parikin sets of ET0L languages in terms of P systems. manuscript, 2000.
• IMVPP02 - IMVeo02
  M. Ionescu, C. Martín-Vide, A. Paun, and G. Paun. Unexpected universality results for three classes of P systems with symport/antiport. In Hagiya and Ohuchi [PP8], pages 281--290.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• IPY01 - WST01
  M. Ito, G. Paun, and S. Yu, editors. Words, Semigroups, and Transductions. World Scientific, Singapore, 2001, ISBN 981-02-4739-7. Festschrift in Honor of Gabriel Thierrin.
  The book contains between others: [CM01], [EPeo01-3], [KP01], [Sal01]
• IS04 - ISvT
  M. Ito and R. Sugiura. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter n-Insertion on Languages, pages 213--218. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Ist03 - Istrail03
  S. Istrail. Principles of computing in genomic regulatory systems: the Davidson model. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 125', 2003.
• Jag - Jag00
  Edwin W. H. Jager. Desktop biofactories? new microrobots might manipulate single cells, http://www.eurekalert.org/releases/aaas-dbn062200.html. Only on the net. Science authors report.
• Ji99 - Ji98
  S. Ji. The cell as the smallest DNA-based molecular computer. In Kari et al. [P4], pages 123--133.
  Abstract: The pioneering work of Adleman (1994) demonstrated that DNA molecules in test tubes can be manipulated to perform a certain type of mathematical computation. This has stimulated a theoretical interest in the possibility of constructing a certain type of mathematical computation. This has stimulated a theoretical interest in the possibility of constructing DNA--based computers. To gauge the practicality of realizing such microscopic computers, it was thought necessary to learn as much as possible from the biology of living cells - presently the only known DNA-based molecular computer in existence. Here the recent development theoretical model of living cell (the Bhopalator) and its associated theories (e.g. cell language), principles, laws and concepts (e.g. conforms, IDS's are briefly reviewers and summarized in the form of a set of live laws of 'molecular semiotics' (synonyms include 'microsemiotics' , 'cellular semiotics', or 'cytosemiotics') - the study of signs mediating measurements, computation, and communication on the cellular and molecular levels. Hopefully, these laws will find practical applications in designing DNA-based computing system.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• JK96 - JonaskaKarl96
  N. Jonoska and S. A. Karl. A molecular computation of the road coloring problem. In Landweber and Baum [2AWDBC].
  Abstract: Two algorithms for molecular computation of the road coloring problem are presented. We present in detail the laboratory techniques to implement these algorithms. In both of these algorithms a new operation of substring matching in the process of separating molecules is introduced. The laboratory techniques of the implementation are discussed.
• JK97 - Jonoska97
  Natasa Jonoska and Stephen A. Karl. Ligation experiments in computing with DNA. In IEEE International Conference on Evolutionary Computation, pages 261--265, 1997.
  Abstract: Relative to a short history, the use of DNA in molecular computing applications has received considerable attention. Although several theoretical and computational studies have been considered, descriptions of laboratory studies have been lacking. In this paper, we detail results from several laboratory experiments that highlight the use of thermostable enzymes in ligation and polymerase chain reactions (LCR and PCR) and explore their utility in DNA-based computing.
• JKS97
  N. Jonoska, S. A. Karl, and M. Saito. Creating 3-dimensional graph structures with DNA. In Rubin and Wood [P3], pages 192--203.
  Abstract: We propose solving computational problems with DNA molecules by physically constructing 3-dimensional graph structures. Building blocks consisting of intertwined strands of DNA are used to represent graph edges and vertices. Different blocks would be combined to form all possible 3-dimensional structures representing a graph. The solution to the Hamiltonian cycle problem provided requires a constant number of steps regardless of the number of vertices. If a solution to the graph problem exists, then a fully closed circular molecule would be formed and can be isolated. This paper introduces a method of using 3D structures in computing which might significantly improve the efficiency of computations with DNA.
• JKS98a - JKS98
  N. Jonoska, S. A. Kari, and M. Saito. Graph structures in DNA computing. In Paun [CBMtitle], pages 93--110.
  Abstract: We show that 3-dimensional graph structures can be used for solving computational problems with DNA molecules. Vertex building blocks consists of k-armed (k = 3 or k = 4) branched junction molecules are used to form the graph. We present the solution to the 3-SAT problem and to the 3-vertex-colorability problem. Construction of one graph structure (in many copies) in both procedures is sufficient for determining the answer to the problem. In our proposed solution, for the 3-SAT, the number of steps required for the algorithm is equal to the number of variables in the formula, and for the 3-vertex-colorability problem, the algorithm requires constant number of steps, regardless of the size of the graph. The vertex and edge building blocks are made of stable molecules.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• JKS98b - JonosEA98
  N. Jonoska, S. A. Karl, and M. Saito. Three dimensional DNA structures in computing. In Kari et al. [P4], pages 143--153.
  Abstract: We show that 3-dimensional graph structures can be used for solving computational problems with DNA molecules. Vertex building blocks consisting of small k-armed (k = 3 or 4) branched junction molecules are used to form graphs. We present solutions to the 3-SAT problem and to the 3-vertex colorability problem. Construction of one graph structure (in many copies) is sufficient to determine the solution to the problem. In our proposed solutions for the 3-SAT, the number of steps required for the algorithm is equal to the number of variables in the formula. For the 3-vertex-colorability problem, the procedure requires a constant number of steps regardless of the size of the graph.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• JKS99
  N. Jonoska, S. A. Karl, and M. Saito. Three dimensional DNA structures in computing. BioSystems, 52:243--253, 1999.
• JLS04 - JLSvT
  N. Jonoska, S. Liao, and N. C. Seeman. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Transducers with Programmable Input by DNA Self-assembly, pages 219--240. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• JM03
  N. Jonoska and K. Mahalingam. Languages of DNA based code words. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 58--68, 2003.
• JM04 - JMvT
  N. Jonoska and K. Mahalingam. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Methods for Constructing Coded DNA Languages, pages 241--253. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• JPR04 - volTH
  N. Jonoska, G. Paun, and G. Rozenberg, editors. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, volume 2950 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, New York, 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• JS01a - JS01
  N. Jonoska and M. Saito. Boundary components of thickened graphs. In Jonoska and Seeman [P7], pages 70--81.
  Abstract: Using linear DNA segments and branched junction molecules many different three-dimensional DNA structures (graphs) could be self-assembled. We investigate maximum and minimum numbers of circular DNA that form these structures. For a given graph G, we consider compact orientable surfaces, called thickened graphs of G, that have G as a deformation retract. The number of boundary curves of a thickened graph G corresponds to the number of circular DNA strands that assemble into the graph G. We investigate how this number changes by recombination or edge additions and relate to some results from topological graph theory.
• JS01b - P7
  N. Jonoska and N. C. Seeman, editors. DNA Computing: 7th International Workshop on DNA-Based Computers, DNA7, Tampa, FL, USA, June 10-13, 2001. Revised Papers, volume 2340. Springer Verlag, Berlin, Heidelberg, New York, 2001.
  The volume contains [SY01], [HHS01], [WBKeo01], [EHPR01], [APa01-1], [MMP01-1], [UHK01], [GO01], [Sak01], [HKK01], [MR01], [MGC01], [PC01], [JS01], [HSc01], [MGLeo01], [FSR01], [BKS01], [WY01], [MY01], [HCNeo01], [MYS01], [RLBeo01], [YHM01], [RFL01]
• JTT+01 - MTeo01
  A. P. Mills Jr., M. Turberfield, A. J. Turberfield, B. Yurke, and P. M. Platzman. Experimental aspects of DNA neural network computation, volume 5(1), pages 10--18. Springer Verlag, Berlin, Heidelberg, New York, 2001, http://link.springer.de/link/service/journals/00500/tocs/t1005001.htm.
• JYP99a - MillsEA98
  A. P. Mills Jr., B. Yurke, and P. M. Platzman. Article for analog vector algebra computation. In Kari et al. [P4], pages 175--180.
  Abstract: We introduce the concept of an analog neural network represented by chemical operations performed on strands of DNA. This new type of DNA computing has the advantage that is should be fault tolerant and thus more immune to DNA hybridization errors than a Boolean DNA computer. We describe a particular set of DNA operations to effect the interconversion of electrical and DNA data and to represent the Hopfield associative memory and the feed-forward neural network of Rumelhart et al. We speculate that networks containing as many as 10⁹ neurons might be feasible.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• JYP99b - MYP99
  A. P. Mills Jr., B. Yurke, and Philip M. Platzman. DNA analog vector algebra and physical constraints on large-scale DNA-based neural network computation. In Winfree and Gifford [P5], pages 65--73.
  Abstract: An analog neural network may be represented by chemical operations performed on strands of DNA. This new type of DNA computing has the possible advantage of being fault tolerant and thus more immune to DNA hybridization errors than a Boolean DNA computer. We describe a particular set of DNA operations to effect the interconversion of electrical and DNA data and to represent the Hopfield associative memory. We consider the constraints imposed by Poisson statistics and diffusion times on the amount of DNA needed and the time required to perform computations using a DNA neural network. For an m-unit Hopfield neural network with mm connections, we derive expressions for these quantities as a function of m. A Hopfield network with a memory capacity of 10¹⁴ bits (comparable to the human brain) would have a cycle time of a few hours and would require about 100 \mumoles of DNA per cycle and 8 cycles for convergence.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• Kar91 - Kari
  L. Kari. On insertion and deletion in formal languages. PhD thesis, University of Turku, 1991.
• Kar96 - Kari96
  L. Kari. DNA computing: tomorrow's reality. Bulletin of the EATCS, 59:256--266, June 1996. See also [Kari01].
• Kar97a - Kar97
  L. Kari. DNA computing: arrival of biological mathematics. The Mathematical Intelligencer, 19(2):9--22, 1997, http://www.csd.uwo.ca/~lila/intel1.ps. Earlier version under the title DNA computers, tomorrow's reality. Bulletin of the European Association for Theoretical Computer Science, (59):256--266, June 1996 http://www.csd.uwo.ca/~lila/amsn.ps.
  Also in [SNAC]
• Kar97b - Kari97
  L. Kari. From Micro-soft to Bio-soft: Computing with DNA. In Fixme[booktitle], 1997. Also in [SNAC].
• Kar01 - Kari01
  L. Kari. DNA Computers: Tomorrow's Reality, volume -, pages 811--829. World Scientific, 2001.
  See also [Kari96].
• Kaz99 - Kazic98
  T. Kazic. After the Turing machine: A metamodel for molecular computing. In Kari et al. [P4], pages 111--122.
  Abstract: Problems implementing DNA computers stem from the physical nature of molecules and their interactions. The current theory of computation requires assumptions, at best, are extremely crude approximations of the physical chemistry. Here I consider the hypothesis that discarding those assumptions in favour of more physically realistic model would produce a more comprehensive theory of computing, yielding both theoretical insights and help in designing better molecular computers. I describe the discordances between the theories of physical biochemistry and computation, indicate some elements of a more comprehensive theory, and discuss some of the challenges of the construction of a unified theory faces.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• KC97
  Kamala Krithivasan and Venkatesan T. Chakaravarthy. Array splicing systems. In G. Paun and A. Salomaa, editors, Lecture Notes in Computer Science, volume 1218, pages 346--365. Springer Verlag, Berlin, Heidelberg, New York, 1997.
  Abstract: In this paper the concept of splicing is extended to arrays and array or 2D splicing systems are defined. Various subclasses of 2D splicing systems are defined and a restricted class viz. finite simple splicing systems is studied. The hierarchy among the various subclasses of finite simple splicing systems and their relationship to the strictly locally testable languages are established.
• KCH - KCH00
  C-Y. Kao, J. Chen, and J-T. Horng. A DNA genetic algorithm for knapsack problems. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• KCL95
  Peter D. Kaplan, Guillermo Cecchi, and Albert Libchaber. Molecular computation: Adleman's experiment repeated. Technical report, NEC Research Institute, 1995.
• KCL96 - KaplanEA96
  P. D. Kaplan, G. Cecchi, and A. Libchaber. DNA based molecular computation: template-template interactions in PCR. In Landweber and Baum [2AWDBC].
  
  • Analysis of Adleman's method on even simpler graphs.
  • Shows PCR (used in `extract' and `amplify') to be a source of errors due to template-template interactions (dsDNA is separated into single strands, that are intended to bind to the primers, but also bind to each other) resulting in ``weird'' DNA (e.g. with folds).
  • Electrophoresis cannot distinguish normal and ``weird'' DNA well enough, but no better method for analysing DNA currently exists.
  • High concentrations of template or product amplify template-template interaction problems.
• KCR97
  Kamala Krithivasan, Venkatesan T. Chakaravarthy, and R. Rama. Array splicing systems. New trends in formal languages. Control, cooperation and combinatorics, 1218:346--365, 1997. Lecture Notes in Computer Science.
• KdMM98 - KoppEA98
  Martin U. Kopp, Andrew J. de Mello, and Andreas Manz. Chemical amplification: Continuous-flow PCR on a chip. Science, 280, May 15, 1998.
  Abstract: A micromachined chemical amplifier was successfully used to perform the polymerase chain reaction(PCR) in continuous flow at high speed. The device is analogous to an electronic amplifier and relies on the movement of sample through thermostatted temperature zones on a glass microchip. Input and output of material (DNA) is continuous, and amplification is independent of input concentration. A 20-cycle PCR amplification of a 176-base pair fragment from the DNA gyrase gene of Neisseria gonorrhoeae was performed at various flow rates, resulting in total reaction times of 90 seconds to 18.7 minutes.
• KG97
  J. Khodor and D. K. Gifford. The efficiency of sequence-specific separation of DNA mixtures for biological computing. In Rubin and Wood [P3], pages 26--34.
  Abstract: We report a series of experimental observations on the efficiency and fidelity of sequence-specific DNA extraction operations. We examined the solution-based annealing of bead-bound probes to target molecules followed by magnetic separation of the annealed probe-target complexes from solution. Our experiments measured how efficiently a 20-mer probe could be used to purify a 40-mer radiolabeled single-stranded target with varying target concentrations. Our results suggest that with perfectly homologous probes and targets, recovery rates of 3-28% can be expected. When the target is not homologous to the probe less than 1% of the target is recovered. The high variance of our recovery rate is consistent with the PNA-DNA results of Orum, et al. [Orum]. Based on our experience we propose that the biological computing community develop a standard set of benchmarks for key primitive operations. To this end, we are making our sequences and oligonucleotides available to other interested research groups.
• KG99 - KhoGif98
  J. Khodor and D. K. Gifford. Design and implementation of computational systems based on programmed mutagenesis. In Kari et al. [P4], pages 93--97.
  Abstract: In a new system for DNA computation called programmed mutagenesis, DNA strands are rewritten according to ``rules'' that are sequence specific. In a programmed mutagenesis reaction DNA sequences undergo programmed changes, and these changes are implemented by an in-vitro mutagenesis system that is based on thermal cycling the rewriting reaction. We describe experimental results that demonstrate the key aspects of programmed mutagenesis. These results include the creation of full-length product DNA molecules that have embedded rewriting, the ability for later sequence changes to depend on earlier sequence changes, and the ability for multiple oligonucleaotides to be active in close proximity on a template sequence. We also discuss the application of programmed mutagenesis to computational problems.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• KH02 - Zimm00
  Zimmermann Karl-Heinz. On applying molecular computation to binary linear codes. submitted to: IEEE Transactions on Information Theory, 48(2):505--509, 2002.
  Abstract: Adleman's successful solution of a seven-vertex instance of the NP complete directed Hamiltonian path problem by a DNA algorithm initiated the field of biological computing. In this correspondence, we describe DNA algorithms based on the sticker model to perform encoding, minimum distance computation, and maximum likelihood decoding to binary linear codes. Finally, we discuss the feasibility and limitations of our sticker algorithms.
• KIAK99 - KBAK99
  J. R. Koza, F. H. Bennett III, D. Andre, and M. A. Keane. Evolution as computation, chapter Genetic programming: biologically inspired computation that creatively solves non-trivial problems, pages 95--124. In Landweber and Winfree [LW99], 1999.
• Kim97
  Sam Myo Kim. Identifying genetically spliced languages. In IEEE International Conference on Evolutionary Computation, pages 231--235, 1997.
  Abstract: A genetic splicing system involves DNA strings mixed with enzymes and a ligase that allow the strings to be cleaved and recombined to produce new strings in addition to the original ones. This paper presents an algorithm which, given a set of enzymes and a set I of DNA strings in terms of the reduced finite state automaton which recognizes the set, decides whether I can be spliced with the given enzymes and a finite number of DNA strings or not. The paper also shows how to find the initial DNA strings, if the answer is positive.
• Kim98
  Sam Myo Kim. Computational modeling for genetic splicing systems. SIAM Journal on Computing, 26(5):1284--1309, 1998, http://epubs.siam.org/sam-bin/getfile/SICOMP/articles/26389.ps.Z.
  Abstract: A genetic splicing system involves DNA molecules mixed with enzymes and a ligase that allow the molecules to be cleaved and recombined to produce other molecules in addition to the original ones. Recently, using formal language theory, several researchers have investigated the string properties of DNA molecules that may potentially arise from the original set of molecules under the effect of the given restriction enzymes. This paper introduces an algorithm which, given a splicing system whose initial set of strings is regular, constructs a finite state automaton that recognizes the set of DNA molecules spliced by the system. This algorithm solves the open problem of constructing such an automaton and shows a direct approach to the proof of regularity of spliced languages.
• KK98
  K. Krithivasan and S. R. Kaushik. Some results on array splicing. In Paun [CBMtitle], pages 295--313.
  Abstract: Array splicing systems were considered in [KC97]. In this paper, we consider persistent and permanent array splicing systems and the concept of constants for such systems. We prove some results about these systems and some reduction theorems. In addition it is shown that there are strictly locally testable array languages that are not splicing languages at all.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• KKA02
  S. Kobayashi, T. Kondo, and M. Arita. On template method for DNA sequence design. In Hagiya and Ohuchi [PP8], pages 205--214.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• KKG01 - KKG
  L. Kari, R. Kitto, and G. Gloor. A computer scientist's guide to molecular biology. Soft Computing, 5(2):95--101, 2001.
• KKJ - KKK01
  Yevgenia Khodor, Julia Khodor, and T. F. Knight Jr. Experimental conformation of the basic principles of length-only discrimination. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• KKL99
  L. Kari, J. Kari, and L. Landweber. Jewels are forever, chapter Reversible molecular computation in ciliates, pages 353--363. Springer Verlag, Berlin, Heidelberg, New York, 1999. J. Karhum\"aki and H. Maurer and G. Paun and G. Rozenberg (eds).
• KKM01
  A. Kelemenova, J. Kememen, and V. Mitrana. Toward biolinguistics. new developments in formal language theory inspired from biology. Grammars, 4:187--203, 2001.
• KKOT - KKeo03
  S. Kobayashi, T. Kondo, K. Okuda, and E. Tomita. Extracting globally structure free sequences by local structure freeness. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• KKW95
  Richard M. Karp, Claire Kenyon, and Orli Waarts. Error resilient DNA computation. Research report 95-20, Laboratoire de l'Informatique du Parallélisme, Ecole Normale Supérieure de Lyon, 46, Allée d'Italie 69364 LYON CEDEX 07 - FRANCE, September 1995, ftp://ftp.lip.ens-lyon.fr/pub/Rapports/RR/RR95/RR95-20.ps.Z.
  Abstract: The DNA model of computation, with test tubes of DNA molecules encoding bit sequences, is based on three primitives, extract-a-bit, merge-two-tubes and detect-emptiness. Perfect operations can test the satisfiability of any boolean formula in linear time. However, in reality the extract operation is faulty. We determine the minimum number of faulty extract operations required to simulate a single highly reliable extract operation, and derive a method for converting any algorithm based on error-free operations to an error-resilient one.
  Achieves a more reliable extract by repeatedly performing extract in a series of test tubes. The DNA strands perform a biased random walk between the tubes.
• KKW96 - KarpEA96-2
  Richard M. Karp, Claire Kenyon, and Orli Waarts. Error-resilient DNA computation. In Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, pages 458--467. SIAM, January28--30 1996.
• KL99
  L. Kari and L. F. Landweber. Computational power of gene rearrangement. In Winfree and Gifford [P5], pages 207--216.
  Abstract: In [LandKari98] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model has the computational power of a Turing machine. This indicates that, in principle, some unicellular organisms may have the capacity to perform any computation carried out by an electronic computer.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• KLR99 - KleinEA98
  J. P. Klein, T. H. Leete, and H. Rubin. A biomolecular implementation of logical reversible computation with minimal energy dissipation. In Kari et al. [P4], pages 15--23.
  Abstract: Energy dissipation associated with logic operations imposes a fundamental physical limit on computation and is generated by the entropic cost of information erasure, which is a consequence of irreversible logic elements. We show how to encode information in DNA and use DNA amplification to implement a logically reversible gate that comprises a complete set of operators capable of universal computation. We also propose a method using this design to connect, or 'wire', these gates together in a biochemical fashion to create a logic network, allowing complex parallel computation to be executed. The architecture of the system permits highly parallel operations and has properties that resemble well known genetic regulatory systems.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• KLR01 - KLeo
  S. N. Krishna, K. Lakshmanan, and R. Rama. Hybrid P systems. Romanian J. of Information Science and Technology, 4(1-2):111--123, 2001.
• KMPR01
  S. Kobayashi, V. Mitrana, G. Paun, and G. Rozenberg. Formal properties of PA-matching. Theoretical Computer Science, 2(262--1):117--131, 2001.
• KMRS - KurtzEA96-2
  Stuart A. Kurtz, Stephen Mahaney, James Royer, and Janos Simon. Biological computing, http://www.cs.uchicago.edu/~stuart/Research/bc.ps. In L. Hemaspaandra and A. Selman, editors, Complexity Retrospective II.
  Abstract: Adleman's [Adl94] successful solution of a seven-vertex instance of the NP-complete Hamiltonian Path problem by recombinant DNA technology initiated the field of biological computing. We propose a very different model of molecular computing based on the biochemistry of RNA editing and RNA translation. In our model, individual molecules become fully capable general purpose computers.
• KMRS96 - KurtzEA96
  S. A. Kurtz, S. R. Mahaney, J. S. Royer, and J. Simon. Active transport in biological computing (preliminary version). In Landweber and Baum [2AWDBC], http://www.cs.uchicago.edu/~stuart/Research/transport.ps.
  Abstract: Early papers on biological computing focused on combinatorial and algorithmic issues, and worked with intentionally oversimplified chemical models. In this paper, we reintroduce complexity to the chemical model by considering the effect problem size has on the initial concentrations of reactants, and the effect this has in turn on the rate of production and quantity of final reaction products. We give a sobering preliminary analysis of Adleman's technique for solving Hamiltonian path. Even on the simplest problems, the annealing phase of Adleman's technique requires time \Omega(n<sup>2</sup>) rather than the O(\log n) complexity given by a computationally inspired but chemically naive analysis. On more difficult problems, not only does the rate of production of witnessing molecules drop exponentially in problems size, the final yield also drops exponentially. These issues are not objections to biological computing per se, but rather difficulties to be overcome in its development as a viable technology.
• KMVP - KMP00
  M. Kudlek, C. Martín-Vide, and G. P/uaun. Toward FMT (formal macroset theory). In Calude et al. [WMP2000], pages 149--158.
• KMVP04 - KVPvT
  L. Kari, C. Martín-Vide, and A. Paun. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter On the Universality of P Systems with Minimal Symport/Antiport Rules, pages 254--265. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Kni99 - Kn99
  R. D. Knight. Evolution as computation, chapter Genetic code evolution in the RNA world and beyond, pages 160--178. In Landweber and Winfree [LW99], 1999.
• KNY+ - KNYeo01
  S. Kashiwamura, M. Nakatsugawa, M. Yamamoto, T. Shiba, and A. Ohuchi. Towards optimization of PCR protocol in DNA computing. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• Kob00 - K00
  S. Kobayashi. Concentration prediction of pattern reaction systems. In Calude et al. [WMP2000], pages 112--123.
  Abstract: In this paper, we will propose a formal system for analyzing the computational capability of chemical reaction systems of linear molecules. In this model, each linear molecule is represented as a string w with a real value c, where c is the concentration of the molecule w. Thus, the system could be regarded as a real-valued multiset system dealing with linear structures (strings). We further discuss on the problem of predicting the concentration of a molecule w at the specific time t in a given chemical reaction system. In particular, we give a polynomial time prediction algorithm for ligation reaction systems.
• KP01
  L. Kari and A. Paun. Words, Semigroups, and Transductions, chapter String Operations Suggested by DNA Biochemistry: The Balanced Cut Operation, page fixme[pages]. World Scientific, Singapore, 2001.
• KPR+96 - KPRSY96
  L. Kari, G. Paun, G. Rozenberg, A. Salomaa, and S. Yu. DNA computing, matching systems, and universality. Technical Report 49, Turku Center for Computer Science, Turku University, Department of Mathematics, 20014 Turku, Finland, October 1996, http://www.tucs.abo.fi/cgi-bin/getps.cgi/publications/techreports/TR49.ps.gz.
  Abstract:: We introduce the matching systems, a computability model which is an abstraction of the way of using the Watson-Crick complementarity when computing with DNA in the Adleman style, [Adl94]. Several types of matching systems are shown to have the same power as finite automata, one variant is proved to be equivalent to Turing machines, and another one is found to have a strictly intermediate power.
• KPR+98 - KPRSY98
  L. Kari., G. Paun, G. Rozenberg, A. Salomaa, and S. Yu. DNA computing, sticker systems and universality. Acta Informatica, 35:401--420, 1998.
• KPS96
  L. Kari, G. Paun, and A. Salomaa. The power of restricted splicing with rules from a regular language. The Journal of Universal Computer Science, 2(4):224--240, April 1996, http://www.iicm.edu/jucs_2_4/the_power_of_restricted/ps/paper.ps.
  Abstract: We continue the investigations begun in [PRS95-1] (Intern. J. Computer Math., to appear) on the relationships between several variants of the splicing operation and usual operations with formal languages. The splicing operations are defined with respect to arbitrarily large sets of splicing rules, codified as simple languages. The closure properties of families in Chomsky hierarchy are examined in this context. Several surprising results are obtained about the generative or computing power of the splicing operation. Many important open problems are mentioned.
• KPTY97
  L. Kari, G. Paun, G. Thierrin, and S. Yu. At the crossroads of DNA computing and formal languages: Characterizing recursively enumerable languages using insertion-deletion systems. In Rubin and Wood [P3], pages 318--333.
• KRa - KR00-6
  S. N. Krishna and R. Rama. Breaking DES using P systems. TCS, to appear.
• KRb - KR01
  S. N. Krishna and R. Rama. Insertion-deletion P systems. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• KR10 - KR00-1
  S. N. Krishna and R. Rama. A note on partial/full parallel rewriting in P systems. Bulletin of EATCS, 73, feb 200r10.
• KR99
  S. N. Krishna and R. Rama. A variant of P systems with active membranes: attacking NP-complete problems. Romanian Journal of Information Science and Technology, 2(4):357--367, 1999.
• KR00a - KrRa00
  S. N. Krishna and R. Rama. On simple P systems. manuscript, 2000.
• KR00b - KR00-2
  S. N. Krishna and R. Rama. On simple P systems with external output. submitted, 2000.
• KR00c - KR99-1
  S. N. Krishna and R. Rama. On the power of P systems with sequential and parallel rewriting. International J. of Computer Math., 1-2(77):1--14, 2000.
• KR00d - KR00-5
  S. N. Krishna and R. Rama. On the power of P systems with sequential/parallel rewriting. Inter. J. Computer Math., 76(1-2):317--330, 2000.
• KR01a - KR00-8
  S. N. Krishna and R. Rama. Insertion-deletion P systems. In preproceedings of DNA Computing, 7th international Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A., 10-13 June 2001, 2001.
• KR01b - KR00-4
  S. N. Krishna and R. Rama. P systems with replicated rewriting. Journal of Automata Languages and Combinatorics, 6(3):345--350, 2001.
• KR01c - KR00-7
  S. N. Krishna and R. Rama. Time-varying and null parallel P systems. submitted, 2001.
• Kri00 - Kr00
  S. N. Krishna. Computing with simple P systems. In Calude et al. [WMP2000], pages 124--137.
  Abstract: The P systems were recently introduced as a new model for distributed parallel computing. We describe in this paper, a new variant of P system: simple P systems. We consider two variants of simple P systems: rewriting simple P systems and splicing simple P systems. Both the variants are proved to be computationally complete. In the case of rewriting simple P systems, computational completeness is achieved using two membranes with priorities, whereas in splicing simple P systems, the same is achieved by systems of degree seven and no priorities.
  TR140, CDMTCS, Univ. Auckland, 2000
• KRK - KR00-9
  S. N. Krishna, R. Rama, and K. Krithivasan. P systems with pictures objects. Acta Cibernetica, to appear.
• KRW99 - P4
  L. Kari, H. Rubin, and D. H. Wood, editors. Proceedings of the 4th DIMACS meeting on DNA based computers, volume 52, (1--3). Elsevier, 1999.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• KS01 - BKS01
  M. Sakthi Balan NAd K. Krithivasan and Y. Sivasubramanyam. Peptide computing: universality and computation. In Jonoska and Seeman [P7], pages 290--299.
  Abstract: This paper considers a computational model using the peptide-antibody interactions. These interactions which are carried out in parallel can be used to solve NP-complete problems. In this paper we show how to use peptide experiments to solve the Hamiltonian Path Problem (HPP) and a particular version of Set Cover problem called Exact Cover by 3-Sets problem. We also prove that this model of computation is computationally complete.
• KSG+00 - KSeo00
  K. Komiya, K. Sakamoto, H. Gouzo, S. Yokoyama, M. Arita, A. Nishikawa, and M. Hagiya. Successive state transitions with i/o interface by molecules. In Condon and Rozenberg [P6], pages 17--26.
  Abstract: This paper reports three experimental achievements in our computation model based on `whiplash' reactions. We first show that a single-stranded DNA (ssDNA) can serve as an independent machine by using a solid support technique. Second, we show how to append an arbitrary sequence, e.g. a transition state or a PCR primer, to the 3'- end of a molecular machine, thus realizing its I/O interface. Finally we demonstrate the successive state transitions for several steps on solid phase with I/O.
• KSLZ - KSLZ02
  D. Kim, S-Y. Shin, I-H. Lee, and B-T. Zhang. NACST/seq: A sequence design system with multiobjective optimization. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• KSO+03 - KSeo03
  T. Kawakami, F. Simiyama, Y. Ogura, A. Suyama, and J. Tanida. Parallel translation of DNA clusters by VCSEL array trapping and temperature control with laser illumination. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 19--27, 2003.
• KT96 - KT97
  L. Kari and G. Thierrin. Contextual insertions/deletions and computability. Information and Computation, 131(1):47--61, November 25 1996, http://www.csd.uwo.ca/~lila/context.ps.
  Abstract: We investigate two generalizations of insertion and deletion of words, that have recently become of interest in the context of molecular computing. Given a pair of words (x; y) called a context, the (x; y)-contextual insertion of a word v into a word u is performed as follows. For each occurrence of xy as a subword in u, we include in the result of the contextual insertion the words obtained by inserting v into u, between x and y. The (x; y)-contextual deletion operation is defined in a similar way. We study closure properties of the Chomsky families under the defined operations, contextual ins-closed and del-closed languages and decidability of existence of solutions to equations involving these operations. Moreover, we prove that every Turing machine can be simulated by a system based entirely on contextual insertions and deletions.
• KTL97
  P. D. Kaplan, D. S. Thaler, and A. Libchaber. Parallel overlap assembly of paths through a directed graph. In Rubin and Wood [P3], pages 127--141.
  Abstract: The first step of extant algorithms for DNA computers require the construction of a computational pool of molecules in which each distinct molecule represents a different computational starting point. We demonstrate the use of parallel overlap assembly to make a pool containing paths through a directed graph.
• Kud04 - KvT
  M. Kudlek. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter On Languages of Cyclic Words, pages 278--288. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• KYGK97 - KYSM97
  S. Kobayashi, T. Yokomori, G.Sanpei, and K.Mizobuchi. DNA implementation of simple Horn clause computation. IEEE International Conference on Evolutionary Computation, 1997, http://ylab-gw.cs.uec.ac.jp/Papers/satoshi/icec97.ps.gz.
  Abstract: In this paper, we propose a method for biologically implementing simple Boolean formulae. This method enables us to compute logical consequences of a given set of simple Horn clauses in parallel and takes advantage of potentially huge number of molecular CPUs of DNA computers. Further, we show that the method is nicely applied to the parallel implementation of a grammatical recognition algorithm which is based on `dynamic programming'.
• KYK+ - KYeo02
  S. Kashiwamura, M. Yamamoto, A. Kameda, T. Shiba, and A. Ohuchi. Hierarchical DNA memory based on nested PCR. Poster paper at the 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• KYS04 - KYSvT
  S. Kobayashi, T. Yokomori, and Y. Sakakibara. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter An Algorithm for Testing Structure Freeness of Biomolecular Sequences, pages 266--277. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• KYSM97 - Kobayashi97
  S. Kobayashi, T. Yokomori, G. Sampei, and K. Mizobuchi. DNA implementation of simple Horn clause computation. In IEEE International Conference on Evolutionary Computation, pages 213--217, 1997, http://ylab-gw.cs.uec.ac.jp/../Papers/satoshi/icec97.ps.gz.
  Abstract: In this paper, we propose a method for biologically implementing simple Boolean formulas. This method enables us to compute logical consequences of a given set of simple Horn clauses in parallel and takes advantage of potentially huge number of molecular CPUs of DNA computers. Further, we show that the method is nicely applied to the parallel implementation of a grammatical recognition algorithm which is based on 'dynamic programming'.
• KYU+03 - KYeo03
  A. Kameda, M. Yamamoto, H. Uejima, M. Hagiya, K. Sakamoto, and A. Ohuchi. Conformational addressing using the hairpin structure of single-stranded DNA. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 197--201, 2003.
• KZW03
  J. Kim, D. Y. Zhang, and E. Winfree. In vitro transcriptional circuits. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 190, 2003.
• Lan97 - Landweber97
  L. F. Landweber. DNA to DNA computations : A potential ``killer app''? In Rubin and Wood [P3], pages 59--68.
• LB96 - 2AWDBC
  L. Landweber and E. Baum, editors. DNA Based Computers II, volume 44 of DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1996.
  The preliminary proceedings contain [Adl96], [Amenyo96], [AGH96], [bioseq]. [BaumBoneh96], [BonehEA96], [DMGFS96], [GuaranieriBancroft96], [JonaskaKarl96], [KaplanEA96], [KurtzEA96], [LeeteEA96], [LiuEA96], [Mir96], [Oliver96], [Paun96], [RoweisEA96], [SeemanEA96], [WilliamsWood96], [Winf96], [Blumb97]. Program committee: E. B. Baum, D. Boneh, P. Kaplan, R. Lipton, J. Reif and N. C. Seeman.
• LFS+ - LFSea00
  L. Landweber, D. Faulhammer, L. L. Sohn, R. J. Lipton, S. J. Freeland, and R. D. Knight. RNA computing: from gels to cells and nanoscale wells. Invited talk at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• LFW+99 - LiuEA98
  Q. Liu, A. G. Frutos, L. Wang, A. J. Thiel, S. D. Gillmor, T. Strother, A. E. Condon, R. M. Corn, M. G. Lagally, and L. M. Smith. Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem. In Kari et al. [P4], pages 25--33.
  Abstract: A multi-base encoding strategy is used in a one word approach to surface-based DNA computation. In this designed DNA model system, a set of 16 oligonucleotides, each a 16mer, is used with the format 5' - FFFFvvvvvvvvFFFF - 3' in which 4-8 bits of data are stored in 8 central variable (``v'') base locations, and the remaining fixed (``F'') base locations are used as a word label. The detailed implementations are reported here. In order to keep perfect discrimination between each oligonucleotide, the efficiency and specificity of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescently tagged complement to an array of 16 addressed immobilized oligonucleotides. A series of preliminary hybridization experiments are presented and further studies about hybridization, enzymatic destruction, read out and demonstrations of a SAT problem are forthcoming.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• LGC+96 - LiuEA96
  Q. Liu, Z. Guo, A. E. Condon, R. M. Corn, M. G. Lagally, and L. M. Smith. A surface-based approach to DNA computation. In Landweber and Baum [2AWDBC]. Later version as a journal publication [LiuEA98-2].
  Abstract: A new model of DNA-based computation is presented. The main difference between this model and that of Adleman is in manipulation of DNA strands that are first immobilized on a surface. This approach greatly reduces losses of DNA molecules during purification steps. A simple, surface-based model of computation is described and it is shown how to implement an exhaustive search algorithm for the SAT problem on this model. Partial experimental progress in solving a 5-variable SAT instance is described, and possible extensions of our model that allow general computations are discussed.
• Li98
  Z. Li. Algebric properties of DNA operations. In Paun [CBMtitle], pages 327--339.
  Abstract: Any DNA strand can be identified with a word in the language X^* where X = \A, C, G, T\. By encoding A as 000, C as 010, G as 101, and T as 111, we treat the DNA operations concatenation, union, reverse, complement, annealing and melting, from the algebraic point of view. The concatenation and union play the roles of multiplication and addition over some algebraic structures, respectively. Then the rest of the operations turn out to be the homomorphisms or anti-homorphisms of these algebraic structures. Using this technique, we find the relationship among these DNA operations.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Li99 - ZLi98-1
  Zhuo Li. Algebraic properties of DNA operations. In Kari et al. [P4], pages 55--61.
  Abstract: Any DNA strand can be identified with a word in the language X^* where X = \A,C,G,T\. By encoding A as 000, C as 010, G as 101, and T as 111, we treat the DNA operations concatenation, union, reverse, complement, annealing and melting, from the algebraic point of view. The concatenation and union play the roles of multiplication and addition over some algebraic structures, respectively. Then the rest of the operations turn out to be homomorphisms or anti-homomorphisms of these algebraic structures. Using this technique, we find the relationship among these DNA operations.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• Lip95a - Lipton95A
  R. J. Lipton. Using DNA to solve NP-complete problems. Science, 268:542--545, April 28, 1995.
  Abstract: DNA experiments are proposed to solve the famous ``SAT'' problem of computer science. This is a special case of a more general method that can solve NP-complete problems. The advantage of these results is the huge parallelism inherent in DNA-base computing. It has the potential to yield vast speedups over conventional electronic-based computers for such search problems.
• Lip95b - Lipton94
  Richard J. Lipton. Speeding up computations via molecular biology. In R. J. Lipton [DBC], pages 67--74, ftp://ftp.cs.princeton.edu/pub/people/rjl/bio.ps.
  Abstract: We show how to extend the recent result of Adleman ([Adl94]) to use biological experiments to directly solve any NP problem. We, then, show how to use this method to speedup a large class of important problems.
• Lip95c - Lipton??
  Richard J. Lipton. Using DNA to solve SAT, 1995. Unpublished draft.
  We show how to use DNA experiments to solve the famous ``SAT'' problem of Computer Science. This is a special case of a more general method of [Lipton94] to solve NP-complete problems. The advantage of these results is the huge parallelism inherit in DNA based computing. It has the potential to yield vast speedups over conventional electronic based computers for such search problems.
• LJH+03 - LJeo03
  H. Lim, H. Jang, S. Ha, Y. Chai, S. Yoo, and B. Zhang. A lab-on-a-chip molecule for bead separation in DNA-based concept learning. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 9--18, 2003.
• LK99a - LK99
  L. F. Landweber and L. Kari. Evolution as computation, chapter Universal molecular computation in ciliates, pages 257--274. In Landweber and Winfree [LW99], 1999.
• LK99b - LandKari98
  L. F. Landweber and L. Kari. The evolution of cellular computing: Nature's solution to a computational problem. In Kari et al. [P4], pages 3--13.
  Abstract: How do cells and nature `compute'? They read and `rewrite' DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a seven-city Directed Hamiltonian Path problem using DNA [Adl94] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, two ciliated protozoans of the genus Oxytricha had solved a potentially harder problem using DNA several million years earlier. The solution to this problem, which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. RNA editing, which can also be viewed as a computational process, offers a second algorithm for the construction of functional genes from encrypted pieces of the genome.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• LKC+03 - LKeo03
  M. Lu, T. Knickerbocker, W. Cai, W. Yang, R. Hamers, and L. Smith. Invasive cleavage reactions on DNA-modified diamond surfaces. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 3, 2003.
• LKR97
  T. H. Leete, J. P. Klein, and H. Rubin. Bit operations using a DNA template. In Rubin and Wood [P3], pages 159--171.
  Abstract: We have derived a new method for encoding information into 30 base pair `bits' of DNA connected together in a linear DNA `bitstring'. The value held at any bit can be changed using a combination of ligase chain reaction mutagenesis (LCRM) and PCR. We have used this method to simulate a reversible logic gate, the Fredkin gate, and have shown by analogy that we can also do simple addition. The salient features of the method are that it requires relatively few steps (for logic gate operations), and that it does not rely upon changing the length or general structure of the bitstring to generate an answer, allowing the products of one reaction to be used as the starting template for the next. We suggest that this method could be used in molecular computations, either as a separate process carried out in parallel or as a subroutine for more complex operations.
• LL99
  Michail G. Lagoudakis and T. H. LaBean. 2D DNA self-assembly for satisfiability. In Winfree and Gifford [P5], pages 141--154.
  Abstract: DNA self-assembly has been proposed as a way to cope with huge combinatorial NP-HARD problems, such as satisfiability. However, the algorithmic designs proposed so far either involve many biosteps or are highly dependent on the particular instance to be solved. This paper presents an algorithmic design for solving satisfiability problems using two-dimensional DNA self-assembly (tiling). The main driving factor in this work was the design and encoding of the algorithm in a general way that separates the algorithm from the data and minimizes the dependency on particular instances. In effect, a large amount of work and preparation can be done in advance as a batch process. In practice, it is likely that the total time for computation will be decreased significantly and laboratory procedures will be simplified.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• LL03
  M. S. Livstone and L. F. Landweber. Mathematical considerations in the design of microreactor-based DNA computers. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 153--159, 2003.
• LLC - LLC03
  Y. Li, H. J. Lee, and R. M. Corn. Controlling hybridization efficiency in DNA microArrays on gold surfaces with SPR imaging for DNA based nanoscale biosensors. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• LLC+03 - LLeo03
  M. Li, H. Lee, Y. Chen, L. Smith, and R. Corn. Attomole detection of DNA in an array format with SPR imaging using rolling cicle amplification for the programmable nanoscale DNA biosensor. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 2, 2003.
• LMS04 - LMSvT
  P. Leupold, V. Mitrana, and J. M. Sempere. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Formal Languages Arising from Gene Repeated Duplication, pages 297--308. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• LPCZ03 - LPeo03
  I.-H. Lee, J. Pack, Y.-G. Chai, and B.-T. Zhang. RCA-based detection methods for resolution refutation. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 42--46, 2003.
• LPJ+ - LPeo02
  I-H. Lee, J-Y. Park, H-M. Jang, Y-G. Chai, and B-T. Zhang. DNA implementation of theorem proving with resolution refutation in propositional logic. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• LPRP04 - LPRvT
  L. Ledesma, J. Pazos, and A. Rodríguez-Patón. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter A DNA Algorithm for the Hamiltonian Path Problem Using Microfluidic Systems, pages 289--296. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• LR97
  E. Laun and K. J. Reddy. Wet splicing systems. In Rubin and Wood [P3], pages 115--126.
  Abstract: Splicing systems were originally developed as a mathematical or dry model of the generative capacity of DNA molecules in the presence of appropriate enzymes. The accuracy with which the model predicts the behavior of the corresponding biological or wet splicing system is investigated. A simple example of a wet splicing system is shown to generate in vitro the splicing language predicted by the corresponding dry splicing system.
• LRBR00
  André Leier, Christoph Richter, Wolfgang Banzhaf, and Hilmar Rauhe. Cryptography with DNA binary strands. BioSystems, 57(1):13--22, 2000.
• LRL02 - LRB02
  D. Liu, J. H. Reif, and T. H. LaBean. DNA nanotubes: construction and characterization of filaments composed of TX-tile lattice. In Hagiya and Ohuchi [PP8], pages 10--21.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• LS - LS00
  J-Q. Liu and K. Shimohara. A DNA computing model for the molecular emergence of genomic dynamics. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• LS00a - LS00-1
  J.-Q. Liu and K. Shimohara. DNA computing by genomic dynamics i: Evolutionary modeling of emergence and context-sensible grammar representation. In Proc.of The Fifth Int. Symp.on Artificial Life and Robotics - AROB 5th'00, pages 781--784, 2000. Oita, Japan, 26-28, January, 2000.
• LS00b - LS00-2
  Jian-Qin Liu and Katsunori Shimohara. DNA computing by genomic dynamics ii: A simulation wetware prototype of dynamical DNA computation. In Proc.of The Fifth Int. Symp.on Artificial Life and Robotics - AROB 5th'00, pages 785--788, 2000. Oita, Japan, 26-28, January, 2000.
• LS01
  Jian-Qin Liu and Katsumori Shimohara. Evolutionary dynamics for heterogeneous P-systems. Journal of Xi'am Mining Institute, 2001.
  To appear
• LS03
  J.-Q. Liu and K. Shimohara. Bio-molecular computation based on regulated phosphorylation-dephosphorylation encoding and kinases-phosphatases logic of rho family GTPase in cells: the first step of our efforts in software simulation. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 192--196, 2003.
• LSA+02 - LSeo02
  J. Y. Lee, S-Y. Shin, S. J. Augh, T. H. Park, and B. T. Zhang. Temperature gradient-based DNA computing for graph problems with weighted edges. In Hagiya and Ohuchi [PP8], pages 156--167.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• LSW+96 - LeeteEA96
  T. H. Leete, M. D. Schwartz, R. M. Williams, D. H. Wood, J. S. Salem, and H. Rubin. Massively parallel DNA computation: Expansion of symbolic determinants. In Landweber and Baum [2AWDBC].
  Abstract: A new type of algorithm is introduced for constructing DNA molecules which encode answers to mathematical problems. Examples include problems from the class \#P-Complete, which are widely considered to be harder than those in the problem classes previously addressed. In particular, algorithms are presented that generate expansions of symbolic determinants given their patterns of zero entries. This is well-known to be exponentially more difficult than evaluating determinants whose entries are merely numerical. Prior approaches to DNA computation were impractical for large problems because they required processing vast quantities of DNA with steps associated with large error propagation. Our new approach to the production of the solution and reading the answer is based on reliable and automatable PCR steps and can solve large problems by processing up to 10¹⁵ or more distinct strands of DNA in parallel. The DNA algorithms described here should be applicable to a wide variety of problems that are intractable using conventional computers.
• LTF+97 - LTFCS97
  Q. Liu, A. J. Thiel, A. G. Frutos, R. M. Corn, and L. M. Smith. Surface-based DNA computation : Hybridization and destruction. In Rubin and Wood [P3], page 239.
• LW94
  N. Littlestone and M. K. Warmuth. The weighted majority algorithm. Information and Computation, 108:212--261, 1994.
• LW99
  L. F. Landweber and E. Winfree, editors. Evolution as computation. Natural computing series. Springer Verlag, Berlin, Heidelberg, New York, 1999.
• LWF+00 - LWeo00
  Q. Liu, L. Wang, A. G. Frutos, A. E. Condon, R. M. Corn, and L. M. Smith. DNA computing on surfaces. Nature, 403, 2000.
• LWR99
  T. H. LaBean, E. Winfree, and J. H. Reif. Experimental progress in computation by self-assembly of DNA tilings. In Winfree and Gifford [P5], pages 123--140, http://www.cs.duke.edu/~reif/paper/DNAtiling/tilings/labean.pdf.
  Abstract: Approaches to DNA-based computing by self-assembly require the use of DNA nanostructures, called tiles, that have efficient chemistries, expressive computational power, and convenient input and output (I/O) mechanisms. We have designed two new classes of DNA tiles, TAO and TAE, both of which contain three double-helices linked by strand exchange. Structural analysis of a TAO molecule has shown that the molecule assembles efficiently from its four component strands. Here we demonstrate a novel method for I/O whereby multiple tiles assemble around a single-stranded (input) scaffold strand. Computation by tiling theoretically results in the formation of structures that contain single-stranded (output) reported strands, which can then be isolated for subsequent steps of computation if necessary. We illustrate the advantages of TAO and TAE designs by detailing two examples of massively parallel arithmetic: construction of complete XOR and addition tables by linear assemblies of DNA tiles. The three helix structures provide flexibility for topological routing of strands in the computation, allowing the implementation of string tile models.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• LYJ+ - LYeo02
  H-W. Lim, J-E. Yum, H-M. Jang, Y-G. Chai, S-I. Yoo, and B-T. Zhang. Version space learning with DNA molecules. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• LYK+00 - BYKL00
  T. H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, H.J. Reif, and N.C. Seeman. The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc., 122:1848--1860, 2000.
• LYQS96 - Li96
  Xiaojun Li, Xiaoping Yang, Jing Qi, and Nadrian C. Seeman. Antiparallel DNA double crossover molecules as components for nanoconstruction. Journal of the American Chemical Society, 118(26):6131--6140, 1996.
  Abstract: Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. We have examined these molecules from the viewpoint of their potential utility in nanoconstruction. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, so these have been characterized in a ligation cyclization assay. In contrast to other molecules that contain branched junctions, we find that these molecules cyclize rarely or not at all. The double crossover molecules cyclize no more readily than the linear molecule containing the same sequence as the ligation domain. We have tested both a conventional DAE molecule and one containing a bulged three-arm branched junction between the crossovers. The conventional DAE molecule appears to be slightly stiffer, but so few cyclic products are obtained in either case that quantitative comparisons are not possible. Thus, it appears that these molecules may be able to serve as the rigid components that are needed to assemble symmetric molecular structures, such as periodic lattices. We suggest that they be combined with DNA triangles and deltahedra in order to accomplish this goal.
• LZ01
  Tangha Tina Lai and Karl-Heinz Zimmermann. A software platform for the sticker model. Technical Report 01.2, TU Hamburg-Harburg, 2001.
  Abstract: The paper describes a software platform for the sticker model of DNA computing. The platform is easy to use and algorithms for the sticker model can be easily implemented by the user.
• LZP - LZP03
  J. Y. Lee, B.-T. Zhang, and T. H. Park. Effectiveness of denaturation temperature gradient-polymerase chain reaction for biased DNA algorithms. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• Mal98 - Maley_98
  Carlo C. Maley. DNA computation: Theory, practice, and prospects. Evolutionary Computation, 6(3):201--229, 1998. Temporarily available at http://mitpress.mit.edu/journals/EVCO/sample-article.html .
• Mal00 - M00
  M. Malita. Membrane computing in Prolog. In Calude et al. [WMP2000], pages 159--175.
  Abstract: This paper presents a simulation environment written in Prolog for the new paradigm of computation proposed by G. Paun in "Computing with membranes" [GPa00]. We present from [GPa00] the concept and our Prolog predicates dealing with the main operations on multisets, on membranes structures and on super cell systems. The program was tested on the examples from [GPa00]. The simulator is conceived to be useful for developing applications, which might test the power of this new computing paradigm.
  TR140, CDMTCS, Univ. Auckland
• Man - Manca00-1
  V. Manca. Monoidal theories and string derivation systems. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• Man98 - Manca98
  V. Manca. String rewriting and metabolism: a logical perspective. In Paun [CBMtitle], pages 36--60.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Man00 - Manca00-2
  V. Manca. Monoidal systems and membrane systems. In Calude et al. [WMP2000], pages 176--190.
  TR140, CDMTCS, Univ. Auckland
• Man04 - MvT
  V. Manca. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter A Proof of Regularity for Finite Splicing, pages 309--317. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Mar74
  S. Marcus. Linguistic structures and generative devices in molecular genetics. Cah. Ling. Th. Appl., 11, 2:77--104, 1974.
• Mar98
  S. Marcus. Language at the crossroad of computation and biology. In Paun [CBMtitle], pages 1--35.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Mar04 - SMvT
  S. Marcus. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter The Duality of Patterning in Molecular Genetics, pages 318--321. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• MAS97
  N. Morimoto, M. Arita, and A. Suyama. Solid phase DNA solution to the Hamiltonian path problem. In Rubin and Wood [P3], pages 83--92.
  Abstract: A new experimental model for solving the Hamiltonian path problem is described. The method is based on a solid phase chemistry and consists of only fast and simple DNA manipulations amenable to full automation. DNA strands representing paths with no city visited twice are synthesized vertex by vertex from the start vertex on a solid support. Each extension cycle takes only about 30 min. In addition, the pruning operations definitely increases the size of the problems solvable on a DNA -based computer. Preliminary experiments using Adleman's seven-city HPP showed that the path extension was very accurate. Our method may be applied to other problems requiring an enormous parallelism in computation.
• Mat98a - Mateescu98
  A. Mateescu. Splicing on routes: a framework of DNA computation. In Calude et al. [UMC98], pages 273--285.
  Abstract: We introduce and investigate a new method to define the splicing of words and languages. The operation is introduced using a uniform method based on the notion of rout. This operation leads in a natural way to a large class of semirings. The approach is amazingly flexible. Several well-known operations used in formal languages theory are just special cases of this operation.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Mat98b - Mat98
  A. Mateescu. Splicing on routes and recognizability. In Paun [CBMtitle], pages 314--326.
  Abstract: Assume that L_1 and L_2 are (regular) languages and that M_1, M_2 are (finite) monoids, such that M_i recognized L_i, i = 1, 2. Moreover assume that \oplus is an operation with languages, such that L_1 \oplus L_2 is a language. The following problem is of a special interest: find a function \Psi such that the language L_1 \oplus L_2 is recognized by the monoid \Psi(M_1, M_2). In this paper we investigate this problem for the case when the operation \oplus is the operation of splicing on routes.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• May - Mayoh4
  Brian Mayoh. Biological computation is universal, http://www.daimi.aau.dk/~brian/biocomputationNat.ps. unpublished.
• May94 - Mayoh2
  Brian Mayoh. Computation = pattern matching \& erasing, http://www.daimi.aau.dk/~brian/patternsIPL94.ps. unpublished, 1994.
• May95a - Mayoh1
  Brian Mayoh. DNA pattern multigrammers, http://www.daimi.aau.dk/~brian/DNApatternmultigrammars.ps. unpublished, 1995.
• May95b - Mayoh3
  Brian Mayoh. On patterns and graphs. Technical Report DAIMI PB 484, Aarhus University, Comp.Sci.Dept., 1995, http://www.daimi.aau.dk/~brian/marcuschapter.ps.
• MBW98
  J.J. Mulawka, P. Borsuk, and P. Weglenski. Implementation of the inference engine based on molecular computing technique. In Proc. IEEE Int. Conf. on Evolutionary Computation (ICEC'98), Anchorage USA, pages 493--498. IEEE, 1998.
  Abstract: In this paper we present a novel application of molecular computing to problems of expert systems. A biochemical reaction on DNA strands is used to realize the backward chaining algorithm. Knowledge base for the expert system is based on the sticker model; memory strands represent rules while stickers represent facts and hypothesis. Series of experiments have been conducted to confirm practical utility of this approach. In these experiments parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try to enhance physical insight into the dominating features of the approach proposed.
• MCC99
  Amit Marathe, Anne E. Condon, and Robert M. Corn. On combinatorial DNA word design. In Winfree and Gifford [P5], pages 75--89.
  Abstract: We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet A,C,G,T that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands, for use in DNA computing or as molecular bar codes in chemical libraries. The primary constraints that we consider, defined with respect to a parameter d, are as follows: for every pair of words w,x in a code, there are at least d mismatches between w and x if w different from x; and also between the reverse of w and the Watson-Crick complement of x. Extending classical results from coding theory, we present several upper and lower bounds on the maximum size of such DNA codes and give methods for constructing such codes. An additional constraint that is relevant to the design of DNA codes is that the free energies and enthalpies of the code words, and thus the melting temperatures, be similar. We describe dynamic programming algorithms that can (i) calculate the total number of words of length n whose free energy value (as approximated by a formula of Breslauer et al.) falls in a given range, and (ii) output a random such word. These algorithms are intended for use in heuristic algorithms for constructing DNA codes.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• McC01 - MCC01
  J. S. McCaskill. Optically programming DNA computing in microflow reactors. BioSystems, 59(2):125--138, February 2001.
• MDF+97 - Murphy97
  R. C. Murphy, R. Deaton, Donald R. Franceschetti, S.E. Stevens, Jr., and Max H. Garzon. A new algorithm for DNA based computation. In IEEE International Conference on Evolutionary Computation, 1997.
  Abstract: A common feature of DNA computing involves the use of molecular biology techniques to extract molecules representing the solution to a computation from a reaction mixture. Current applied extraction methods often employ PCR and/or gel electrophoresis, both of which we believe are too time consuming and error prone to yield a practical DNA -based molecular computing capability. This paper suggests a new approach toward solving the Hamiltonian Graph and similar combinatorial problems that avoids these traditional techniques in favor of a purely enzymatic methodology.
• MdG97 - Manganaro97
  Gabriele Manganaro and Jose Pineda de Gyvez. DNA computing based on chaos. In IEEE International Conference on Evolutionary Computation, pages 255--260, 1997.
  Abstract: In this paper a new approach for the realization of the DNA computing paradigm is presented. It exploits the natural richness of the chaotic dynamics to efficiently generate and process coded binary sequences following the DNA computing framework introduced by Leonard M. Adleman. The new method is discussed and some simulation results regarding the directed Hamiltonian path problem are presented.
• Mih97 - Mihalache97
  Valeria Mihalache. Prolog approach to DNA computing. In IEEE International Conference on Evolutionary Computation, pages 249--254, 1997.
  Abstract: The paper addresses the realization of an implementation of Prolog programming language by means of DNA molecules. To this ultimate goal, representation of Prolog statements as DNA stretches is proposed. Matching of the facts, the basic operation a Prolog system has to perform in an attempt to answer the questions of a user, is modeled in terms of the Watson-Crick complementarity of DNA molecules. The automatic backtracking of Prolog language can be simulated by parallelism in a test tube.
• Mir96
  K. U. Mir. A restricted genetic alphabet for DNA computing. In Landweber and Baum [2AWDBC].
  Introduction: Since Adleman demonstrated his original groundbreaking scheme [Adl94], a simpler approach suggested by Lipton [Lipton95A] has widened the range of problems that can be addressed by DNA computing. A single molecular operation, DNA annealing, is required for Lipton's scheme. This also forms the basis of Baum's proposal for a content-addressable DNA memory [Baum95]. In both cases an extractor or cue oligonucleotide, most likely to be in the solid-phase, attached to beads, would anneal to a longer single-stranded target present in the graph or memory. So far, most work on DNA computing has rightly concentrated on what is theoretically possible. Here however, I will discuss some practical issues and offer a means to overcome some practical obstacles.
• Mit97a - MitBook97
  V. Mitrana, editor. Bioinformatics. L. and S. Informat, Bucharest, 1997. in Romanian.
• Mit97b - Mit97-1
  V. Mitrana. Crossover systems. a generalization of splicing systems. Journal of Automata, Languages and Combinatorics, 3(2):151--160, 1997.
• Mit97c - Mit97
  V. Mitrana. On the interdependence between shuffle and crossing-over operations. Acta Informatica, 34, 4:257--266, 1997.
• Mit01 - MitBook-2
  V. Mitrana, editor. New Developments in Formal Language Theory Inspired from Biology. University of Bucharest Publishing House, 2001.
• MK00a - MaKr00
  M. Madhu and K. Krithivasan. Computing with dynamic polarized membranes. manuscript, 2000.
• MK00b - MK00
  M. Mutyam and K. Krithivasan. P systems with communicating rules. manuscript, 2000.
• MK00c - MK00-1
  M. Mutyam and K. Krithvasam. Inter-membrane communication in P systems. Romanian Journal of Information Science and Technology, 3(4):335--352, 2000.
• MK01a - MMKK01
  M. Madhu and K. Krithivasan. P systems with active objects: Universality and efficiency. In Margenstern and Rogozhin [MCU01], pages 276--287.
• MK01b - MK00-2
  M. Mutyam and K. Krithvasam. P systems with membrane creation: universality and efficiency. In Margenstern and Rogozhin [MCU01], pages 276--287.
• MLRS00 - MBRS00
  C. Mao, T.H. LaBean, J.H. Reif, and N.C. Seeman. An algorithmic self-assembly. Nature, September 28, 2000.
• MM - MC00
  H. P. Mathis and J. S. McCaskill. Potential of a spatially resolved single molecule i/o interface for DNA computing. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• MMAPJ02 - MAP02
  F.J. Martín-Mateos, J.A. Alonso, and M.J. Perez-Jimenez. Molecular computation models in ACL2: a simulation of lipton's SAT experiment in the adleman's restricted model. In Proceedings of the Third International Workshop on the ACL2 Theorem Prover and Its Applications, pages 175--187, 2002.
  Abstract: In this paper we present an ACL2 formalization of a molecular computing model: Adleman's restricted model. This is a first step to formalize unconventional models of computation in ACL2. As an application of this model, an implementation of Lipton's experiment solving SAT is described. We use ACL2 to make a formal proof of the completeness and soundness properties of the function implementing the experiment.
• MMVP99 - MancaEA98
  V. Manca, C. Martín-Vide, and G. Paun. New computing paradigms suggested by DNA computing: Computing by carving. In Kari et al. [P4], pages 47--54.
  Abstract: Inspired by the experiments in the emerging area of DNA computing, a somewhat unusual type of a computation strategy was recently proposed by one of us: generate a (large) set of candidate solutions of a problem, then remove the non-solutions such that what remains is the set of solutions. This has been called a computation by carving. This idea leads both to a speculation with possible important consequences -- computing non-recursively enumerable languages -- and to interesting theoretical computer science (formal language) questions.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• MMVP01a - MMP01
  V. Manca, C. Martín-Vide, and G. Paun. On P systems with replicated rewriting. Journal of Automata Languages and Combinatorics, 6(3):359--374, 2001.
• MMVP01b - MMP01-1
  M. Margenstern, C. Martín-Vide, and G. Paun. Computing with membranes: variants with an enhanced membrane handling. In Jonoska and Seeman [P7], pages 340--349.
  Abstract: Membrane computing is a recently introduced (very general) computing framework which abstracts from the way the living cells process chemical compounds in their compartmental structure. Many variants considered in the literature are computationally universal and/or able to solve NP complete problems in polynomial (even linear) time - of course, by making use of an exponential working space created in a natural way (for instance, by membrane division). In the present paper we propose a general class of membrane systems, where besides rules for objects evolution (the objects are described by strings over a finite alphabet), there are rules for moving objects from a compartment to another one (this is done conditionally, depending on the strings contest), and for handling membranes. Especially this latter feature is important (and new in many respects), because it makes possible to interpret several DNA computing experiments as membrane computations. Specifically, rules for dividing membranes (with the contents replicated or separated according to a given property of strings), creating, merging, or dissolving them are considered. Some of these variants generalize certain previous variants of membrane systems, for the new variants we investigate their power and computational efficiency (as expected, universality results, as well as polynomial solutions of NP-complete problems are found; the latter case is illustrated with the SAT problem). Due to space restrictions, the paper is a preliminary, partially formalized one; more mathematical details are given in the appendices available at http://bioinformatics.bio.disco.unimib.it/psystems, where also current information about the membrane computing area can be found.
• MN00 - CN00
  J. McCaskill and U. Niemann. Graph replacement chemistry for DNA processing. In Condon and Rozenberg [P6], pages 103--116.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• MP98 - MaPa98
  V. Manca and G. Paun. Arithmetically controlled H systems. Computer Science Journal of Moldova, 6(2):103--118, 1998.
• MPG+00 - CPeo00
  J. S. McCaskill, R. Penchovsky, M. Gohlke, J. Ackermann, and T. Rucker. Steady flow micro-reactor module for pipelined DNA computation. In Condon and Rozenberg [P6], pages 239--246.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• MPRS96 - MPRS
  V. Mihalache, G. Paun, G. Rozenberg, and A. Salomaa. Generating strings by replication: a simple case. Report. TUCS No. 17, 1996. Turku, Finland.
• MPRS98 - MPRS96
  Alexandru Mateescu, G. Paun, G. Rozenberg, and A. Salomaa. Simple splicing systems. Discrete Applied Mathematics, 84:145--163, 1998. Also: Technical Report TR95-09 (March 1995), Department of Computer Science, Leiden University, P.O. Box 9512, 2300 RA Leiden, The Netherlands.
  Abstract: We consider one of the most restrictive classes of splicing (H) systems, namely based on splicing rules of the form (a,\lambda; a,\lambda), where a is a symbol in a given set and \lambda is the empty string. (They correspond to a special class of ``null context splicing systems'', as introduced in [Head87].) A series of language-theoretic properties of languages generated by such systems with finite sets of axioms are investigated.
• MR98
  Maurice Margenstern and Yurii Rogozhin. Time-varying distributed H systems of degree 2 generate all RE languages. MFCS 1998 workshop on frontiers of universality, 1998.
  Brno
• MR99 - MargRo98
  Maurice Margenstern and Yurii Rogozhin. A universal time-varying distributed H-system of degree 2. In Kari et al. [P4], pages 73--80.
  Abstract: A time-varying distributed H system is a slicing system which has the following features: at different moments one uses different sets of splicing rules. The number of these sets is called the degree of the system. The passing from a set of rules to another is specified in a cycle. It is a well known fact that any formal language can be generated by a time--varying distributed H--system of degree at least 7. Here we prove that there are universal time--varying distributed H--systems of degree 2. The question of weather or not there are universal time--varying distributed H--systems of degree 1 remains open.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• MR00
  M. Margenstern and Y. Rogozhin. About time-varying distributed H systems. In Condon and Rozenberg [P6], pages 53--62.
  Abstract: A time-varying distributed H system (TVDH system) is a splicing system which has the following feature: at different moments one uses different sets of splicing rules (these sets are called components of TVDH system). The number of components is called the degree of the TVDH system. The passing from a component to another one is specified in a cycle. It was proved by both authors (1999) that TVDH systems of degree 2 generate all recursively enumerable languages. It was made by modeling Turing machines and, in that modeling, every language is generated "step by step" or "word by word". This solution is not a fully parallel one. A.Paun (1999) presented a complete parallel solution for TVDH systems of degree 4 by modeling type 0 formal grammars. Now we improved A.Paun's result by reducing the number of components of such TVDH systems down to 3. This question is open for 2 components, i.e. is it possible to construct TVDH systems of degree 2 which completely uses the parallel nature of molecular computations based on splicing operations (say model type 0 formal grammars)? We consider also original G.Paun's definition of TVDH systems and suggest a slightly different definition of TVDH systems based on the definition of H systems extended time-varying distributed H systems (ETVDH systems). For this new definition we proved that ETVDH systems with one component generate exactly the set of all regular languages and that with two components, they generate exactly the set of all recursively enumerable languages.
• MR01a - MCU01
  M. Margenstern and Y. Rogozhin, editors. Machines, Computations, and Universality: Third International Conference, MCU 2001 Chisinau, Moldavia, May 23-27, 2001, Proceedings, volume 2055 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, New York, 2001.
• MR01b - MR01
  M. Margenstern and Y. Rogozin. A universal time-varying distributed H system of degree 1. In Jonoska and Seeman [P7], pages 371--380.
  Abstract: Time-varying distributed H system (TVDH system shortly) of degree n is a well known model of splicing computations which has the following special feature: at different moments one uses different sets of splicing rules (the number of these sets of splicing rules is called the degree of the TVDH system). It is known that there is a universal TVDH system of degree 2. Now we prove that there is a universal TVDH system of degree 1. It is a surprising result because we did not thought that these systems are so powerful.
• MRV - MRV02
  M. Margenstern, Y. Rogozin, and S. Verlan. Time-varying distributed H systems of degree 2 can carry out parallel computations. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• MRV03
  M. Margenstern, Y. Rogozhin, and S. Verlan. Time-varying distributed H systems with parallel computations: the problem is solved. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 47--51, 2003.
• MS97
  V. Mihalache and A. Salomaa. Lindenmayer and DNA: Watson-crick d0l systems. Bulletin of the EATCS, 62:160--175, June 1997. See also [MS01].
• MS01
  V. Mihalache and A. Salomaa. Lindenmayer and DNA: Watson-Crick D0L Systems, volume -, pages 740--751. World Scientific, 2001.
  See also [MS97].
• MT - MT01
  Ernesto Acosta Martin and Jorge Eduardo Ortiz Trivino. A general model for artificial neural network (ANN) encoding using DNA sequences and a learning method based on natural selection. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• MVM00a - CVMBook00
  C. Martíin-Vide and V. Mitrana, editors. Where Do Mathematics, Computer Science and Biology Meet. Kluwer Academic, Dortrecht, 2000.
  The book contains [DHV00], [APMP00] and [EPeo01-1].
• MVM00b - MVM00-11
  C. Martín-Vide and V. Mitrana. P systems with valuations. In Antoniou et al. [UMC2K], pages 154--166.
  Abstract: We propose a new variant of P systems having a simple evolution rules in which the communication of objects and the membrane dissolving are regulated by a valuation mapping (a morphism which assigns to each word an integer value). Two NP-complete problems are solved by P systems with valuation in linear time.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• MVM01 - CMBook01
  C. Martíin-Vide and V. Mitrana, editors. Grammars and Automata for Sequence Processing. From Mathematics and Computer Science to Biology and Back. Gordon and Breach, London, 2001.
• MVMP02 - MVMP
  C. Martíin-Vide, V. Mitrana, and G. Paun. On the power of valuations in P systems. Computacion y Systemas, 5(2):120--127, 2002.
• MVP97
  C. Martín-Vide and G. Paun. Cooperating distributed splicing systems. Workshop on molecular computing, 1997.
  Mangalia, Romania
• MVP00a - MVP00-1
  Carlos Martíin-Vide and G. Paun. Computing with membranes: One more collapsing hierarchy. Bulletin of the European Association for Theoretical Computer Science, -(72):183--187, October 2000.
• MVP00b - MvP00
  C. Martín-Vide and G. Paun. String objects in P systems. Proc. of Algebraic Systems, Formal Languages and Computations Workshop, pages 161--169, 2000. Kyoto, RIMS Kokyuroku, Kyoto Univ.
• MVPR00a - MVPR00
  C. Martín-Vide, G. Paun, and G. Rozenberg. Membrane systems with carriers. unpublished, 2000.
• MVPR00b - MvPR00-1
  C. Martín-Vide, G. Paun, and G. Rozenberg. Plasmid-based P systems. manuscript, 2000.
• MVPRP01 - MVP01
  C. Martín-Vide, G. Paun, and A. Rodriguez-Paton. P systems with immediate communication. Romanian J. of Information Science and Technology, 4(1-2):171--182, 2001.
• MVPRS98 - MPRS98
  C. Martíin-Vide, G. Paun, G. Rozenberg, and A. Salomaa. Universality results for finite H systems and for Watson-Crick finite automata. In Paun [CBMtitle], pages 200--220.
  Abstract: Because "computers" based on uncontrolled splicing with respect with respect to a finite set of splicing rules can only compute at the level of finite automata, it is of interest to have universality result at this level of computability. We find finite automata which are universal for the class of finite automata with a bounded number of states (and of input symbols). This directly leads to universal extended H systems with finite sets rules applied without any additional control. Another "implementation" of this result is in terms of so-called Watson-Crick finite automata, a kind of device similar to finite automata and working on double stranded tapes. Also Watson-Crick automata which are universal for the class on Watson-Crick finite automata with a bounded number of states and of symbols are found. The constructions are significantly simpler when one of the heads of the Watson-Crick automaton works in a two-way manner (the other works in the usual left-to-right one0way manner) and when one uses a triple-stranded tape (on one of them we work in the two-way manner).
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• MW00 - McW00
  J. S. McCaskill and P. Wagler. From reconfigurability to evolution in construction systems: spanning the electronic, microfuidic and biomolecular domains. In R. W. Hartenstein and H. Grunbacher, editors, Field-Programmable Logic and Applications. The Roadmap to Reconfigurable Computing: 10th International Conference, FPL 2000, Villach, Austria, August 27-30, 2000. Proceedings, volume 1896 of Lecture Notes in Computer Science, pages 286--299. Springer Verlag, Berlin, Heidelberg, New York, 2000.
• MWP99a - MWP99
  J. J. Mulawka, P. Wasiewicz, and K. Pietak. Virus-enhanced genetic algorithms inspired by DNA computing. Lecture Notes in Computer Science, 1609:527--537, 1999, http://www.springer.de/comp/lncs/.
  Abstract: DNA computing is a new promising paradigm to develop an alternative generation of computers. Such approach is based on biochemical reactions using DNA strands which should be carefully designed. To this purpose a special DNA sequences design tool is required. The primary objective of this contribution is to present a virus-enhanced genetic algorithms for global optimization to create a set of DNA strands. The main feature of the algorithms are mechanisms included specially for searching solution space of problems with complex bounds. Formulae, describing bounds of power of sequences' sets, which satisfy criteria and estimation functions are expressed. A computer program, called Mismatch, was implemented in C++ and runs on Windows NT platform.
• MWP99b - MWP99-1
  J.J. Mulawka, P. Wasiewicz, and A. Plucienniczak. Another logical molecular NAND gate system. In Proc. of the 7th Int. Conf. on Microelectronics for Neural, Fuzzy, and Bio-Inspired Systems (MicroNeuro'99), pages 340--345, 1999. Granada, Spain.
  Abstract: In this paper we implement a new logic NAND gate using standard operations on DNA strands as well as digestion by the restriction nuclease class II. This concept despite some difficulties looks in general more elegant and can be utilized with fluorescent probes. Some experimental results demonstrating implementation of a single logic NAND gate are provided. The derived logic gates are proposed to be implemented on DNA chips.
• MY - MY02
  D. Matsuda and M. Yamammura. Cascading whiplash PCR with a nicking enzyme. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• MY01
  J. C. Mitchell and B. Yurke. DNA scissors. In Jonoska and Seeman [P7], pages 258--268.
  Abstract: Designed strands of DNA were used to construct a nanomachine with appearance of a pair of scissors. Further strands of DNA were then employed to close and reopen the handles of the scissor with result closing and reopening of the jaws with a change in angle of 10<sup>o</sup>. It was further shown that it is possible to open the handles wider than their equilibrium position, with resultant widening of the jaws.
• MYS+01 - MYS01
  N. Matsuura, M. Yamamoto, T. Shiba, Y. Kawazoe, and A. Ohuchi. Solutions of shortest path problems by concentration control. In Jonoska and Seeman [P7], pages 203--212.
  Abstract: In this paper, we present a concentration control method that may become a new framework of DNA computing. In this method, the concentration of each DNA is used as input and output data. By encoding the numeric data into concentrations of DNAs, a shortest path problem, which is a combinatorial optimization problem, can be solved. The method also enables local search among all candidate solutions instead of a exhaustive search. Furthermore, we can reduce the cost of some experimental operations in detecting process of DNA computing, because we have only to extract and analyze relatively intensive bands. Solutions of a shortest path problem by using simulator and y laboratory experiments are presented to show the effectiveness of the concentration control method.
• MZ01 - MGLeo01
  V. Manca and C. Zandron. A DNA algorithm for 3-SAT(11,20). In Jonoska and Seeman [P7], pages 172--181.
  Abstract: We present a DNA solution for an instance of 3-SAT, the satisfiability for a formula of propositional logic constituted by 11 propositional variables and 20 clauses (each clause is the disjunction of 3 literals). The algorithm transforms the given instance in an equivalent combinatorial formulation where 22 different double stranded DNA dominoes with sticky ends encode clauses. Solutions are obtained by a suitable ligation of 11 dominoes, where all the clauses are encoded.
• Nar97 - Narayanan97
  Ajit Narayanan. Representing arc labels in DNA algorithms. Technical Report R360, Department of Computer Science, Exeter University, Computer and Cognitive Sciences, University of Exeter, Exeter EX4 4PT, UK, 1997, ftp://ftp.dcs.ex.ac.uk/pub/artificial_intelligence/360.ps.
  Abstract: DNA computing has recently generated much interest as a result of pioneering work by Adleman and Lipton, who described DNA algorithms for solving problems considered NP-hard by computer scientists. Their DNA algorithms worked on graph representations of the problem, but no indication was provided about how information on the arcs between nodes on a graph could be handled. The aim of this paper is extend the basic DNA algorithmic techniques of Adleman and Lipton by demonstrating a method for representing simple arc information --- in this case, distances between cities in a simple map. The work described here significantly advances our understanding of DNA computational processes and identifies the potential for DNA algorithms for addressing problems in the NP class.
• nID99 - BD99
  E. B. Bauma nd I. Durdanovic. Evolution as computation, chapter Toward code evolution by artificial economies, pages 314--332. In Landweber and Winfree [LW99], 1999.
• NS03
  N. Nitta and A. Suyama. Autonomous biomolecular computer modelled after retroviral replication. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 180--189, 2003.
• NYH01
  A. Nishikawa, M. Yamamura, and M. Hagiya. DNA computation simulator based on abstract bases, volume 5(1), pages 25--38. Springer Verlag, Berlin, Heidelberg, New York, 2001, http://link.springer.de/link/service/journals/00500/tocs/t1005001.htm.
• NZ98
  A. Narayanan and S. Zorbalas. DNA algorithms for computing shortest paths. In J. Koza et al, editor, Proceedings of the 3rd Genetic Programming Annual Conference, pages 718--724, 1998.
• NZ03
  A. Narayanan and S. Zorbalas. DNA algorithms for computing shortest paths. In Koza et al, editor, Proceedings of the 3rd Genetic Programming Annual Conference, 2003.
  Abstract: DNA computing has recently generated much interest as a result of pioneering work by Adleman and Lipton. Their DNA algorithms worked on graph representations but no indication was provided as to how information on the arcs between nodes on a graph could be handled. The aim of this paper is to extend the basic DNA algorithmic techniques of Adleman and Lipton by proposing a method for representing simple arc information - in this case, distances between cities in a simple map. It is also proposed that the real potential of DNA computing for solving computationally hard problems will only be realised when algorithmic steps which currently require manual intervention are replaced by executable DNA which operate on DNA strands in test-tubes.
• OA99
  C. Ofria and C. Adami. Evolution as computation, chapter Evolution of genetic organization in digital organims, pages 296--313. In Landweber and Winfree [LW99], 1999.
• Obt01a - Ob01-1
  A. Obtulowicz. Deterministic P systems for solving SAT problem. Romanian J. Information Sci. and Technology, 4(1-2), 2001.
• Obt01b - Ob01-2
  A. Obtulowicz. Membrane computing and one-way functions. Inter. J. Fond. Computer Sci., 2001.
  to appear
• OGB97
  M. Orlian, F. Guarnieri, and C. Bancroft. Parallel primer extension horizontal chain reactions as a paradigm of parallel DNA-based computation. In Rubin and Wood [P3], pages 142--158.
  Abstract: The ability of DNA to store, process, and transmit large quantities of information suggests that it may be possible to construct a powerful computer based upon the molecular biology of DNA. To harness DNA's computational capabilities in a way that may be competitive with modern computers, it will probably be necessary to perform DNA computations in a massively parallel fashion. A prerequisite, however, for constructing any computer is the ability to perform controlled bit-flipping operations. We have recently demonstrated how DNA can be employed to carry out binary addition, and thus how DNA can be used to flip bits. The procedure to carry out this simple computation uses successive primer extension reactions. We demonstrate here that this process, called a horizontal chain reaction, can be employed to solve a simple graph problem, thus illustrating the feasibility of running a chain of controlled primer extension reactions in parallel. We further show how incorporation into input DNA strands of unique restriction sites permits the application of a simple and straightforward readout mechanism. Combined with our previous study, these results demonstrate the ability of DNA to carry out parallel bit-flipping operations.
• Ogi96 - Ogihara96
  M. Ogihara. Breadth first search 3SAT algorithms for DNA computers. Technical Report TR 629, University of Rochester, Computer Science Department, July 1996, ftp://ftp.cs.rochester.edu/pub/papers/theory/96.tr629.Breadth_first_search_3SAT.ps.gz.
  Abstract: This paper demonstrates that some practical 3SAT algorithms on conventional computers can be implemented on a DNA computer as a polynomial time breadth first search procedure based only on the fundamental chemical operations identified by Adleman and Lipton's method. In particular, the Monien-Speckenmeyer algorithm, when implemented on DNA , becomes an O(n\cdot\max \m<sup>2</sup>,n\) time, 2<sup>0.6942 n</sup> space algorithm, with significant increase in time and significant decrease in space. This paper also proposes a fast breadth first search method with fixed split points. The running time is at most twice as that of Lipton. Although theoretical analysis of the algorithm is yet to be done, simulations on a conventional computer suggest that the algorithm could significantly reduce the search space for 3SAT for most cases. If the observation is correct, the algorithm would allow DNA computers to handle 3SAT formulas of more than 120 variables, thereby doubling the limit given by Lipton.
• Oit00 - AROB5
  Oita, Japan, 26-28, January, 2000. Proc.of The Fifth Int. Symp.on Artificial Life and Robotics - AROB 5th'00, Artificial life and Robotics, Applied Mathematics and Computation. Springer Verlag, Berlin, Heidelberg, New York, 2000.
  The preliminary proceedings contain [LS00-1], [LS00-2]
• OKLL97 - OuyangEA
  Q. Ouyang, P. D. Kaplan, S. Liu, and A. Libchaber. DNA solution of the maximal clique problem. Science, 278:446--449, 1997.
  Abstract: The maximal clique problem has been solved by means of molecular biology techniques. A pool of DNA molecules corresponding to the total ensemble of six-vertex cliques was built, followed by a series of selection processes. The algorithm is highly parallel and has satisfactory fidelity. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.
• Oli96 - Oliver96
  J. S. Oliver. Computation with DNA-matrix multiplication. In Landweber and Baum [2AWDBC], http://www.chem.brown.edu/brochure/people/jso/DNA.html.
  Abstract: If chemical reactions are to be used as the basis for computers, efficient instruction sets will need to be developed. A chemically based computation can not at this time be expected to compete with an electronic computer. However, the potential usefulness of a chemical computer provides a compelling reason to investigate and design procedures for the solution of varied problems. DNA based methods which may be used to calculate the product of Boolean matrices or matrices containing positive, real numbers are represented. This provides a method to perform a quantitative calculation with DNA.
• ONJ+95 - Orum
  H. Orum, P. E. Nielsen, M. Jorgensen, C. Larsson, and C. Staneley. Sequence-specific purification of nucleic-acids by DNA-controlled hybrid selection. Biotechniques, 19(3):472--480, 1995.
• OR97a - OR97
  M. Ogihara and A. Ray. DNA-based parallel computation by ``counting''. In Rubin and Wood [P3], pages 265--274.
  Abstract: The potential of DNA as a truly parallel computing device is enormous. Solution-phase DNA chemistry, though not unlimited, provides the only currently-available experimental system. Its practical feasibility, however, is controversial. We have sought to extend the feasibility and generality of DNA computing by a novel application of the theory of counting. The biochemically equivalent operation for DNA counting is well known. We propose a DNA algorithm that employs this new operation. We also present an implementation of this algorithm by a novel DNA-chemical method. Preliminary computer simulations suggest that the algorithm can significantly reduce the DNA space complexity (i.e., the maximum number of DNA molecules that must be present in the test tube during computation) for solving 3SAT to O(2^{0.4 n}). If the observation is correct, our algorithm can solve 3SAT instances of size up to or exceeding 120 variables.
• OR97b - OR97-2
  Mitsunori Ogihara and Animesh Ray. The minimum DNA computation and its computational power. Technical Report TR 672, University of Rochester, Computer Science Department, December 1997, ftp://ftp.cs.rochester.edu/pub/papers/theory/97.tr672.Minimum_DNA_computation_model_and_its_computational_power.ps.gz.
  Abstract: This paper studies seemingly the smallest DNA computational model. This model assumes as its computation basis merge, detect, synthesize, anneal, and length-specific separation, but does not assume sequence-specific separation as in many other DNA computational models. Uncertainty occurring in some of the operations is taken into consideration, and the decision by computation under the model is defined in terms of robustness. This paper shows tight upper bounds on the power of this computational model in terms of circuits. For every k\geq 1, the languages robustly accepted by programs under this model in O(\log^k n) steps using polynomially many DNA molecules resides between NC^k and SAC^k+1. ,
• OR98a - OR98
  M. Ogihara and A. Ray. Circuit evaluation: thoughts on a killer application in DNA computing. In Paun [CBMtitle], pages 111--126.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• OR98b - OgiRay98
  M. Ogihara and A. Ray. The minimum DNA computation model and its computational power. In Calude et al. [UMC98], pages 309--322.
  Abstract: This paper studies seemingly the smallest DNA computational model. This model assumes as its computation basis merge, detect, synthesize, anneal, and length-specific separation, but does not assume sequence-specific separation as in many other DNA computational models. Uncertainty occurring in some of the operations is taken into consideration, and the decision by computation under the model is defined in terms of robustness. This paper shows tight upper bounds on the power of this computational model in terms of circuits. For every k \leq 1, the languages robustly accepted by programs under this model in O(\log^k n) steps using polynomially many DNA molecules resides between NC^k and SAC^k+1.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• otCoECC99 - Erk99
  Proceedings of the Congress on Evolutionary Computation (CEC'99), editor. Simulating Boolean circuits by finite splicing, July 6--9 1999, http://www.ps.uni-sb.de/~erk/boolcirc.ps.gz. Washington D.C., USA.
• PAM00 - WHAM00
  K. Grabowski P. Arsenics and J.J. Mulawka. Optimal sequence design for DNA computing. In -, pages 245--254, 2000. In Proceedings of the IV Polish Conference on Evolutionary Algorithms and Global Optimization.
  Abstract: In this paper the method of automatic string sets generation for DNA computing was described. A computer program written in C++ called Mismatch [1] with our new improvements was used. We described changes in the input files and examples of string generation. These new optimized DNA structures are useful in the implementation of molecular inference systems. The models of DNA computing are helpful in developing alternative generation of extremely miniaturized computers.
  Ladek Zdro
• Pau95a - Paun95-3
  G. Paun. SPLICING a challenge for formal language theorists. Bulletin of the European Association for Theoretical Computer Science, 57:183--194, October 1995.
  Abstract: A series of basic notions and results related to the splicing operation, introduced by T. Head as a language-theoretic model of DNA recombination, are presented. Further bibliographical hints, open problems and directions for further research are also mentioned.
• Pau95b - Paun95-4
  G. Paun. The splicing as an operation on formal languages. In Proceedings of IEEE Conference on Intelligence in Neural and Biological Systems, pages 176--180, Herndon-Washington, 1995.
• Pau96a - Paun96-5
  G. Paun. Computing by splicing: How simple rules? Bulletin of the European Association for Theoretical Computer Science, 60:145--150, October 1996.
  Abstract: Extended H systems with permitting/forbidding contexts having the splicing rules of radius at most two can characterize the recursively enumerable languages. How powerful are the systems with rules of radius one? We conjecture that they characterize the context-free languages (we only prove that they can generate all linear languages, as well as all Dyck languages).
• Pau96b - Paun96
  G. Paun. Five (plus two) universal DNA computing models based on the splicing operation. In Landweber and Baum [2AWDBC].
  Abstract: We briefly present five types of mechanisms (and we mention two other related devices) based on the splicing operation (a model of the recombinant behavior of DNA sequences under the influence of restriction enzymes and ligases). All these models characterize the recursively enumerable languages, hence all are equal in power to the Turing machines. On the basis of the constructions in the proofs of this assertion, one can obtain universal (hence programmable) computing devices.
• Pau96c - Paun96-2
  G. Paun. On the power of splicing grammar systems. Ann. Univ. Buc., Matem.-Inform. Series, 45(1):93--106, 1996.
• Pau96d - Paun96-3
  G. Paun. On the splicing operation. Discrete Applied Mathematics, 70(1):57--79, September 10, 1996.
  Abstract: We propose here a systematic formal study of the splicing operation introduced by Head as a model of recombinant behavior of DNA . We consider both simple and iterated splicing, with respect to a finite or an infinite set of splicing rules, in the latter case the whole set of rules constituting a regular language. Relations between these operations and usual operations with languages are investigated, as well as the closure of Chomsky language families under these splicing operations. A series of open problems are formulated too.
• Pau96e - Paun96-4
  G. Paun. Regular extended H systems are computationally universal. Journal of Automata, Languages, Combinatorics, 1(1):27--36, 1996.
• Pau96f - Paun96-6
  G. Paun. Splicing systems with targets are computationally complete. Information Processing Letters, 59:129--133, 1996.
• Pau98a - Paunbook
  G. Paun, editor. Computing With Bio-molecules: Theory and Experiments. Springer Series in Discrete Mathematics and Theoretical Computer Science. Springer Verlag, Berlin, Heidelberg, New York, October 1998, ISBN 981-4021-05-9.
  Description Molecular computing (especially DNA computing) means using bio-molecules as a support for computations and devising computers. This is in contrast to the current opposite direction of research, the classic one, where computers are used in studying molecules (especially DNA ), a field now commonly termed the science of bioinformatics. Using DNA as a "chip" or support for computation is not a new idea, and has been speculated upon since the 1950's. Adleman's 1994 report on solving the Hamiltonian Path Problem in a graph, using only biochemical laboratory techniques, was the revolutionary turning point in making possible the construction of large computers of huge parallelism, which are able to incorporate the features of matching, splicing (cross-over), insertion, deletions, etc., of data structures (strings and languages) - all features typical of the living DNA molecule. DNA computing is a domain of clear interdisciplinary work, and is definitely a field in rising expansion. Still, a lot of work has to be done, both from a mathematical and a biochemical point of view. This book brings together over 20 international contributions on the theoretical and experimental works of scientists in search of the bio-computer. The style of the contributions are that of research papers and surveys. Being one of the first volumes of its type in this new exciting field, this book will be of equal interest to computer scientists, mathematicians, and biochemists alike.
• Pau98b - Paun98-1
  G. Paun. Distributed architectures in DNA computing based on splicing: Limiting the size of components. In Calude et al. [UMC98], pages 323--335.
  Abstract: Splicing systems (also called H systems) with a finite set of rules generate only regular languages. Thus, it is necessary to supplement such a system with a control mechanism on the use of rules. Many possibilities were explored in the literature. One fruitful idea is to use distributed architectures as suggested by the grammar systems theory. All the results obtained up to now in this area try to simulate Turing machines or type-0 Chomsky grammars by H systems with a minimal number of components. Here we approach an ``orthogonal'' problem: find computationally complete distributed H systems with as reduced as possible components (as the number of splicing rules; this is of practical interest, because the splicing rules correspond to restriction enzymes, and it is in general difficult to put several enzymes to work together, in the same reaction conditions). We prove that communicating splicing systems where each component consists of only one splicing rule characterize the recursively enumerable languages.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Pau00a - APa00-2
  A. Paun. On P systems with active membrane. In Antoniou et al. [UMC2K], pages 187--201.
  Abstract: The paper deals with the vivid area of computing with membranes (P systems). We improve here two recent results about the so called systems with active membranes. First, we show that the Hamiltonian Path Problem can be solved in polynomial time by P systems with active membranes where the membranes are only divided into two new membranes (a result of this type was obtained by Krishna and Rama, [KR99], but making use of the possibility of dividing a membrane in an arbitrary number of new membranes). We also show that HPP can be solved in polynomial time also by a variant of P systems, with the possibility of dividing non-elementary membranes under the influence of objects present in them. Then, we show that membrane division (and even membranes dissolving) is not necessary in order to show that such systems are computationally complete.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• Pau00b - Paun00
  G. Paun. Computing with membranes: attacking NP-complete problems. In Antoniou et al. [UMC2K], pages 94--115.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• PCMS+00 - PCOeo00
  Michael C. Pirrung, Richard V. Connors, Michael P. Montague-Smith, Amy L. Odenbaugh, Nathan G. Walcott, and Jeff J. Tollett. The arrayed primer extension method for DNA microchip analysis. molecular computation of satisfaction problems. J. Am. Chem. Soc., 122:1873, 2000, http://pubs.acs.org/reprint-request?ja992392j/36uF.
  Abstract: A high fidelity, surface-based method of nucleic acid analysis has been developed based on DNA polymerase extension of primer-template complexes on DNA microchips. The method's ability to discriminate against mismatches and provide an almost ``digital" signal recommended it for molecular computation. A DNA computer with the capability of solving NP-complete problems in polynomial time using this Arrayed Primer Extension (APEX) method was experimentally demonstrated. An algorithm involving extension of surface-bound primer-template complexes, representing solutions and clauses of a Boolean formula, is described for the solution of two-, three-, and four-variable satisfiability problems, including a 3SAT, exploiting the theoretical concepts of Lipton. A discussion of the principles of non-deterministic computing with APEX is also provided.
• Pet99 - Pe99
  I. Petre. A normal form for P systems. Bulletin of the EATCS, 67:165--172, February 1999.
• PG99
  M. Ptashne and A. Gann. Evolution as computation, chapter Imposing specificity by localization: mechanism and evolvability, pages 179--200. In Landweber and Winfree [LW99], 1999.
• Pie99 - Pieri00
  Matteo Di Pieri. Computazione molecolare. Master's thesis, Universita Ca' Foscari - Venezia - Italy, 1999, http://digilander.libero.it/mdipieri/tesi/molecular.tgz http:digilander.libero.it/mdipieri/tesi/molecularPDF.tgz.
  Abstract: La computazione molecolare e` una delle aree di ricerca piu` interessanti e recenti dell'Informatica. Essa prevede l'uso di materiale genetico e cellulare come mezzo per effettuare dei calcoli matematici. Alla fine del 1994, Adleman ha descritto un esperimento in cui e` stato possibile risolvere un noto problema sui grafi elaborando appunto delle molecole di DNA. Successivi algoritmi hanno poi dimostrato i vantaggi e le potenzialita` del DNA Computing, la sottoarea della computazione molecolare che usa il materiale genetico. La completezza computazionale di questo modello di calcolo viene inoltre messa in luce dai sistemi formali che ne astraggono i meccanismi funzionali. L'uso della cellula come formalismo di calcolo e` alla base dell'altra sottoarea della computazione molecolare, che e` detta Membrane Computing. Sebbene l'uso della membrana cellulare come modello computazionale non sia stato sperimentato in laboratorio, la potenzialita` di tale modello di calcolo e` stata dimostrata da recenti ricerche nella teoria dei linguaggi formali. Questo lavoro di tesi presenta una rassegna esauriente dello stato attuale dell'area di ricerca della computazione molecolare. L'enfasi e` posta sull'organizzazione unitaria con cui vengono presentati i diversi filoni di ricerca, e sui problemi implementativi dei relativi sistemi di calcolo.
  In italian
• Pis97 - Pisanti97
  Nadia Pisanti. A survey on DNA computing. Technical Report TR-97-07, Univerità di Pisa, April 1997, ftp://ftp.di.unipi.it/pub/techreports/TR-97-07.ps.Z.
  Abstract: The aim of this report is to make a review on DNA computing: molecular biology is used to suggest a new way of solving a NP-complete problem. The idea (due to Leonard Adleman in [Adl94]) is to use strands of DNA to encode the (instance of the) problem, and to manipulate them using techniques commonly available in any molecular biology laboratory, in order to simulate operations that select the solution of the problem, if it exists. After Adleman's paper ---appeared on Science in November 1994--- many authors have been interested in DNA computing. We will try to give a description of the discussions and the results which appeared in literature.
• Pis98 - Pisanti98
  Nadia Pisanti. DNA Computing: A Survey. Bulletin of the European Association for Theoretical Computer Science, 64:188--216, February 1998.
• Pis00
  Nadia Pisanti. DNA computing: a new computational paradigm using molecules. In Bulzoni Editore, editor, Grounding effective processes in empirical laws. Reflections on the notion of algorithm, pages 101--116. Rossella Lupacchini and Guglielmo Tamburrini, 2000, http://www.filosofia.unibo.it/Enriques/Enriques.htm. Research papers in philosophy of science 1, Centro interdipartimentale di ricerca "F. ENRIQUES", Universita' di Bologna.
  Abstract: DNA computing appeared in the literature in 1994 when Leonard Adleman suggested to solve an NP-complete problem by using DNA molecules. Since one can store a large amount of molecules in a small volume, and since it is possible to apply operations to all of them in parallel, the result is a surprisingly interesting performance of DNA computations. In recent years, possible computationally complete models that might be implemented in a molecular biology laboratory have been suggested. Experiments are being performed in order to test the feasibility of DNA computations by using such models. We will report on some of the ideas, discussions, and results that have appeared in the literature so far, and we will stress some new issues in DNA computing that suggest a revisitation of complexity theory.
• Pix95a - Pixton95-2
  Dennis Pixton. Linear and circular splicing systems. In Proceedings of the 1st International Symposium on Intelligence in Neural and Biological Systems, pages 181--188. IEEE, May 1995.
• Pix95b - Pix95
  Dennis Pixton. Regular splicing systems. Manuscript, 1995.
• Pix96 - Pixton96
  D. Pixton. Regularity of splicing languages. Discrete Applied Mathematics, 69(1--2):101--124, August 1996.
  Abstract: Motivated by the recombinant behavior of DNA , T. Head introduced a scheme for the evolution of formal languages called splicing. We give a simpler proof of the fundamental fact that the closure of the regular language under iterated splicing using a finite number of splicing rules is again regular. We then extend this result in two directions, by incorporating circular strings and by using infinite, but regular, sets of splicing rules.
• Pix00 - Pixton00
  Dennis Pixton. Splicing in abstract families of languages. Theoretical Computer Science, 234:135--166, 2000. Also Technical report of SUNY Univ. at Binghamton, New York, 1997.
  Abstract: We show that the iterated splicing operation determined by a regular H scheme (with some additional restrictions) preserves membership in any full abstract family of languages. This involves translation of an H scheme into two alternative forms. The first form, which is closely related to the underlying biochemical operations, uses cutting and pasting rather than splicing. The second form uses matrices of languages, and in this formulation the splicing operation is translated into standard formal language operations (concatenation and quotient). Moreover, in the matrix formulation the splicing language itself may be expressed in terms of standard formal language operations, and this provides an algorithm for calculating the splicing language. As an application we use the cutting and pasting approach to extend the closure result to circular strings.
• PJGDRJSC02 - PGRS02
  M.J. Perez-Jimenez, C. Graciani-Diaz, A. Romero-Jimenez, and F. Sancho-Caparrini. Formalizaciòn computacional del experimento de lipton sobre el problema SAT. In Actas del Primer Congreso Espanol sobre Algoritmos Evolutivos y Bio-inspirado, (AEB'02), pages 326--332, 2002.
• PJRJ02 - PR02-1
  M.J. Perez-Jimenez and A. Romero-Jimenez. Generation of diophantine sets by computing p systems with external output. Lecture Notes in Computer Science, 2509:176--190, 2002.
  Abstract: In this paper a variant of P system with external output designed to compute functions on natural numbers is presented. These P systems are stable under composition and iteration functions. We prove that every Diophantine set can be generated by such P systems; then, the universality of this model can be deduced from the theorem by Matiyasevich, Robinson, Davis and Putnam in which they established that every recursively enumerable set is a Diophantine set.
• PJRJSC02a - PRS02
  M.J. Perez-Jimenez, A. Romero-Jimenez, and F. Sancho-Caparrini. Decision p systems and the p \neq NP conjecture. Lecture Notes in Computer Science, 2597, 2002. To appear.
  Abstract: In this paper we present the model, using symbol--objects, of decision P systems with external output and prove the following main result: if there exists an NP--complete problem that cannot be solved in polynomial time, with regard to the input length, by the deterministic variant of such P systems, constructed in polynomial time, then P \neq NP. From Zandron-Ferretti-Mauri's theorem it follows that if P \neq NP then no NP--complete problem can be solved in polynomial time, with regard to the input length, by a deterministic P system with active membranes but without membrane division, constructed in polynomial time from the input. Both results give a characterization of P\neq NP through the solvability by deterministic P systems.
• PJRJSC02b - PRS02-1
  M.J. Perez-Jimenez, A. Romero-Jimenez, and F. Sancho-Caparrini. Teoría de la Complejidad en Modelos de Computaciòn Celular con Membranas. Kronos, 2002, ISBN 84-86273-57-9.
• PJRJSC04 - PRCvT
  M. J. Pérez-Jiménez, A. Romero-Jiménez, and F. Sancho-Caparrini. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter The P Versus NP Problem Through Cellular Computing with Membranes, pages 338--352. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• PJSC01a - PS01-1
  M.J. Perez-Jimenez and F. Sancho-Caparrini. Minimal set cover problem: On a DNA solution of selection stage. In G. Paun C. Martíín-Vide, editor, Pre-proceedings of Workshop on Membrane Computing, pages 251--258, 2001. Report 17/01 of the Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain.
  Abstract: The introduction of Sticker Model by S. Roweis et al. is illustrated with a solution in this model of a NP-complete problem: Minimal Set Cover Problem. The molecular solution given has three stages, the last one is a subroutine to select a minimal set cover of a finite set from a collection of covers of it. In this work a formal verification of this subroutine is given through a systematic method using a labeling procedure and invariant formulas searching.
• PJSC01b - PS01
  M. J. Perez-Jumenez and F. Sancho-Caparrini. Solving knapsack problems in a sticker based model. In Jonoska and Seeman [P7], pages 94--106.
  Abstract: Our main goal in this paper is to give molecular solutions for two NP-complete problems, namely Subset-sum and Knapsack, in a sticker based model for DNA computations. In order to achieve this, we have used a finite set sorting subroutine together with the description of a procedure to formally verify the designed programs through the labeling of the test tubes using inductive techniques.
• PJSC02a - PS02-3
  M.J. Perez-Jimenez and F. Sancho-Caparrini. Computaciòn Celular con Membranas: Un modelo no convencional. Kronos, 2002, ISBN 84-86273-52-8.
• PJSC02b - PS02-2
  M.J. Perez-Jimenez and F. Sancho-Caparrini. A formalization of transition p systems. Fundamenta Informaticae, 49(1-3):261--272, 2002.
  Abstract: In this paper we give a complete formalization of a new computability model of a distributed parallel type which is inspired by some basic features of living cells: transition P systems, addressed with completely different techniques than other previous papers. For this, we present a formal syntax and semantic of the transition P systems capturing the synchronized work of P systems, and the nondeterministic and maximally parallel manner in which the rules of the system can be applied.
• PJSC02c - PS02-1
  M.J. Perez-Jimenez and F. Sancho-Caparrini. Simulating turing machines by p systems with external output. Fundamenta Informaticae, 49(1-3):273--287, 2002.
  Abstract: Another proof of the universality of Membrane Computing with External Output is presented. The proof is carried out associating to each deterministic Turing Machine a P System with External Output that simulates its running. Thus we generate directly all recursively enumerable languages, instead of modulo Parikh mapping.
• PJSC02d - PS02
  M.J. Perez-Jimenez and F. Sancho-Caparrini. Verifying a p system generating squares. Romanian Journal of Information Science and Technology, 5(1-2):181--191, 2002.
  Abstract: In the foundational paper of P systems, G. Paun gives an example of a P system generating exactly all the squares of natural numbers greater than 1 is given. In this paper we study a similar P system to it (only one evolution rule is modified). A formalization of the syntax of the P system is given, and then we establish its formal verification through the study of the critical points of the computations of the P system that give to us important information to characterize the successful computations.
• PM01 - PC01
  R. Penchovsky and J. S. McCaskill. Cascadable hybridization transfer of specific DNA between microreactor selection modules. In Jonoska and Seeman [P7], pages 46--56.
  Abstract: The paper demonstrates experimentally the basic principle of DNA transfert between magnetic bead based selection stages, which can be used in steady flow microreactors for DNA computing [MCC01] and molecular diagnostic. Short DNA oligomers, which can be attached covalently to magnetic beads by a light programmable photochemical procedure [Penchovsky et.al.: Nucleic Acid Res., 22 (2000) e98], are used to bind matching ssDNA from a flowing solution. The beads are restrained in a two reaction chambers (molecules) by etched ledges in a bonded microreactor made of silicon and glass, with the solution flowing in closed micro-channels. The action of a steady flow network of selection molecules is studied in this two chamber microreactor using a succession of different buffer solutions at alternate pH to simulate the transfer between parallel flows in a former system. The pH changes causes successive hybridization and dissociation of ssDNA to matching sequences on the beads. Detection of DNA is by fluorescence from rhodamine-labeled target DNA. The result demonstrate the successful selection of specific DNA in one module and its subsequent transfer to and pickup on the magnetic beads of a second module. This verifies the biochemical operation of the basic processing step for optically programmable DNA computing in micro-flow reactors.
• Poo95 - Poole95
  Robert Pool. A boom in plans for DNA computing. Science, 268:498--499, April 28, 1995.
• Poo96 - New_Scientist_96
  Robert Pool. Forget silicon, try DNA. New Scientist, 151(2038):26--31, July 13, 1996.
• Poo97 - Pool97
  Robert Pool. Dr. tinkertoy. Discover Magazine, February 1997, http://www.enews.com/magazines/discover/magtxt/9702-1.html.
  Abstract: Ned Seeman has been playing around in his lab for more than a decade and has nothing to show for it--other than a few miraculous toys made from the molecule of life.
• PP98 - PaPa98
  A. Paun and M. Paun. Controlled and distributed H systems of small diameter. In Paun [CBMtitle], pages 239--254.
  Abstract: This paper is a direct continuation of [APa97]. Characterizations of recursively enumerable language are given, by means of H systems with permitting context or with target language and by means of communicating distributed H systems having splicing rules of small size (that is, involving short context strings). Representations of context-free languages are also obtained in certain particular cases.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• PP99 - PePe99
  I. Petre and L. Petre. Mobile ambients and P systems. Journal of Universal Computer Science, 5(9):588--589, 1999.
  Also in Workshop on Formal Languages, FTC'99, Iasi, Romania
• PP01 - APMP00
  A. Paun and M. Paun. Where Do Mathematics, Computer Science, Linguistic and Biology Meet, chapter On the membrane computing based on splicing, pages 409--422. Kluwer, Dordrecht, 2001. C. Martín-Vide and V. Mitrana (eds).
• PPJ03
  G. Paun and M.J. Perez-Jimenez. Recent computing models inspired from biology: DNA and membrane computing. To appear in Theoria, 2003.
  Abstract: We briefly present two areas of natural computing, vividly investigated in the recent years: DNA computing and membrane computing. Both of them have the roots in cellular biology and are rather developed at the theoretical level (new concepts, models, paradigms of computer science, with mathematical and epistemological significance have been considered in this framework), but both areas are still looking for implementations of a practical interest.
• PPJSC02 - PPS02
  G. Paun, M.J. Perez-Jimenez, and F. Sancho-Caparrini. On the reachability problem for p systems with porters. In Proceedings of the 10^th International Conference on Automata and Formal Languages, 2002.
  Abstract: We address the problem of deciding whether or not a given configuration of a P system can be reached by correct transitions starting from a given initial configuration. Specifically, we consider P systems with symport/antiport rules, an attractive class which was recently introduced. As expected, the problem is undecidable in general, due to the large generative power of P systems, but, somewhat surprisingly, the reachability is decidable for configurations which take into account also the objects which are sent out of the system during the computation (the language describing such configurations is proved to be context-sensitive, hence recursive). These assertions are true both for halting configurations and for arbitrary configurations
• PPP96
  J. Parkkinen, S. Parkkinen, and G. Paun. Computing by splicing: gsm's working on circular words. -, 1996.
  Manuscript
• PPZ97
  R. Paturi, P. Pudlak, and F. Zane. Satisfiability coding lemma. Proceedings of the 38th annual symposium on foundations of computer science, pages 566--574, October 1997. Miami Beach, Florida.
• PR98 - GPGR98
  G. Paun and G. Rozenberg. Sticker systems. Theoretical Computer Science, 205, 1998.
• PR00
  G. Paun and G. Rozenberg. A guide to membrane computing. unpublished, 2000.
• PR02
  D. M. Prescott and G. Rozenberg. How ciliates manipulate their own DNA. A splendid example of natural computing. Natural Computing, 1(2-3):165--183, 2002.
• Pre96 - GP96
  MIT Press, editor. First Conference on Genetic Programming, Stanford University, 1996. -, ISBN 0-262-61127-9, http://www.cs.brandeis.edu/~zippy/gp-96.html.
• PRM98 - PRM97-1
  L. Priese, Y. Rogozhin, and M. Margenstern. Finite H-systems with 3 test tubes are not predictable. In Altman et al. [PSB98], pages 547--558, http://www.uni-koblenz.de/fb4/publikationen/gelbereihe/RR-24-97.ps.gz.
  Abstract: Finite H-systems with n test tubes are splicing systems of n test tubes over a common molecular alphabet, \Sigma, with a filter F_i\subseteq\Sigma for each test tube. Initially, arbitrary many copies of molecules and enzymes (splicing rules) from a finite set of molecules and enzymes are given to the test tubes that produce new molecules by splicing and filtering. It is known that any formal language can be generated by a finite H-system with 9 test tubes and that the results of finite H-systems with 6 test tubes are unpredictable. Here we present a rather simple proof that the results of finite H-systems with only 3 test tubes are unpredictable and that 4 test tubes suffices to generate any formal language.
• Pro - Profir03
  A. Profir. Bistable self-organizing biocomputing model. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• PRS95 - PRS95-1
  G. Paun, G. Rozenberg, and A. Salomaa. Restricted use of the splicing operation. Technical Report TR95-16, Department of Computer Science, Leiden University, P.O. Box 9512, 2300 RA Leiden, The Netherlands, June 1995.
  Abstract: Splicing is a new powerful tool, stemming originally from molecular genetics but investigated extensively also in language theory. In this paper we investigate variants of splicing inspired partly by regulating mechanism customarily studied in language theory, partly by imposing restrictions on the pairs to be spliced or on the result of splicing. The Chomsky hierarchy constitutes a very suitable test bed for the resulting families, because it is classical and well understood. In contrast to the usual, nonrestricted splicing, we find several cases when the families of regular or of context-free languages are not closed under the new types of splicing. On the other hand, our results give new characterizations for families in the Chomsky hierarchy and for closure properties in general.
• PRS96a - PRS
  G. Paun, G. Rozenberg, and A. Salomaa. Computing by splicing. Theoretical Computer Science, 168(2):321--336, 1996.
• PRS96b - PRS96-1
  G. Paun, G. Rozenberg, and A. Salomaa. Restricted use of the splicing operation. International Journal of Computer Mathematics, 60:17--32, 1996. Also Technical Report TR95-16, Department of Computer Science, Leiden University, The Netherlands June 1995.
  Abstract: Splicing is a new powerful tool, stemming originally from molecular genetics but investigated extensively also in language theory. In this paper we investigate variants of splicing inspired partly by regulating mechanism customarily studied in language theory, partly by imposing restrictions on the pairs to be spliced or on the result of splicing. The Chomsky hierarchy constitutes a very suitable test bed for the resulting families, because it is classical and well understood. In contrast to the usual, nonrestricted splicing, we find several cases when the families of regular or of context-free languages are not closed under the new types of splicing. On the other hand, our results give new characterizations for families in the Chomsky hierarchy and for closure properties in general.
• PRS97 - PRS96
  G. Paun, G. Rozenberg, and A. Salomaa. Computing by splicing. Programmed and evolving splicing systems. In IEEE International Conference on Evolutionary Computation, pages 273--277, 1997. Indiana University Purdue University, Indianapolis, Illinois, USA.
  Abstract: Computing by splicing is a new powerful tool stemming originally from molecular genetics. This new model of computing, spicing systems, is investigated here. Several variants, resulting from the use of the rules in different ways, are considered. The power of such systems with very weak structure imposed on rules turns out to be very large. Characterizations of recursively enumerable languages are obtained for many variants. In this way our study is analogous to the early studies concerning variations of the Turing machines. Other classes of such splicing systems generate only regular or context-free languages (giving, in fact, characterizations of these families). With a few exceptions, we are able to obtain precise characterizations for all resulting families.
• PRS98 - PRSbook
  G. Paun, G. Rozenberg, and A. Salomaa. DNA Computing: New Computing Paradigms. Springer Verlag, Berlin, Heidelberg, New York, September 1998, ISBN 3-540-64196-3.
  Description This is both a text and a monograph about DNA computing, a field of rapidly growing interest during the past few years. As indicated in the title, special emphasis is laid on underlying ideas concerning computing and computability in general: what happens when the sequential computing of Turing's diligent clerk is replaced by, or taken in conjunction with the massive parallelism of DNA strands acting in a test tube. The research traditions, let alone idioms and vocabulary, are rather different within the communities of molecular biologists and theoretical computer scientists. The book provides relevant introductory material from both fields, molecular biology and theoretical computer science. The book consists of two parts. The first part, written in a narrative style, begins with the basics of biochemistry and DNA -related matters, and then proceeds to the DNA -based computing itself, its experimental history, laboratory techniques used so far, its problems, hopes, as well as warnings presented against it. The first part also contains a brief account "DNA computing in a nutshell". The second part is a monograph about the mathematical theory of DNA computing, based mainly on the authors' own work. The table of contents given below should give an idea about the topics covered. The reader will learn the significance of the Watson-Crick complementarity: it guarantees universal computations in any model of DNA computers having sufficient capabilities for handling inputs and outputs. Watson-Crick complementarity is closely related to the twin-shuffle language, known to be universal and built from four letters. What a coincidence: DNA molecules are built from four nucleotides! To aid the reader, the second part is provided with a lengthy introduction to the prerequisites needed in the theory. The theory also indicates directions, where progress in laboratory techniques is very much needed.
• PRS00 - PRS99
  G. Paun, G. Rozenberg, and A. Salomaa. Membrane computing with external output. Fundamenta Informaticae, 3(41):259--266, 2000.
  See also TUCS research report No. 218, December 1998, http://www.tucs.fi
• PRS01 - ctt01
  G. Paun, G. Rozenberg, and A. Salomaa, editors. Current Trends in Theoretical Computer Science. Entering the 21st Century. Worlds Scientific Publishing Co. Pte. Ltd., 2001, ISBN 981-02-4473-8.
  The book contains: [Amos01], [MS01], [Kari01], [GP01] and [GP01-1].
• PS96a - PS96
  G. Paun and A. Salomaa. From DNA recombination to DNA computing via formal languages. Technical Report 43, Turku Center for Computer Science, Turku University, Department of Mathematics, 20014 Turku, Finland, October 1996, http://www.tucs.abo.fi/publications/techreports/TR43.ps.gz.
  Abstract: We briefly present notions and results from three directions of research which use formal language theory tools for modeling operations specific to DNA (and RNA) recombinations; in all cases one obtains computability models which are universal (language generating devices are obtained which are equivalent in power with Turing machines). The basic operations are those of matching (a model of the Watson-Crick complementarity), of splicing (a model of the recombinant behaviour of DNA sequences under the influence of restriction enzymes), and of insertion/deletion (known to hold both for DNA and for RNA sequences).
• PS96b - MFCS96
  Penczek and Szalas, editors. Proc. Mathematical Foundations of Computer Science, volume 1113, Cracow, Poland, 1996. Springer Verlag, Berlin, Heidelberg, New York. Lecture Notes in Computer Science.
• PS96c - PaSa96
  G. Paun and A. Salomaa. From DNA recombination to DNA computing. Proc. of Fis German Conf. on Bioinformatics, 1996. Leipzig.
  Also in [PaSa97]
• PS97 - PaSa97
  G. Paun and A. Salomaa. From DNA recombination to DNA computing. Lecture Notes in Computer Science, 1278:210--220, 1997.
  Also in [PaSa96]
• PST01 - PST00
  G. Paun, Y. Suzuki, and H. Tanaka. P system with energy accounting. Inter. J. Computer Math., 79, 2001.
• PSTY00
  G. Paun, Y. Suzuki, H. Tanaka, and T. Yokomori. On the power of membrane division in P systems. manuscript, 2000.
• PSY01 - PSY00
  G. Paun, Y. Sakakibara, and T. Yokomori. P systems on graphs of restricted forms. Publicationes Mathematicae Debrecen, 2001.
  To appear
• PT99
  G. Paun and G. Thierrin. Multiset processing by means of systems of finite state transducers. In O. Boldt, H Jurgensen, and L. Robbins, editors, Pre-Proc. of Workshop on Implementing Automata WIA99, volume 15, pages 1--17. Potsdam, Preprint 5/1999 of Univ. Potsdam, August 1999.
  See also Auckland University, CDMTCS Report No. 101, 1999 http://www.cs.auckland.ac.nz/CDMTCS
• PTY00
  G. Paun, G. Thierrin, and S. Yu. Tree-systems of morphisms. manuscript, 2000.
• P\u95 - Paun95
  G. Paun. On the power of the splicing operation. International Journal of Computer Mathematics, 59:27--35, 1995.
• P\u96a - Paun95-2
  G. Paun. Computationally universal distributed systems based on the splicing operation. J. Automata, Languages, Combinatorics, 1(1):27 -- 36, 1996.
• P\u96b - Paun96-7
  G. Paun. DNA computing based on the splicing operation. Mathematica Japonica, 43(3):607--632, 1996.
• P\u97a - APa97
  A. Paun. Controlled H systems of small radius. Fundamenta Informaticae, 31, 2:185--193, 1997.
• P\u97b - GPa97-1
  G. Paun. Controlled H systems and chomsky hierarchy. Fundamenta Informaticae, 30, 1:45--57, 1997.
• P\u97c - GPa97
  G. Paun. Structures in Logic and Computer Science. A Selection of Essays in Honor of A. Ehrenfeucht, volume 1261 of Lecture Notes in Computer Science, chapter DNA computing: distributed splicing systems, pages 351--370. Springer Verlag, Berlin, Heidelberg, New York, 1997. J. Mycielsky and G. Rozenberg and A. Salomaa (eds).
• P\u97d - GPa97-2
  G. Paun. Two-level distributed H systems. Proc. of the Third Conf. on Developments in Language Theory, pages 309--327, 1997. Aristotele Univ. of Thessaloniki, Thessaloniki.
• P\u98a - CBMtitle
  G. Paun, editor. Computing with Bio-Molecules. Theory and Experiments. Springer Verlag, Berlin, Heidelberg, New York, 1998, ISBN 981-4021-05-9.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• P\u98b - GPa98
  G. Paun. DNA computing based on splicing: universality results. In Proceedings of the Second International Colloquium on Universal Machines and Computations, Metz, volume 1, pages 67--91, 1998.
• P\u99a - GhP11
  G. Paun. Computing with membranes. a correction, two problems, and some bibliographical remarks. Bulletin of the EATCS, 68:141--144, 1999.
• P\u99b - GhP1
  G. Paun. Computing with membranes. An introduction. Bulletin of the European Association for Theoretical Computer Science, 67:139--152, February 1999.
  See also [GP01-1].
• P\u99c - GPa97-3
  G. Paun. (DNA) computing by carving. Soft Computing, 3(1):30--36, 1999.
• P\u00a - APa00-1
  A. Paun. On P systems with global rules. unpublished, 2000.
• P\u00b - APa00-3
  A. Paun. On rewriting P systems with partial parallelism. unpublished, 2000.
• P\u00c - GPa00
  G. Paun. Computing with membranes. Journal of Computer and System Sciences, 1(61):108--143, 2000.
• P\u00d - GhP2
  G. Paun. Computing with membranes. A variant: P systems with polarized membranes. International Journal of Foundations of Computer Science, 1(11):167--182, 2000.
  See also CDMTCS research report No. 098, 1999, Auckland Univ., New Zealand. http://www.cs.auckland.ac.nz/CDMTCS
• P\u00e - GhPa00
  G. Paun. Computing with membranes; attaching NP-complete problems. Unconventional Models of Computing, pages 94--115, 2000.
• P\u00f - GP00-1
  G. Paun. Computing with membranes (P systems): twenty six research topics. In Calude et al. [WMP2000], pages 203--217, http://www.cs.auckland.ac.nz/CDMTCS.
  Abstract: The aim of these notes is to state a series of open problems and, mainly, research topics about P systems. They can be clustered in three classes: questions dealing with "classic" topics in automata and language theory, questions motivated by the possible usefulness of P systems as computing models (implementation and complexity issues), and questions related to the fields where the P systems are inspired from, biology and biochemistry. Precise open problems can be found practically in all papers published or distributed so far on the web; here we are mainly interested in research directions, in classes of problems.
• P\u00g - GP00
  G. Paun. From cells to computers: computing with membranes (P-systems). In International Workshop Grammar Systems 2000 (R. Freund, A. Kelemenova), Bad Ischl, Austria, July 2000, pages 9--40, 2000.
  Abstract: The aim of this paper is to introduce to the reader the main ideas of Computing with Membranes, a recent branch on (theoretical) Molecular Computing. In short, in a cell-like system, multisets of objects evolve in a membrane structure and compute natural number as the result of halting sequences of transitions. The model is parallel, nondeterministic. Many variant have been already considered and many problems about them were investigated. We present here some of these variants, focusing on two central classes of results: (1) characterization or recursively enumerable sets of numbers and (2) possibilities to solve NP-complete problems in polynomial (even linear) time. Only samples of typical proofs are given. A complete bibliography of the domain, at the middle of April 2000, is also provided.
  Also in Bio Systems, Volume 59, Issue 3, Pages 139-158 (March 2001)
• P\u00h - GPa00-3
  G. Paun. From cells to computers: computing with membranes (P systems). manuscript, 2000.
• P\u00i - GPa00-1
  G. Paun. On P systems with membrane division. In Antoniou et al. [UMC2K], pages 187--201.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• P\u00j - GhPa00-1
  G. Paun. On the generative power of P systems. Theorietag 2000, Workshop on New Computing Paradigms, pages 59--78, 2000.
  TU Vienna, Austria
• P\u01a - APa01-1
  A. Paun. On P systems with global rules. In Jonoska and Seeman [P7], pages 329--339.
  Abstract: We contribute to the vivid area of membrane computing (P systems) by considering the case when the same evolution rules are valid in all regions of the system. Such a P system is called with global rules. We consider the case of string-objects, with the evolution rules based on splicing and by rewriting. Universality results are proved for both types of systems. For splicing we also try to minimize the diameter of the used rules, while for rewriting systems we improve a result from the literature, proving that two membranes suffice for simulating Turing machines.
• P\u01b - APa01
  A. Paun. On P systems with partially parallel rewriting. Romanian J. Inform. Sci. and Technology, 4(1-2), 2001.
• P\u01c - Pa01
  A. Paun. P systems with string-objects: universality results. In pre-proceedings of Workshop on Membrane Computing, WMC-CdeA2001, pages 229--241, 2001.
  Abstract: We contribute to the area of membrane computing (P systems) by considering several types of systems having string-objects and presenting some results concerning the universality of these devices. The case when the same evolution rules are valid in all regions (such a system is said to be with global rules) is considered for splicing P systems and rewriting P systems, which are proved to be computationally universal. We also consider the case of partial parallelism, as recently introduced by Krishna and Rama, and we settle an open problem formulated by Krishna and Rama by proving that such systems having six membranes are universal. For splicing P systems we also try to minimize the diameter of the used rules.
• P\u01d - GP01-1
  G. Paun. Computing with Membranes (P Systems): an Introduction, volume -, pages 845--866. World Scientific, 2001.
  See also [GhP1].
• P\u01e - GhP3
  G. Paun. P systems with active membranes: attacking NP complete problems. Journal of Automata, Languages and Combinatorics, 1(6):75--90, 2001.
  See also CDMTCS research report No. 102, 1999, Auckland Univ., New Zealand. http://www.cs.auckland.ac.nz/CDMTCS
• P\u01f - GP01
  G. Paun. Splicing: a Challenge for Formal Language Theorist, volume -, pages 830--844. World Scientific, 2001.
• P\u04 - PvT
  G. Paun. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Membrane Computing: Some Non-standard Ideas, pages 322--337. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• PY99a - PY99-1
  G. Paun and T. Yokomori. Membrane computing based on splicing. In Winfree and Gifford [P5], pages 217--232.
  Abstract: Membrane computing devices were recently introduced (under the name of P systems) as distributed parallel computing models of a biochemical type. Multisets of objects are placed in a cell-like hierarchical structure of membranes and they evolve according to given rules, which are applied in a synchronous manner: at each step, all objects which can evolve, from all membranes, must evolve. The result of a computation consists of objects which exit the system. Here we consider objects described by strings, which evolve by means of splicing rules. Both usual P systems based on membrane structures and systems working on planar maps are considered. Several simple variants are shown to be computationally universal: systems with only a few number of membranes (described by a star tree or a linear tree) or working on maps described by asymmetric graphs and without any target indication when communicating strings characterize the recursively enumerable languages.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• PY99b - PYu99
  G. Paun and S. Yu. On synchronization in P systems. Fundamenta Informaticae, 34(4):397--410, 1999.
  see also University of Western Ontario Report TR 539, 1999, http://www.csd.uwo.ca/faculty/syu/TR539.html
• PY00 - PaYo00
  G. Paun and T. Yokomori. Simulating H systems by P systems. Journal of Universal Computer Science, 6(2):178--193, 2000. http://www.iicm.edu/jucs.
• QL98
  Z. F. Qiu and M. Lu. Arithmetic and logic operations for DNA computers. Second IASTED International Conference on Parallel and Distributed Computing and Networks, pages 481--486, December 1998, http://ee.tamu.edu/~zhiquan/dna/pub/iasted.ps.
  Brisbane, Australia
• QL00a - QL00-1
  Z. F. Qiu and M. Lu. A surface-based DNA algorithm for the expansion of symbolic determinants. Accepted to the Third Workshop on Bio-inspired solutions to parallel problems (BioSP3), May 2000, http://ee.tamu.edu/~zhiquan/dna/pub/symb.ps.
• QL00b - QL00-2
  Z. F. Qiu and M. Lu. Take advantage of the computing power of DNA computers. Accepted to the Third Workshop on Bio-inspired solutions to parallel problems (BioSP3), May 2000, http://ee.tamu.edu/~zhiquan/dna/pub/logical.ps.
• R. 00 - WGS2000
  R. Freund and F. Freund. International Workshop Grammar Systems 2000 (R. Freund, A. Kelemenova), Bad Ischl, Austria, July 2000, Edicni stredisko FPF SU, Opava, 2000, ISBN 80-7248-067-7.
  The proceedings contain [GP00], [Sir00], [BMFZ00], [ZMF00].
• Ram00 - R00
  R. Rama. Computing with P systems. In Calude et al. [WMP2000], pages 218--235.
  Abstract: P systems, introduced by G. Paun form a new class of biologically inspired distributed computing models. Several variants of P systems were already shown to be computationally universal. In this paper, we establish that rewriting P systems with priorities and two membranes is computationally universal, improving the existing result that RE \subseteq RP_3(Pri). We give a new model in P systems stressing the importance of parallelism and investigate its power. We also propose a class of P systems capable of solving NP-complete problems like HPP and NCD in linear time. We also show that this class of P systems can break the most widely used cryptosystem, DES in linear time.
• RD00
  J. A. Rose and R. J. Deaton. The fidelity of annealing-ligation: a theoretical analysis. In Condon and Rozenberg [P6], pages 231--246.
  Abstract: Understanding the nature of the error propagation through successive biosteps is critical to modeling the overall fidelity of computational DNA architectures. In this work, the fidelity of the compound biostep annealing-ligation is discussed in the limit of zero dissociation, within the framework of a simple statistical thermodynamic model. For simplicity, a DNA ligase of ideal infidelity is assumed, with its error behavior taken as bounding that of real DNA ligases. The derived expression for the fidelity of annealing-ligation indicates that the error coupling is both strong and dependent on sequence. Estimates of the fidelities of annealing and annealing-ligation have also been calculated for various encodings of Adleman's graph, assuming a staggered zipper model of duplex formation. Results indicate the necessity of including information regarding the specific free energies and/or occupancies of accessible duplex states, in addition to information based purely on sequence comparison.
• RDG+97 - RDGMFS97
  J. A. Rose, R. Deaton, M. Garzon, R. C. Murphy, D. R. Franceschetti, and S.E. Stevens, Jr. The effect of uniform melting temperatures on the efficiency of DNA computing. In Rubin and Wood [P3], pages 35--42, http://www.msci.memphis.edu/~garzonm/dna97umelt.ps.
  Abstract: Differences in the binding energies between nitrogenous bases cause a large variation in the melting temperatures of oligonucleotides of a given length. This non uniformity restricts the maximum graph size that can be reliably and efficiently solved by DNA computation with compositionally random encodings. It is shown that homogenizing the encodings into alternating regions of A-T's and C-G's substantially increases this size. The consequent uniformity in melting temperatures among codewords also allows the application of DNA chip (SbH) extraction methods.
• RDHS - RDHS01
  J. A. Rose, R. J. Deaton, M. Hagia, and A. Suyama. The fidelity of the tag-antitag system. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• RE97
  M. P. Robertson and A. D. Ellington. New directions in nucleic acid computing: Selected ribosomes that can implement re-write rules. In Rubin and Wood [P3], pages 69--73.
• Rea01 - PRe
  Patricia Reaney. Scientists build tiny computer from DNA, November 22, 2001, http://in.news.yahoo.com/011121/107/199x5.html.
  Abstract: Following Mother Nature's lead, Israeli scientists have built a DNA computer so tiny that a trillion of them could fit in a test tube and perform a billion operations per second with 99.8 percent accuracy ...
  Yahoo! India News: World
• Rei95 - Reif95
  J. H. Reif. Parallel molecular computation: models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA95), Santa Barbara, June 1995, pages 213--223, 1995, http://www.cs.duke.edu/~reif/paper/Molecular.ps, http://www.cs.duke.edu/~reif/paper//mole.fig.ps, http://www.cs.duke.edu/~reif/paper/Molecular.pdf.
• Rei97 - Reif97
  J. H. Reif. Local parallel biomolecular computing. In Rubin and Wood [P3], pages 243--264.
• Rei98a - Reif98-2
  J. H. Reif. Paradigms for biomolecular computation. In Calude et al. [UMC98], pages 72--93, http://www.cs.duke.edu/~reif/paper/paradigm.ps, http://www.cs.duke.edu/~reif/paper/paradigm.pdf.
  Abstract: Biomolecular Computation (BMC) is computation done at the molecular scale, using biotechnology techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental milestones for the field of BMC.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Rei98b - Reif98
  J. H. Reif. Parallel molecular computation: Models and simulations. Algorithmica, 1998, http://www.cs.duke.edu/~reif/paper/Molecular.ps, http://www.cs.duke.edu/~reif/paper//mole.fig.ps, http://www.cs.duke.edu/~reif/paper/Molecular.pdf. Special issue on Computational Biology.
• Rei02 - Reif02
  J. Reif. The design of autonomous DNA nanomechanical devices: Walking and rolling DNA. In Hagiya and Ohuchi [PP8], pages 22--37.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• Rei03 - Reif03
  J. H. Reif. The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA. Natural Computing, 2(4):439--461, 2003.
• RFL01
  A. J. Ruben, S. J. Freeland, and L. Landweber. PUNCH: an evolutionary algorithm for optimizing bit set selection. In Jonoska and Seeman [P7], pages 150--160.
  Abstract: Nearly every nucleotide-based computing problem attempted thus far has involved the prearranged assignment of nucleotide sequences to represents bits. However, no general program is yet available to optimize those bit sequences. In this paper, we present a program that uses an evolution algorithm to generate optimum bit sets using given (changeable) criteria. We also test some properties of the program and discuss future applications.
  The volume contains [SY01], [HHS01], [WBKeo01], [EHPR01], [APa01-1], [MMP01-1], [UHK01], [GO01], [Sak01], [HKK01], [MR01], [MGC01], [PC01], [JS01], [HSc01], [MGLeo01], [FSR01], [BKS01], [WY01], [MY01], [HCNeo01], [MYS01], [RLBeo01], [YHM01], [RFL01]
• RHB - RHB03
  S. Raikin, C. Henkel, and T. B\"ack. An evolutionary algorithm for DNA sequence design. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• RHCE99 - RHeo99
  Michael P. Robertson, Jay Hesselberth, J. Colin Cox, and Adrew D. Ellington. Designing and selection components for nucleic acid computers. In Winfree and Gifford [P5], pages 183--193.
  Abstract: Just as the design and function of modern electronic computers is dependent on the nature of their components, the design and function of nucleic acid computers will likely be dependent on the types of molecules used in their construction. We show that ribozymes can function as switches and as molecular logic gates, and propose that nuclei acid catalysts might therefore be used to generate circuitry for biological computation. Nucleic acids can also self-assemble into stochastic, organized architectures that may prove to be the equivalent of circuits boards for nucleic acid components.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• RI - RI00
  P. Raj and N. Ishii. A generalization of splicing system. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• RJ90 - RobertsonJoyce90
  D. L. Robertson and F. G. Joyce. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 344(6265):467--468, March 29 1990.
• RJL95 - DBC
  E. B. Baum R. J. Lipton, editor. DNA based computers, volume 27 of DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1995.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• RK00
  R. Rama and S. N. Krishna. On some classes of deterministic P systems. unpublished, 2000.
• RKM+97 - GP97
  Koza John R., Deb Kalyanmoy, Dorigo Marco, Fogel David B.and Garzon Maxand Iba Hitoshi, and Riolo Rick L., editors. Conference on Genetic Programming, GP-97, Stanford University, Stanford, California, July13--16, 1997. -, http://www.msci.memphis.edu/~garzonm/csys/gp97.html. Special Track on DNA computing.
• RL00 - RLB00
  J. H. Reif and T. H. LaBean. Computationally inspired biotechnologies: improved DNA synthesis and associative search using error-correcting codes and vector-quantization. In Condon and Rozenberg [P6], pages 145--172.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• RLBR - RLBR00
  C. Richter, A. Leier, W. Banzhaf, and H. Rauhe. Private and public key DNA steganography. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• RLP+01 - RLBeo01
  J. H. Reif, T. H. LaBean, M. Pirrug, V. S. Rana, B. Guo, C. Kingsford, and G. S. Wickham. Experimental construction of a very large scale DNA database with associative search capability. In Jonoska and Seeman [P7], pages 231--247.
  The volume contains [SY01], [HHS01], [WBKeo01], [EHPR01], [APa01-1], [MMP01-1], [UHK01], [GO01], [Sak01], [HKK01], [MR01], [MGC01], [PC01], [JS01], [HSc01], [MGLeo01], [FSR01], [BKS01], [WY01], [MY01], [HCNeo01], [MYS01], [RLBeo01], [YHM01], [RFL01]
• RLS00 - RBS00
  J. Reif, T. H. LaBean, and N. Seeman. Challenges and applications for self-assembled DNA nanostructures. In Condon and Rozenberg [P6], pages 173--198.
  The volume contains [KSeo00], [BJeo00], [Fri00], [MR00], [WER00], [Hagi00], [CN00], [BFMZ00], [FrFr00], [RLB00], [RBS00], [CR00], [DEO00], [Sak00], [GWC00], [CPeo00]
• RNP01 - NWMP01
  J.J. Mulawka R. Nowak, P. Wasiewicz and A. Plucienniczak. Processing DNA tokens in parallel computing. In Proc. International Parallel and Distributed Processing Symposium, 2001.
  Abstract: In this paper a new technique of sending data between molecular processors is presented. The molecular processor is a processing data unit. Its computation results have to be sent to other units in the form of addressed messages - tokens. Necessary experiments were performed. All operations were implemented in DNA . DNA processors and tokens were specially designed DNA strings. Results of experiments prove our assumptions.
  San Francisco - USA
• Ros - Ros00
  Bill Rosato. DNA motors promise faster, smaller electronics, http://dailynews.yahoo.com/h/nm/20000809/sc/dna_dc_1.html. Only on the net.
• Rot95 - Roth96
  P. W. K. Rothemund. A DNA and restriction enzyme implementation of Turing machines. In R. J. Lipton [DBC], pages 75--120, http://www.ugcs.caltech.edu/~pwkr/oett/dimacs/dimacs.ps, http://www.ugcs.caltech.edu/~pwkr/oett.html.
  Abstract: Bacteria employ restriction enzymes to cut or restrict DNA at or near specific words in a unique way. Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA . Two pieces of DNA may be rejoined or ligated if their terminal overhangs are complementary. Using these operations fragments of DNA , or oligonucleotides may be inserted and deleted from a circular piece of plasmid DNA . We propose an encoding for the transition table of a Turing machine in DNA oligonucleotides and a corresponding series of restrictions and ligations of those oligonucleotides that, when performed on circular DNA encoding an instantaneous description of a Turing machine, simulate the operation of the Turing machine encoded in those oligonucleotides. DNA based Turing machines have been proposed by Charles Bennet but they invoke imaginary enzymes to perform the stat-symbol transitions. Our approach differs in that every operation can be performed using commercially available restriction enzymes and ligases.
  A very detailed scheme for simulation Turing machines in DNA. Provides references to papers prior to [Adl94] containing some of the ideas of Molecular Computation.
• Roz00
  G. Rozenberg. DNA processing in ciliates - the wonders of DNA computing in vivo. In Antoniou et al. [UMC2K], pages 116--118. Invited paper.
  The proceedings contain [MVM00-11], [APa00-2], [ZFM00-3], [Head00], [Roz00], [GPa00-1] and [Paun00].
• RP01 - Rod01
  A. Rodriguez-Paton. Computing with membranes: P systems with DNA-worms. unpublished, 2001.
• RPW03
  P. W. K. Rothemund, N. Papadakis, and E. Winfree. Algorithmic self-assembly of DNA sierpinski triangles. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 125, 2003.
• RS92 - Lsystems92
  G. Rozenberg and A. Salomaa, editors. Lindenmayer Systems: Impacts on Theoretical Computer Science, Computer Graphics and Developmental Biology. Springer Verlag, Berlin, Heidelberg, New York, 1992, ISBN 3-540-55320-7.
  Description L systems are language-theoretic models for developmental biology. They were introduced in 1968 by Aristid Lindenmayer (1925-1989) and have proved to be among the most beautiful examples of interdisciplinary science, where work in one area induces fruitful ideas and results in other areas. L systems are based on relational and set-theoretic concepts, which are more suitable for the discrete and combinatorial structures of biology than mathematical models based on calculus or statistics. L systems have stimulated new work not only in the realistic simulation of developing organisms but also in the theory of automata and biology as well as professionals in computer graphics.
• RS96a - Handbook96
  G. Rozenberg and A. Salomaa, editors. Handbook of Formal Languages. Springer Verlag, Berlin, Heidelberg, New York, October 1996, ISBN Vol 1: 3-540-60420-0, Vol 2: 3-540-60648-3, Vol 3: 3-540-60649-1.
  Description
  Volume 1: Word, Language, Grammar
  This first volume of the Handbook of Formal Languages gives a comprehensive authoritative exposition on the core of language theory. Grammars, codes, power series, L systems, and combinatorics on words are all discussed in a thorough, yet self-contained manner. This is perhaps the most informative single volume in the history of theoretical computer science.
  Volume 2: Linear Modeling: Background and Application
  This second volume of the Handbook of Formal Languages contains the most fundamental applications of language theory. Various aspects of linguistics and parsing, both natural and programming languages, symbolic manipulation, and pattern matching are discussed. A special feature is the recently very active field of DNA computing.
  Volume 3: Beyond Words
  This third volume of the Handbook of Formal Languages discusses language theory beyond linear or string models: trees, graphs, grids, pictures, computer graphics. Many chapters offer an authoritative self-contained exposition of an entire area. Special emphasis is on interconnections with logic.
  Volume 2 contains [HPP96].
• RS96b - RozSal96
  G. Rozenberg and A. Salomaa. Watson-Crick complementarity, universal computations and genetic engineering. Technical Report TR96-28, Department of Computer Science, Leiden University, P.O. Box 9512, 2300 RA Leiden, The Netherlands, October 1996.
• RS97 - HFL
  G. Rozenberg and A. Salomaa. Handbook of Formal Languages, 3 volumes. Springer Verlag, Berlin, Heidelberg, New York, 1997.
  Present articles are: [HPP]
• RSHD - RSHD01
  J. A. Rose, A. Suyama, M. Hagia, and R. J. Deaton. PNA-mediated whiplash PCR. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• RT00a - RT00
  Mark A. Reed and James M. Tour. Computing with molecules. Scientific American, 2000, http://www.sciam.com/2000/0600issue/0600reed.html.
  Abstract: How fast and powerful can computers become? Will it be possible someday to create artificial "brains" that have intellectual capabilities comparable--or even superior--to those of human beings? The answers to these questions depend to a very great extent on a single factor: how small and dense we can make computer circuits.
• RT00b - DLT99
  G. Rozenberg and W. Thomas, editors. Developments in Language Theory, Foundations, Applications, and Perspectives. World Scientific Publishing Company, 2000.
• RTS02
  J. A. Rose, M. Takano, and A. Suyama. A PNA-mediated whiplash PCR-based program for in vitro protein evolution. In Hagiya and Ohuchi [PP8], pages 47--60.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• Rub96
  Harvey Rubin. Looking for the DNA killer app. Nature Structural Biology, 3(8):656--658, August 1996. Editorial.
  Abstract: The structural and functional properties of nucleic acids may form the basis for carrying out elementary and complex computational operations with biological molecules. A recent meeting on computing with DNA explored the potential of this approach.
• RVF+ - RVeo00
  H. Rauhe, G. Vopper, U. Feldkamp, W. Banzhaf, and J. C. Howard. Digital DNA molecules. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• RW95 - RoossWagner95
  Diana Rooss and Klaus W. Wagner. On the power of DNA-computers. Technical report, University of Wurzburg, 1995, ftp://haegar.informatik.uni-wuerzburg.de/pub/TRs/ro-wa95.ps.gz.
  Abstract: In [Adl94] Adleman used biological manipulations with DNA strings to solve some instances of the Directed Hamiltonian Path Problem. Lipton [Lipton94] showed how to extend this idea to solve any NP problem. We prove that exactly the problems in P^NP = [Captial delta]_{P^NP = [Captial delta]}^p can be solved in polynomial time using Lipton's model. Various modifications of Lipton's model are investigated, and it is proved that their computational power in polynomial time can be characterized by one of the complexity classes P, [Captial delta]_{[Captial delta]}^p, [Captial delta]_{[Captial delta]}^p or even PSPACE. Restricting Lipton's model to DNA strings of logarithmic length one can compute exactly the problems in L.
• RW97 - P3
  H. Rubin and D. H. Wood, editors. DNA Based Computers III, volume 48 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1997.
• RWB+96 - RoweisEA96
  S. Roweis, E. Winfree, R. Burgoyne, N. V. Chelyapov, M. F. Goodman, P. W. K. Rothemund, and L. M. Adleman. A sticker based model for DNA computation. In Landweber and Baum [2AWDBC], ftp://hope.caltech.edu/pub/roweis/DIMACS/stickers.ps.
  Abstract: We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is represented and of separation by hybridization as a central mechanism. However, unlike previous models, the stickers model has a random access memory that requires no strand extension, uses no enzymes, and (at least in theory) its materials are reusable. The paper describes computation under the stickers model and discusses possible means for physically implementing each operation. We go on to propose a specific machine architecture for implementing the stickers model as a microprocessor-controlled parallel robotic workstation. Finally, we discuss several methods for achieving acceptable overall error rates for a computation using basic operations that are error prone. In the course of this development a number of previous general concerns about molecular computation [SmithSchweitzer95][ Hartmanis95], [Letters to Science] are addressed. First, it is clear that general-purpose algorithms can be implemented by DNA-based computers, potentially solving a wide class of search problems. Second, we find that there are challenging problems, for which only modest volumes of DNA should suffice. Third, we demonstrate that the formation and breaking of covalent bonds is not intrinsic to DNA-base computation. This means that costly and short-lived materials such as enzymes are not necessary, nor are energetically costly processes such as PCR. Fourth, we show that a single essential biotechnology, sequence-specific separation, suffices for constructing a general-purpose molecular computer. Fifth, we illustrate that separation errors can theoretically be reduced to tolerable levels by invoking a trade-off between time, space, and error rates at the level of algorithm design; we also outline several specific ways in which this can be done and present numerical calculations of their performance. Despite these encouraging theoretical advances, we emphasize that substantial engineering challenges remain at almost all stages and that the ultimate success or failure of DNA computing will certainly depend on whether these challenges can be met in laboratory investigations.
• Ryu - Ryu00
  Will Ryu. DNA computing: A primer, http://www.arstechnica.com/reviews/2q00/dna/dna-1.html. Only on the net.
• SA99
  G. Sella and D. H. Ardell. Evolution as computation, chapter The impact of message mutation on the fitness of a genetic code, pages 140--159. In Landweber and Winfree [LW99], 1999.
• SAJS02 - AJS02
  P. Sa-Ardyen, N. Jonoska, and N C. Seeman. Self-assembling DNA graphs. In Hagiya and Ohuchi [PP8], pages 1--9.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• SAJS03a - SJS03
  P. Sa-Ardyen, N. Jonoska, and N. C. Seeman. The assembly of graphs whose edges are DNA helix axes. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 126, 2003.
• SAJS03b - SAeo03
  P. Sa-Ardyen, N. Jonoska, and N. C. Seeman. Self-assembling DNA graphs. Natural Computing, 2(4):427--438, 2003.
• Sak00
  Y. Sakakibara. Solving computational learning problems of boolean formulas on DNA computers. In Condon and Rozenberg [P6], pages 220--230.
  Abstract: We apply a DNA-based massively parallel exhaustive search to solving the computational learning problems of DNF (disjunctive normal form) Boolean formulas. Learning DNF formulas from examples is one of the most important open problems in computational learning theory and the problem of learning 3-term DNF formulas is known a s intractable unless RP \not= NP. We propose new methods to encode any k-term DNF formula to a DNA strand, evaluate the encoded DNF formula for a truth-value assignment by using hybridization and PCR, and find a consistent DNF formula with the given examples. By employing these methods, we show that the class of k-term DNF formulas (for any constant k) and the class of general DNF formulas are efficiently learnable on DNA computer.
• Sak01
  Y. Sakakibara. Population computation and majority inference in test tube. In Jonoska and Seeman [P7], pages 82--91.
  Abstract: We consider a probabilistic interpretation of the test tube which contains a large amount of DNA strands, and propose a population computation using a number of DNA strands in the test tube and and a probabilistic logical inference based on the probabilistic interpretation. Second, in order for the DNA-based learning algorithm [Sak00] to be robust for errors in the data, we implement the weighted majority algorithm [LW94] on DNA computers, called DNA-based majority algorithm via amplification (DNAMA), which take a strategy of "amplifying" the consistent (correct) DNA strands while the usual weighted majority algorithm decreases the weights of inconsistent ones. We show a theoretical analysis for the mistake bound of the DNA-based majority algorithm via amplification, and imply that the amplification to "double the volume" of the correct DNA strands in the test tube works well.
• Sak03
  Y. Sakakibara. DNA-based algorithms for learning boolean formulae. Natural Computing, 2(2):153--171, 2003.
• Sal97 - Salomaa97
  A. Salomaa. Turing, Watson-Crick and Lindenmayer. Aspects of DNA Complementarity. Technical Report 128, Turku Center for Computer Science, September 1997, http://www.tucs.abo.fi/publications/techreports/TR128.ps.gz.
  Abstract: Watson-Crick complementarity is one of the very central components of DNA computing, the other central component being the massive parallelism of DNA strands. While the latter component drastically reduces time complexity, the former component is the cause behind the Turing universality of models of DNA computing. This paper makes this cause explicit and also discusses it in terms of some specific models. Finally, another aspect of complementarity, the operational one, will be discussed in terms of Lindenmayer systems.
• Sal98a - Salomaa98
  A. Salomaa. Turing, Watson-Crick and Lindemayer: Aspects of DNA complementarity. In Calude et al. [UMC98], pages 94--107.
  Abstract: Watson-Crick complementarity is one of the very central components of DNA computing, the other central component being the massive parallelism of DNA strands. While the latter component drastically reduces time complexity, the former component is the cause behind the Turing universality of models of DNA computing. This paper makes this cause explicit and also discusses it in terms of some specific models. Finally, another aspect of complementarity, the operational one, will be discussed in terms of Lindenmayer systems.
  Contains [AWHOG98], [Reif98-2], [Salomaa98] [Alf98], [BPL98], [FreMi98], [Mateescu98], [OgiRay98], [Paun98-1].
• Sal98b - Sal98
  A. Salomaa. Turing, Watson-Crick and lindenmayer. aspects of DNA complementarity. Unconventional Models of Computation, pages 94--107, 1998.
• Sal01
  A. Salomaa. Words, Semigroups, and Transductions, chapter Iterated Morphisms with Complementarity on the DNA Alphabet, page fixme[pages]. World Scientific, Singapore, 2001.
• SBP85 - SBP91
  G. Stefan, V. Bistriceanu, and A. Paun. Toward a natural mode of the LISP implementation (in romanian). Comm. to the Second National Symposium on Artificial Intelligence, September 1985.
  Also in: Systems for Artificial Intelligence, Romanian Academy Pub. House, Bucharest, 1991
• SCA+03 - SCeo03
  M. R. Shortreed, S. B. Chang, M. Andronescu, D. Tulpan, H. Hoos, A. Condon, and L. M. Smith. An algorithm for designing structure-free concatenated DNA word set. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 69, 2003.
• SCC+88 - LiuEA98-2
  Lloyd M. Smith, Robert M. Corn, Anne E. Condon, Max G. Lagally, Anthony G. Frutos, Qinghua Liu, and Andrew J. Thiel. A surface-based approach to DNA computation. Journal of Computational Biology, 5(2):255--267, 1988. Reworked version of [LiuEA96].
  A scalable approach to DNA-based computations is described. Complex combinatorial mixtures of DNA molecules encoding all possible answers to a computational problem are synthesized and attached to the surface of a solid support. This set of molecules is queried in successive MARK (hybridization) and DESTROY (enzymatic digestion) operations. Determination of the sequence of the DNA molecules remaining on the surface after completion of these operations yields the answer to the computational problem. Experimental demonstrations of aspects of the strategy are presented.
• Sch - Sch00
  T. Schmidt. Single molecule detection. Invited talk at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• Sch94 - Schneider.nano2
  T. D. Schneider. Sequence logos, machine/channel capacity, Maxwell's demon, and molecular computers: a review of the theory of molecular machines. Nanotechnology, 5:1--18, 1994, ftp://ftp.ncifcrf.gov/pub/delila/nano2.ps.
• SCH+95 - StemmerEA95
  Willem P.C. Stemmer, Andreas Crameri, Kim D. Ha, T. M. Brennan, and Herbert L. Heyneker. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene, 164(1):49--53, 1995.
• Sch99
  U. Schoning. A probabilistic algorithm for k-SAT and constraint satisfaction problems. Proceedings of 40th symposium on foundations of computer science, pages 410--414, 1999. IEEE computer society press, Los Alamos, CA.
• SD04 - SDvT
  R. Siromoney and B. Das. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Plasmids to Solve \#3SAT, pages 361--366. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• Sea92a - Sear92
  David B. Searls. The linguistic of DNA. American Scientist, 80:579--591, 1992.
• Sea92b - searls92
  David B. Searls. The linguistics of DNA. American Scientist, 80:579--591, 1992.
• See96 - Seeman96
  Nadrian C. Seeman. The design and engineering of nucleic-acid nanoscale assemblies. Current Opinion in Structural Biology, 6(4):519--526, 1996.
  Abstract: It is possible to design DNA molecules that can form unusual structures and topologies. Stable DNA-branched junctions have been used to construct polyhedral catenated molecules with the connectivities of a cube and of a truncated octahedron. The truncated octahedron has been constructed following a solid-support-based methodology. Branched-DNA molecules are flexible, suggesting that triangular and deltahedral DNA objects should be favored as the components of two- and three-dimensional nucleic acid arrays. DNA polyhedra are complex catenanes. The engineering of single-stranded DNA knots and catenanes exploits the fact that a node can be equated with a half-turn of DNA.
• See02
  N. C. Seeman. It started with Watson and Crick, but it sure didn't end there: Pitfalls and possibilities beyond the classic double helix. Natural Computing, 1(1):53--84, 2002.
• SF97
  Y. Sakakibara and C. Ferretti. Splicing on tree-like structures. In Rubin and Wood [P3], pages 348--358.
  Abstract: In this paper, we provide a method to accelerate the power of splicing systems. We introduce the splicing systems on trees to be built as partially annealed single strands, that is a quite similar notion and a natural extension of splicing systems on strings. Trees are a common and useful data structure in computer science and have a biological counterpart such as molecular sequences with secondary structures, which are typical structures in RNA sequences. Splicing on trees involves (1) complete subtrees as axioms, (2) restriction operated on the annealed subsequences, (3) rules to substitute a complete subtree with another. We show that splicing systems on trees with finite sets of axioms and finite sets of rules can generate the class of context-free languages without the need of multiplicity constraints.
• SGK+00 - SGeo00
  K. Sakamoto, H. Gounzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, and M. Hagiya. Molecular computation by DNA hairpin formation. Science, 288:1223--1226, May 19, 2000.
• SH00
  M. Sturm and T. Hinze. Distributed splicing of RE with 6 test tubes. In Calude et al. [WMP2000], pages 236--248.
  Abstract: This paper introduces a functional approach to distributed splicing systems for generation of recursive enumerable languages with 6 test tubes. The specification of this systems serves both, the formal mathematical and the lab-experimental aspect. The implementation of the splicing system using a functional description of laboratory operations supports particularly the last-mentioned aspect. Advantages of this approach consist in large experimental practicability as well in the independence of certain Chomsky type-0 grammar parameters.
• SH03 - SH03-1
  Y. Sakakibara and T. Hohsaka. In vitro translation-based computations. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 175--179, 2003.
• Sha99 - Shap99
  J. A. Shapiro. Evolution as computation, chapter Genome system architecture and natural genetic engeneering, pages 1--14. In Landweber and Winfree [LW99], 1999.
• SHRS03 - SH03-2
  K. A. Schmidt, C. V. Henkel, G. Rozenberg, and H. P. Spaink. Experimental single-molecule DNA computing. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 191, 2003.
• SI - SI02
  Y. Sakakibara and H. Imai. A DNA-based computational model using a specific type of restriction enzymes. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• Sir00
  Rani Siromoney. Distributed circular systems. In International Workshop Grammar Systems 2000 (R. Freund, A. Kelemenova), Bad Ischl, Austria, July 2000, pages 41--54, 2000.
  Abstract: The main aim of the talk is to consider some of the splicing systems for circular strings introduced so far, and examine which of the distributed architecture (sequential/parallel) are feasible and give interesting or new results. It is intended to motivate into this not so well-trodded path of work on circular splicing and contains preliminary results.
• SKK+99a - SKeo99
  K. Sakamoto, D. Kiga, K. Komiya, H. Gouzu, S. Yokoyama, S. Ikeda, H. Sugiyama, and M. Hagiya. State transitions by molecules. BioSystems, 52:81--91, 1999.
• SKK+99b - SakaEA98
  K. Sakamoto, D. Kiga, K. Komiya, H. Gouzu, S. Yokoyama, S. Ikeda, H. Sugiyama, and M. Hagiya. State transitions by molecules. In Kari et al. [P4], pages 81--91.
  Abstract: In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3'-end sequence encodes the current state of the machine. Successive state transitions are performed in such a way that the current state is annealed onto an appropriate portion of DNA encoding the translation table of the state machine and the next state is copied to the 3'-end by extension with polymerase. In this paper, we first show that combined with parallel overlap assembly, a single series of successive transitions can solve NP-complete problems. This means that the number of necessary laboratory steps is independent from the problem size. We then report the results of two experiments concerning the implementation of our method. One is on isothermal reactions which greatly increase the efficiency of state transitions compared with reactions controlled by thermal cycles. The other is on the use of unnatural bases for avoiding out-of-frame annealing. The latter result can be applied to many DNA-based computing paradigms.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• SKZ+03 - SKeo03
  Y. Y. Shi, DeX. Kong, GuoB. Zhou, ZhenDe Huang, and L. He. How to make an authomatic DNA computer practicable: a new mathematical model based on the oscillatory and dissipative mechanism. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 57, 2003.
• SLPW03 - SLeo03-1
  R. Schulman, S. Lee, N. Papadakis, and E. Winfree. One dimensional boundaries for DNA tile self-assembly. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 111--124, 2003.
• SLPZ - SLeo03-2
  S.-Y. Shin, E. J. Lee, T. H. Park, and B.-T. Zhang. DNA computing compkexity analysis using DNA/DNA hybridization kinetics. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• SM97 - Stefan97
  G. Stefan and M. Malita. The splicing mechanism and the connex memory. In IEEE International Conference on Evolutionary Computation, pages 225--229, 1997.
• Smi95a - Smith1
  W. D. Smith. DNA computers in vitro and vivo. In R. J. Lipton [DBC], pages 121--186.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• Smi95b - Smith
  Warren D. Smith. An opinionated, but reasonably short, summary of the Mini DIMACS workshop on DNA based computers, April 5 1995, http://www.neci.nj.nec.com/homepages/wds/workshop.summary.ps.
• SS - SS03
  X. Su and L. M. Smith. Circuit SAT. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• SS95 - SmithSchweitzer95
  Warren D. Smith and Allan Schweitzer. DNA computers in vitro and vivo. Technical report, NEC Research Institute, March 20, 1995. Manuscript of 3/20/95, presented at DIMACS Workshop on DNA Based Computing, Princeton, 4/4/95.
  Abstract: We show how DNA molecules and standard lab techniques may be used to create a nondeterministic Turing machine. This is the first scheme that shows how to make a universal computer with DNA. We claim that both our scheme and previous ones will work, but they probably cannot be scales up to be of practical computational importance. In vivo, many limitations on our and previous computers are much less severe or do not apply. Hence, lifeforms ought, at least in principle, to be capable of large Turing universal computations. The second part of our paper is a loose collection of biological phenomena that look computation and mathematical models of computation that look biological. We observe that cells face some daunting computational problems, e.g., gene regulation, assembly of complex structures and antibody synthesis. We then make simplified mathematical models of certain biochemical processes and investigate the computational power of these models. The view of ``biology as a computer programming problem'' that we espouse, can be useful for biologists. Thus our particular Turing machine construction bears a remarkable resemblance to (and probably explains) recently discovered ``RNA editing'' processes. In fact it may be that the RNA editing machine in T. Brucei is clonable, extractable and runnable in vitro, in which case one would have a better performing Turing machine than with our construction. The fact that RNA editing is a Turing machine may in turn have a lot to do with the origins of life. We also have a possible explanation for ``junk DNA''.
• SSD92 - SSR92
  Rani Siromoney, K.G. Subramanian, and V. Rajkumar Dare. Circular DNA and splicing systems. In A. Nakamura, M. Nivat, A. Saoudi, P.S.P. Wang, and K. Inoue, editors, Proceedings of Parallel Image Analysis, 2nd International Conference ICPIA '92, Ube, Japan, 21-23 Dec 1992., number 654 in Lecture Notes in Computer Science, pages 260--273, Ube, Japan, 1992. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-56346-6.
  Abstract: Circular strings representing DNA molecules and certain recombinant behaviour are formalized. Various actions of splicing schemes on linear and circular DNA molecules are examined. It is shown that there is a difference in the regularity result of [CulikHarju91] between the linear and circular strings. A consequence of this result is that a conjecture of Head [Splicing schemes and DNA, manuscript] that the circular string language of a splicing system under an action on circular strings is regular, when the set of initial circular strings is regular, is disproved.
• ST94 - KY94
  S.Kobayashi and T.Yokomori. Modeling RNA secondary structures using tree grammars. In Proc. of 5th Genome Informatics Workshop, pages 29--38, 1994, http://ylab-gw.cs.uec.ac.jp/Papers/satoshi/giw94.ps.gz.
  Abstract: This paper proposes a grammatical tool, called tree adjunct grammar with tag for RNA ( denoted by TAG 2 RNA ), for representing secondary structures of RNAs, and shows some example TAG 2 RNA grammars for fairly complicated RNA secondary structures. We then demonstrate the appropriateness of the grammars for modeling RNA secondary structures by discussing its formal language and/or graph theoretic properties, including closure properties of TAG 2 RNA and graph planarity of secondary structures generated by TAG 2 RNA , the latter of which would provide a biologically reasonable constraint.
• ST00a - ST00
  Y. Suzuki and H. Tanaka. Artificial life and P systems. In Calude et al. [WMP2000], pages 265--285.
  Abstract: Artificial chemical system is well studied in Artificial life and complexity. Here we introduce a new artificial chemical system: abstract rewriting system on multiset (ARMS). The system belongs to P systems and is able to show complex phenomena such as non-linear oscillations. We introduce a membrane that is composed of "chemical compounds (denoted by symbols)", and the compounds are generated through chemical reactions in the cell. Furthermore, we apply a genetic method to the system and find some interesting result.
• ST00b - ST00-2
  Y. Suzuki and H. Tanaka. Chemical evolution among artificial proto-cells. Artificial Life, 7:54--63, 2000.
• ST00c - ST00-3
  Y. Suzuki and H. Tanaka. A new molecular computing model, artificial cell systems. GECCO2000, pages 833--840, 2000.
• ST00d - SuTa99
  Y. Suzuki and H. Tanaka. On a LISP implementation of a class of P systems. Romanian J. of Information Science and Technology, 2(3):173--186, 2000.
• ST00e - ST00-1
  Y. Suzuky and H. Tanaka. Computational living systems based on an abstract chemical system. CEC2000, pages 1369--1376, 2000.
• Ste - Stevens99
  Joel Stevens. DNA model of computation of a sub-set sum, http://www.lcc.net/~dmjs/Dna.htm. -.
  Abstract: The purpose of this experiment was to use DNA computation to solve the nondeterministic polynomial bounded complete problem (NP-Complete) of Sub-Set Sum. The Sub-Set Sum problem contains several variables. It has a container size C and a set of n objects. The object is to add the n objects together to reach as closely as possible to C, but not exceeding. The sample problem used in this experiment was a container size of thirty and a set of six objects (5, 10, 12, 13, 15, 18). The objects were encoded into synthetic DNA samples with restriction enzymes specially encoded to each object. The strands were added together using linkers (Watson-Crick complements of six base pairs of one strand and six base pairs of the other strand). These strands were amplified together in a PCR reaction, run on a gel, gel purified, phenol-chloroform extracted, and cut with restriction enzymes. By progressively cutting the strands with the assigned restriction enzymes, the objects within the containers can be found. For example, if a container was cut with EcoRI, the assigned RE for object 12, two bands should remain, those without any objects of 12, and those with objects of 12. The objects that had 12 would have a remaining band length of the object 18, giving a solution to the Sub-Set Sum problem. This experiment produced negative results, but with a few modifications, the model will become feasible.
• Ste94a - Stemmer94a
  Willem P.C. Stemmer. DNA shuffling by random fragmentation and reassembly: In-vitro recombination for molecular evolution. Proceedings of the National Academy of Science, U.S.A., 91:389--391, 1994.
• Ste94b - Stemmer94b
  Willem P.C. Stemmer. Rapid evolution of a protein by DNA shuffling. Nature, 370:389--391, 1994.
• Ste95a - Stemmer95
  Willem P.C. Stemmer. The evolution of molecular computation. Science, 270:1510--1510, December 1, 1995.
  Molecular computation in the style of [Adl94] and [Lipton95A] requires too much DNA even for rather small problem instances. Nature has sought through such a large search space using a much smaller pool of sequences, by evolution: repeated cycles of selection from small pools. The author suggests to use similar methods in attacking problems using molecular computation: approximate solutions by treating a problem with a dynamic programming approach.
• Ste95b - Stemmer95b
  Willem P.C. Stemmer. Searching sequence space. Bio/Technology, 13:549--553, 1995.
• Ste96 - Stemmer_sexual_PCR
  Willem P.C. Stemmer. Sexual PCR and assembly PCR. In Robert M. Meyers, editor, The Encyclopedia of Molecular Biology and Molecular Medicine, volume 5, pages 447--457. 1996, VCH, New York, year.
• Ste98 - Stefan98
  G. Stefan. Silicon or molecules? What's the best for splicing? In Paun [CBMtitle], pages 158--181.
  Abstract: We present the main ideas concerning the implementation in the solid state circuits of some molecular mechanism: the splicing operation and the insert/delete operation. The physical support for these operations is based on the Connex Memory concept first introduced in [SBP91]. We promote this solution because a pure biological process is very hard to be interfaced with machines in nowadays technologies. At the same time we believe that the mechanism emphasized in the molecular process of computation are very good suggestion for silicon based machines devoted to perform a fine grain parallelism. Using a Connex Memory the splicing operation or the insert/delete operation is performed in linear time related to the length of the rules; the time does not depend on the length of the processed strings. In order to perform in parallel all possible applications of a rule in a set of strings, the function of the Connex Memory is extended over a cellular automaton, thus defining the EcoChip.
  The book contains [Mar98], [Manca98], [Ciob98], [Head97-5], [JKS98], [OR98], [DAG98], [DG98], [Biswas98], [Stefan98], [Fre98], [MPRS98], [FMF98], [PaPa98], [HvV], [Head97-3], [DM98], [KK98], [Mat98], [Li98], [Cet98].
• Ste00 - Stefan00
  G. Stefan. Membrane computing with cellular automata on a dedicated hardware. In Calude et al. [WMP2000].
  The pre proceedings contain [Ata00], [BCM00], [CV00], [F00], [K00], [Kr00], [M00], [GP00-1], [R00], [SH00], [ST00], [ZFM00-1], [BCAG00], [KMP00], [Fr00-1], [Manca00-2], [Stefan00], [BCMeo01].
• STT00a - STT00-1
  Y. Suzuki, J. Takabayashi, and H. Tanaka. Adaptive behavior in a tritrophic interactions consisting of plants, herbivores and carnivores. From animals to animat2000, 2000.
• STT00b - STT00
  Y. Suzuki, J. Takabayashi, and H. Tanaka. Investigation of an ecological system by using an abstract rewriting system on multisets. Recent topics in mathematical and computational linguistic, pages 300--309, 2000. Academy Publishing House, Bucharest.
• Sul00 - Sulliv00
  Peggy Sullivan. Cut, paste and filter. manuscript, 2000.
• SWL+96 - SeemanEA96
  N. C. Seeman, H. W., B. L., J. Qi, X. Li, X. Yang, F. Liu, W. Sun, Z. Shen, R. Sha, C. Mao, Y. Wang, S. Zhang, T.-J. Fu, S. Du, J. E. Mueller, Y. Zhang, and J. Chen. The perils of polynucleotides: The experimental gap between the design and assembly of unusual DNA structures. In Landweber and Baum [2AWDBC].
  Abstract: DNA computing relies on the successful implementation of physical chemistry techniques involving oligonucleotides of prescribed sequence. Our laboratory has been involved in genetic recombination and nanofabrication. We have constructed a large number of unusual DNA molecules, including branched DNA molecules, DNA polyhedra, DNA knots, DNA double crossover molecules, and DNA anti junctions and mesojunctions. Our experience with these systems has uncovered a large number of experimental pitfalls that may confront individuals working with DNA computing. We present our experience in this area with the hope that we can help investigators to anticipate the experimental problems that may affect their DNA computing schemes.
  
  • DNA computing will have to use physical chemistry in order to get substantial --- detectable --- yields of desired results. The molecular biological techniques (e.g.\ PCR) are not sufficient since they only work well when sequence properties of the desired solution are known; this is generally not the case.
  • The main problem in building unusual DNA structures is one of control. In general, multiple outcomes are (nearly) equivalent from the standpoint of free energy. The undesired alternatives must be made sufficiently unfavourable in relation to the target. Since --- under certain reaction circumstances --- Watson-Crick bonds are highly favoured, one can try to choose the base sequence in such a way that Watson-Crick pairing favours the intended design.
  • Reaction circumstances are very important.
  • The 3D structure of molecules is important (e.g. the twist in the double helix), as is the flexibility of the structure.
  • Some ligases used to ligate sticky ends are ``hungry'' and will settle for an end that is close to its optimal one.
• SY01
  F. C. Simmel and B. Yurke. Operation of a purified DNA nanoactuator. In Jonoska and Seeman [P7], pages 248--257.
  Abstract: During the self-assembly and operation of DNA-based nanochemical devices like the previously reported molecular tweezers or actuators, unwanted dimerization can occur. Here we show that in the case of the DNA nanoactuator dimerization predominantly occurs at the assembly stage. Correctly formed molecular devices can be purified and subsequently operated without interference by dimers.
  The volume contains [SY01], [HHS01], [WBKeo01], [EHPR01], [APa01-1], [MMP01-1], [UHK01], [GO01], [Sak01], [HKK01], [MR01], [MGC01], [PC01], [JS01], [HSc01], [MGLeo01], [FSR01], [BKS01], [WY01], [MY01], [HCNeo01], [MYS01], [RLBeo01], [YHM01], [RFL01]
• SZC94 - Seeman94
  Nadrian C. Seeman, Yuwen Zhang, and Junghuei Chen. DNA nanoconstructions. Journal of Vacuum Science \& Technology A: Vacuum Surfaces and Films, 12(4):1895--1903, 1994.
  Abstract: The control of structure on the nanometer scale is central to nanotechnology. We are pursuing this end with synthetic DNA, whose sequence is selected by sequence symmetry minimization algorithms, so that it can form branched junctions. These structures can be ligated together in the same way that linear DNA is ligated in molecular cloning. Ligating branched structures generates stick figures whose edges consist of double helical DNA and whose vertices are branch points. We have built a DNA molecule whose helix axes have the connectivity of a cube. The vertices are separated by two helical turns of DNA; hence the plectonemic nature of DNA makes this molecule a hexacatenane, each of whose cyclic strands corresponds to a face. We have developed a solid-support-based procedure to implement these constructions. Using the solid-support-based methodology we have constructed a molecule whose helix axes have the connectivity of a truncated octahedron. This figure contains 14 faces, of which six are ideally square and eight are hexagonal; this Archimedean polyhedron contains 24 vertices and 36 edges. Control of topology is strong in this system, but control of three-dimensional (3D) structure remains elusive. Our key aim is the formation of prespecified two-dimensional and 3D periodic structures. Applications envisioned include nanomanipulators and scaffolding for molecular electronic devices.
• Szo92 - Szostak92
  Jack W. Szostak. In vitro genetics. Trends in Biochemical Sciences, 172(3):89--93, 1992.
• TB90 - Bach90
  H. J. Thiesen and C. Bach. Target detection assay (TDA) - A versatile procedure to determine DNA-binding sites as demonstrated on SP1 protein. Nucleic Acids Research, 18(11):3203--3209, 1990.
• Tem - Temkin02
  A. Ya. Temkin. On laser light damage to biomolecular computing, http://www.eng.tau.ac.il/~temkin/LasBioComp.ps.zip. In [Temkin02].
  Abstract: The damage of laser radiation to biomolecular computers and computing is considered. The consideration is focused on the case when this radiation is not able to destroy biocomputer hardware. In this case the damage is produced by the formal language alphabet alteration as result of molecular quantum level's excitations by the laser light. These excitations break the identity of chemically identical groups creating extra letters of the alphabet. As a result the information written by the original alphabet is distorted or even completely destroyed. Formulas are deduced for the estimation of the upper limit of the permissible light intensity when the computing still remains reliable and correct.
• Tem00 - Temkin00
  Alexander Ya. Temkin. Neuron, biomolecular computing, genetics, thinking, http://www.eng.tau.ac.il/~temkin/Neuron&Biocomp.html. In [temk03], 2000.
• Tem02 - Temkin
  A. Ya. Temkin. Whether homo sapiens thinking is carried out by biomolecular information processors in the brain? Frontier Perspectives, 11(1):36--38, 2002, http://www.eng.tau.ac.il/~temkin.
  Abstract: Leonard M. Adleman [Adl94] found out that computers can be built of DNA and other biomolecules instead electronic devices. Taking this fact into account, one can suppose that network(s) of an enormous number of biomolecules in the brain is able to process the information and that this is precisely the equipment that carry out the human thinking. If yes, in this case the information processing is not limited with the execution of sequences of logical operations, but creates also illogical thoughts and operates with them, possesses such qualities of human intellectual activity as creative thinking, emotions, intuition, consciousness etc.. It could be achieved, if the information processing by the brain be performed with the participation of such virtual complex combinations of chemical groups that, from the mathematical point of view, form chains of relations defined on subsets of the set of all chemical groups forming all biomolecules of the brain or its certain part.
• Tem03 - temk03
  A. Y. Temkin. Papers in different fields, May 2003, http://eng.tau.ac.il/~temkin/SB1.zip http://eng.tau.ac.il/~temkin/SB2.zip. [Temkin02] and [Temkin00] are in this book.
• TG90 - TuerkGold90
  C. Tuerk and L. Gold. Systematic evolution of ligands by exponential enrichment - RNA ligands to bacteriophage-T4 DNA-polymerase. Science, 249(4968):505--510, August 3 1990.
• TH03 - TH03-1
  D. C. Tulpan and H. H. Hoos. Hybrid randomised neighbourhoods improve stochastic local search for DNA code design. In Canadian AI Conference, 2003, http://www.cs.ubc.ca/spider/hoos/Publ/TulHoo03.pdf.
• THC - THC02
  D. C. Tulpan, H. Hoos, and A. Condon. Stochastic local searching algorithms for DNA word design. Poster paper at 8th International Workshop on DNA-Based Computers, DNA 2002, Sapporo, Japan, 10-13 June 2002.
• TKYO03 - TKeo03
  F. Tanaka, A. Kameda, M. Yamamoto, and A. Ohuchi. Nearest-neighbor thermodynamics od DNA sequences with single bulge loop. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 150--152,160--166, 2003.
• TNY+ - TNYeo01
  F. Tanaka, M. Nakatsugawa, M. Yamamoto, T. Shiba, and A. Ohuchi. Developing support system for sequence design in DNA computing. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• TRB99
  C.T. Taylor, V. Risca, and C. Bancroft. Hiding messages in DNA microdots. Nature, 399:533--534, 1999, http://www.nature.com/server-java/Propub/nature/399533A0.frameset?context=search.
• TS92 - TakSir92
  Yuji Takada and Rani Siromoney. On identifying DNA splicing systems from examples. In K.P. Jantke, editor, Proceedings of the International Workshop on Analogical and Inductive Inference (AII'92), 5-9 Oct 1992., number 642 in Lecture Notes in Artificial Intelligence, pages 305--319, Dagstuhl Castle, Germany, October 1992. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-56004-1.
  Abstract: DNA sequences are recombined with restriction enzymes and ligases. Splicing systems, generative devices introduced by [Head87], represent this DNA recombinant behaviors as operations on pairs of strings over a finite alphabet. [CulikHarju91] proved that a language generated by a splicing system is regular. We give a method to construct a splicing system from a deterministic finite state automaton. By combining a conventional inductive inference/learning method for deterministic finite state automata with our method, we have an effective inductive inference/learning method for splicing systems.
• TS95 - YK95
  T.Yokomori and S.Kobayashi. DNA evolutionary linguistics and RNA structure modeling : A computational approach. In Proc.of 1st International IEEE Symposium on Intelligence in Neural and Biological Systems, pages 38--45, 1995, http://ylab-gw.cs.uec.ac.jp/Papers/yokomori/dnarna.ps.gz.
  Abstract: In this paper, we are concerned with analysing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including ``pseudoknots'', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.
• TSD+ - TSeo00
  D. G. Thimas, K. G. Subramanian, V. R. Dare, T. Robinson, and B. Le Saec. Learning algorithms for subclasses of circular DNA molecules. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• TT99
  P. K. Theodosopoulus and T. V. Theodosopoulus. Evolution as computation, chapter Evolution at the edge of chaos: a paradigm for the maturation of the humoral immune response, pages 41--66. In Landweber and Winfree [LW99], 1999.
• TTBN - TTB00
  A. Tamulis, J. Tamuliene, M. L. Balevicius, and J-M. Nunzi. Quantum chemical design of light inducer logically controlled multivariable anisotropic random-walk molecular deviced. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• TY02
  A. Takahara and T. Yokomori. On the computational powers of insertion-deletion systems. In Hagiya and Ohuchi [PP8], pages 269--280.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• TY03
  A. Takahara and T. Yokomori. On the computational power of insertion-deletion systems. Natural Computing, 2(4):321--336, 2003.
• TYAPM99 - TYM99
  A. J. Turberfield, B. Yurke, and Jr. A. P. Mills. DNA hybridization catalysts and molecular tweezers. In Winfree and Gifford [P5], pages 171--182.
  Abstract: We demonstrate new methods for the control of DNA hybridization: formation of a loop with a protective strand is used to inhibit hybridization, and a DNA catalyst that opens the loop is used to catalyze hybridization. A combination of inhibition and catalysis will allow control of the bonds formed between elements of a self-assembled structure. We also demonstrate a new class of nanomachine, made of DNA and using the hybridization of DNA as a source of chemical energy to produce repeated movement.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• UH03a - UH03-2
  H. Uejima and M. Hagiya. Analyzing secondary structure transition paths of DNA/RNA molecules. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 92--96, 2003.
• UH03b - UH03-1
  H. Uejima and M. Hagiya. Secondary structure design of multi-state DNA machines based on sequential structure transition. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 80--91, 2003.
• UHK01
  H. Uejima, M. Hagiya, and S. Kobayashi. Horn clause computation by self assembly of DNA molecules. In Jonoska and Seeman [P7], pages 308--320.
  Abstract: Kobayashi proposed Horn clause computation by DNA molecules, which is more suitable for expressing complex algorithms than other models for DNA computing. This paper describes a new implementation of Horn clause computation by DNA. It employs branching DNA molecules for representing Horn clauses. As derivations are realized by self-assembly of such molecules, the implementation requires only a constant number of laboratory operations. Furthermore, it deals with first order Horn clauses with some restrictions. In order to realize first order logic, we implement variable substitution by string tiling proposed by Winfree, et al. As we show the computational power of a Horn clause program in our model, we give another proof that a polynomial number of operations using self-assembly of DNA molecules can compute any problem in NP.
• UHKY95
  Y. Uemura, A. Hasegawa, S. Kobayashi, and T. Yokomori. Grammatically modeling and predicting RNA secondary structures. In Proceedings Genome Informatics Workshop, pages 67--76, 1995, http://ylab-gw.cs.uec.ac.jp/Papers/uemura-y/giw95-final.ps.gz. Extended abstract?
  Abstract: Tree Adjunct Grammar for RNA (T AG 2 RNA ) is a new grammatical device to model RNA secondary structures including pseudoknots. An efficient parsing algorithm for this grammar is developed, and applied to some computational problems concerning RNA secondary structures. With this parser, we first try to predict secondary structures of RNA sequences which are known to form pseudoknots structures, and show prediction results which nicely match the known structures. Further, a (--1) frame shift grammar is constructed based on a biological observation that a (--1) frame shift might be caused from some structural features of RNA sequences. The proposed grammar is used to find candidate sequences for (--1) frame shift in Human spumaretrovirus gag and pol genes.
• Uni99 - WIA99
  University of Potsdam. Pre-Proc. of Workshop on implementing automata WIA99, Preprint 5/1999 of University of Potsdam, 1999.
• Uni01 - CT01-1
  University of Tarragona (Spain). Coordination of Gene Expression by Pipes and Signals, 2001.
  Proceedings of the Workshop on Membrane Computing, Report 17/01
• UT - UT03
  O. Unold and M. Troc. Simulator of molecular finite state machines. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• V.99 - Manca99
  Manca V. Logical Splicing in Natural languages, volume 47, pages 131--143. ISSN 0165-7712. Martín-Vide C., 1999. Issues in Mathematical Linguistics.
  Also in Studies in Functional and Structural Linguistics, Vol. 47, John Benjamins Publishing Co., Amsterdam, 1999
• V.00 - Manca00
  Manca V. Splicing Normalization and Regularity, volume 15, pages 199--215. Calude C., Paun C., 2000. Finite Versus Infinite. Contribution to an Eternal Dilemma.
  Series in Discrete Mathematics and Theoretical Computer Science
• VCG99 - MMP99
  Manca V., Martín-Vide C., and Paun G. New computing paradigms suggested by DNA computing: Computing by carving. BioSystems, 52(1-3):47--54, 1999.
• VD99 - MaMa99
  Manca V. and Martino M. D. From String Rewriting to Logical Metabolic Systems, volume 8, pages 297--315. Gordon and Breach Science Publishers, London, 1999, ISBN 90-5699-177-9. in Grammatical Models of Multiagent Systems.
  Paun G., Salomaa A. editors, Series in Topics in Computer Mathematics
• Ver - Verlan00
  S. Verlan. On extended time-varying distributed H systems. Poster at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• Ver04 - VvT
  S. Verlan. Aspects of Molecular Computing: Essays Dedicated to Tom Head, on the Occasion of His 70th Birthday, chapter Communicating Distributed H Systems with Alternating Filters, pages 367--384. Volume 2950 of Jonoska et al. [volTH], 2004. It contains [AvT], [ACDvT], [BGHvT], [CSvT], [CVSvT], [VSvT], [CKSvT], [FMvT], [FFOvT], [GBHvT], [GBRvT], [GPvT], [HPRvT], [ISvT], [JLSvT], [JMvT], [KVPvT], [KYSvT], [KvT], [LPRvT], [LMSvT], [MvT], [SMvT], [PvT], [PRCvT], [BKvT], [SDvT], [VvT], [AVPvT].
• VGC99 - MPM99
  Manca V., Paun G., and Martín-Vide C. Iterated GSM Mappings: A Collapsing Hierarchy, pages 182--193. Springer Verlag, Berlin, Heidelberg, New York, Salomaa A., Maurer H., Paun G. editors 1999, ISBN 3540658946. Jewels Are Forever.
  Series in Discrete Mathematics and Theoretical Computer Science
• vNGM01 - MGC01
  D. van Noort, Frank-Ulrich Gast, and J. S. McCaskill. DNA computing in microreactors. In Jonoska and Seeman [P7], pages 33--45.
  Abstract: The goal of this research is to improve the programmability of DNA based computers. Novel clockable microreactors can be connected in various ways to solve combinatorial optimization problems, such as Maximum Clique or 3-SAT. This work demonstrates by construction how one micro-reactor design can be programmed optically to solve any instance of Maximum Clique up to its given maximum size (N). It reports on an implementation of the concept proposed previously [MCC01]. The advantage of this design is that it is generically programmable. This contrast with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. Presently, in ongoing research, we are solving a graph for the Maximum Clique problem with N=6 nodes and have completed the design of a micro-reactor for N=20. Furthermore, the design of the DNA solution space will be presented, with solution encoded in customized word-structured sequences.
• vNL03 - NL03
  D. van Noort and L. F. Landweber. Towards a re-programmable DNA computer. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 167--174, 2003.
• vV04 - vVliet04
  R. van Vliet. Combinatorial aspects of minimal dna expressions (ext.). Technical Report 2004-03, Leiden Institute of Advanced Computer Science, Leiden University, 2004, http://www.liacs.nl/home/rvvliet/mindnaexpr.html.
• VZ03
  S. Verlan and R. Zizza. 1-splicing vs. 2-splicing: separating results. In WORDS 2003, Turku, Finland, 1-14 September 2003, 2003. Pre-proceedings TUCS Report, University of Turku.
  Abstract: Splicing systems, or H systems, were proposed as a generative device of languages: starting from a set of words, by repeated application of the splicing operation, new words may be generated. When we consider Paun's definition, two types of H systems may be defined, according to the fact that one word or two words are produced as a result of the splicing operation, called 1-splicing and 2-splicing operation, respectively. In this paper we present non trivial classes of regular languages which are generated by using the 1-splicing operation (over a finite H system) but which cannot be generated by using the 2-splicing operation. Thus, we show that 1-splicing operation is more powerful than the 2-splicing operation.
• WBH+03 - Weo03
  R. Weiss, S. Basu, S. Hooshangi, A. Kalmbach, D. Karig, R. Mehreja, and I. Netravali. Genetic circuit building blocks for cellular computation, communications, and signal processing. Natural Computing, 2(1):43--84, 2003.
• WBK+01 - WBKeo01
  D. H. Wood, H. Bi, S. O. Kimbrough, D. Wu, and J. Chen. DNA starts to learn poker. In Jonoska and Seeman [P7], pages 92---103.
  Abstract: DNA is used to implement a simplified version of poker. Strategies are evolved that mix bluffing with telling the truth. The essential features are (1) to wait your turn, (2) to default to the most conservative course, (3) to probabilistically override the default in some cases, and (4) to learn from payoffs. Two players each use an independent population of strategies that adapt and learn from their experiences in competition.
• WBMW99
  Potr Wasiewicz, P. Borsuk, Jan J. Mulawka, and Piotr Weglenski. Implementation of data flow logical operations via self-assembly of DNA. Lecture Notes in Computer Science, 1586:174--182, 1999.
  Abstract: Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This technique employs standard operations of genetic engineering including radioactive labeling. To check practical utility of the method a series of genetic engineering experiments have been performed. The obtained results confirm interesting properties of the DNA -based molecular data flow logic gates. This technique may be utilized in massively parallel computers.
• WBSL03 - WBeo03
  S. D. Wetting, G. A. Bare, R. J. S. Skinner, and J. S. Lee. Chemical switching and molecular logic in fluorescent-labelled M-DNA. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, pages 29--41, 2003.
• WCA+99 - WCAeo99
  David Herlan Wood, Junghuei Chen, Eugene Antipov, Bertrand Lemieux, and Walter Cedeno. In vitro selection for onemax DNA evolutionary computation. In Winfree and Gifford [P5], pages 23--37.
  Abstract: Aspects of Evolutionary Computation, DNA computing, and in vitro evolution are combined in proposed laboratory procedures. Preliminary experimental results are shown. The traditional test problem for Evolutionary Computation known as the OneMax problem is addressed. The preliminary experimental results indicate successful laboratory "separation by fitness" of DNA encoded candidate solutions.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• WCA+01 - WCeo01
  D. H. Wood, J. Chen, E. Antipov, B. Lemieux, and W. Cedeño. A design for DNA computation of the OneMax problem, volume 5(1), pages 19--24. Springer Verlag, Berlin, Heidelberg, New York, 2001, http://link.springer.de/link/service/journals/00500/tocs/t1005001.htm.
• WCCN+02 - WCNeo02
  K. Wickiser, S. Chalamish-Chohen, S. Narashimhan, B. Sawichi, D. C. Ward, and R. R. Breaker. Oligonucleotide sensitive hammerhead ribosomes as logic gates. In Preproceedings DNA Computing : 8th International Workshop on DNA-Based Computers, DNA8 Sapporo, Japan, June 10-13, 2002. page 19.
• WER00
  E. Winfree, T. Eng, and G. Rozenberg. String tile models for DNA computing by self-assembly. In Condon and Rozenberg [P6], pages 63--88.
  Abstract: This paper investigates computation by linear assemblies of complex DNA tiles, which we call string tiles. By keeping track of the strands as they weave back and forth through the assembly, we show that surprisingly sophisticated calculations can be performed with linear assembly. Examples range from generating an addition able to providing O(1) solutions to CNF-SAT and DHPP. We classify the families of languages that can be generated by various types of DNA molecules, and establish a correspondence to the existing classes ETL0Lml and ETL0Lfin. Thus, linear self-assembly of string tiles can generate the output languages of finite-visit Turing Machines.
• Wet97 - Wetmur
  J. G. Wetmur. Physical chemistry of nucleic acid hybridization. In Rubin and Wood [P3], pages 1--14.
  Introduction The goal of this review is to describe a unified approach to all types of nucleic acid hybridization (adapted from Wetmur, 1996; see Wetmur, 1991 and Wetmur and Sninsky, 1995 for additional references). In addition, new data are presented describing the thermodynamics of stacking, dangling and branch migration structures and the advantage of experimental conditions limited by dissociation kinetics rather than equilibria for achieving maximum discrimination against mis paired structures. Hybrid duplexes containing DNA and/or RNA strands are the products of hybridization reactions between partially or completely complementary single-stranded molecules. Reassociation or renaturation are alternative terms used to describe hybridization of completely complementary DNA or RNA strands. The reverse reaction is called strand separation or dissociation. The structural differences between deoxyribose and ribose in DNA and RNA strands are reflected in different forms of the antiparallel double-helices and in quantitative differences in hybrid stability and the rate of hybrid formation. Nevertheless, they are qualitatively the same, and the basic concepts may be treated together. Most of the illustrations are for DNA:DNA hybridization.
• WG99 - P5
  E. Winfree and D. K. Gifford, editors. DNA Based Computers V, volume 54 of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, 1999.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• WHJ99 - WHTK99
  R. Weiss, G. E. Homsy, and T. F. Kinght Jr. Evolution as computation, chapter Toward in vivo digital circuits, pages 275--295. In Landweber and Winfree [LW99], 1999.
• Win95a - Winf95
  E. Winfree. Complexity of restricted and unrestricted models of molecular computation. In R. J. Lipton [DBC], pages 187--198, http://dope.caltech.edu/winfree/Papers/models.ps.gz.
  Description: Here I show some limits on what can be computed using some proposed operations on DNA. These limits have since been overcome by the inclusion of additional operations.
  Abstract: In [Lipton94] and [Adl94] a formal model for molecular computing was proposed, which makes focused use of affinity purification. The use of PCR was suggested to expand the range of feasible computations, resulting in a second model. In this note, we give a precise characterization of these two models in terms of recognized computational complexity classes, namely branching programs (BP) and nondeterministic branching programs (NBP) respectively. This allows us to give upper and lower bounds on the complexity of desired computations. Examples are given of computable and uncomputable problems, given limited time.
• Win95b - Winf2
  E. Winfree. On the computational power of DNA annealing and ligation. In R. J. Lipton [DBC], pages 199--210, http://dope.caltech.edu/winfree/Papers/ligation.ps.gz.
  Description: Here I show how one might create a "one-pot" mixture of DNA which can perform universal computation. A.k.a. "weaving the tapestry of life". [Note, there are strand polarity errors in several figures. EW, 5/96]
  Abstract: In [Winf95] it was shown that the DNA primitives of Separate, Merge and Amplify were not sufficiently powerful to invert functions defined by circuits in linear time. Dan Boneh et al [biocircuit] show that the addition of a ligation primitive, Append, provides the missing power. The question becomes, ``How powerful is ligation? Are Separate, Merge, and Amplify necessary at all?'' This paper proposes to informally explore the power of annealing and ligation for DNA computation. We conclude, in fact, that annealing and ligation alone are theoretically capable of universal computation.
  It contains: [Adl95], [Baum], [Beav95D], [BDL96], [Lipton94], [Roth96], [Smith1], [Winf95] and [Winf2].
• Win98 - Winf98-4
  E. Winfree. Algorithmic Self-Assembly of DNA. PhD thesis, California Institute of Technology, Pasadena, California, May 19 1998, http://hope.caltech.edu/winfree/Papers/thesis.ps.gz.
  Abstract: How can molecules compute? In his early studies of reversible computation, Bennett imagined an enzymatic Turing Machine which modified a hetero-polymer (such as DNA) to perform computation with asymptotically low energy expenditures. Adleman's recent experimental demonstration of a DNA computation, using an entirely different approach, has led to a wealth of ideas for how to build DNA-based computers in the laboratory, whose energy efficiency, information density, and parallelism may have potential to surpass conventional electronic computers for some purposes. In this thesis, I examine one mechanism used in all designs for DNA-based computer -- the self-assembly of DNA by hybridization and formation of the double helix -- and show that this mechanism alone in theory can perform universal computation. To do so, I borrow an important result in the mathematical theory of tiling: Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. I propose constructing molecular Wang tiles using the branched DNA constructions of Seeman, thereby producing self-assembled and algorithmically patterned two-dimensional lattices of DNA. Simulations of plausible self-assembly kinetics suggest that low error rates can be obtained near the melting temperature of the lattice; under these conditions, self-assembly is performing reversible computation with asymptotically low energy expenditures. Thus encouraged, I have begun an experimental investigation of algorithmic self-assembly. A competition experiment suggests that an individual logical step can proceed correctly by self-assembly, while a companion experiment demonstrates that unpatterned two dimensional lattices of DNA will self-assemble and can be visualized. We have reason to hope, therefore, that this experimental system will prove fruitful for investigating issues in the physics of computation by self-assembly. It may also lead to interesting new materials.
• WJMP99 - WJM99
  P. Wasiewicz, T. Janczak, J.J. Mulawka, and A. Plucienniczak. The inference via DNA computing. In -, pages 988--993, 1999. In Proc. Congress on Evolutionary Computation (CEC'99).
  Abstract: DNA computing is a new paradigm to perform calculations using genetic engineering technology. This paper presents the overall research direction from which molecular inference and expert systems are emerging. It provides an introduction to the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA strands, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing.
  Washington, USA
• WJMP00
  P. Wasiewicz, T. Janczak, J.J. Mulawka, and A. Plucienniczak. The inference based on molecular computing. Int. Journal of Cybernetics and Systems, 3(31):283--315, 2000, http://www.tandf.co.uk/journals/tf/01969722.html.
  Abstract: Molecular computing is a new paradigm to perform calculations using nanotechnology. This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing. Series of experiments have been conducted to confirm practical utility of this approach. In these experiments, parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try to enhance physical insight into the dominating features of the approach proposed.
• WLC+ - WLeo00
  L. Wang, Q. Liu, R. M. Corn, A. E. Condon, and L. M. Smith. DNA computing on surfaces. Invited talk at 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000.
• WLF+99 - WangEA98
  L. Wang, Q. Liu, A. G. Frutos, S. D. Gillmor, A. J. Thiel, T. C. Strother, A. E. Condon, R. M. Corn, Max G. Lagally, and L. M. Smith. Surface-based DNA computing operations: DESTROY and READOUT. In Kari et al. [P4], pages 189--191.
  Abstract DNA computing on surfaces is where complex combinatorial mixtures of DNA molecules are immobilized on a substrate and subset are tagged and enzymatically modified (DESTROY) in repeated cycles of the DNA computation. A restriction enzyme has been chosen for the surface DESTROY operation. For the READOUT operation, both cycle sequencing and PCR amplification followed by addressed array hybridization were studied to determine the DNA sequences after the computations.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• WLWS98 - Winf98-2
  E. Winfree, F. Lin, L. A. Wenzler, and N. C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693):539--545, August 6 1998.
  Abstract: The mathematical theory of tiling has been used as a basis for a new approach to two-dimensional crystal design in which three 2-D lattices with two distinct topologies have been assembled from double-crossover (DX) molecules. The periodic blocks used in this research are made up of either two or four individual DX units. It has been possible to indicate the potential of using DNA to form self-assembly periodic nanostructures. The two-dimensional lattices demonstrated in this research could be extended into three dimensions.
• WM01
  P. Wasiewicz and J.J. Mulawka. Molecular genetic programming. Soft Computing, 2(5), 2001, http://link.springer.de/link/service/journals/00500/index.htm.
  Abstract: The paper addresses a new implementation of genetic (or evolutionary) programming by using molecular approach. Our method is based on dataflow techniques in DNA computing. After description of fundamental operations on DNA molecules and construction of logical functions the genetic programming method is introduced. We propose a way to handle these graph encoding molecules and which can be considered a genetic programming algorithm; a short discussion about experiments in implementing parts of this procedure is added.
• WMN+01 - WMN01
  P. Wasiewicz, A. Malinowski, R. Nowak, J.J Mulawka, P. Borsuk, P. Weglenski, and A. Plucienniczak. DNA computing: Implementation of data flow logical operations. Future Generation Computer Systems, 4(17):361--378, 2001, http://www.elsevier.nl/locate/future/.
  Abstract: elf-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This technique employs standard operations of genetic engineering including radioactive labeling as well as digestion by the second class restriction nuclease and Polymerase Chain Reaction (PCR). To check practical utility of the method a series of genetic engineering experiments have been performed. The obtained information confirms interesting properties of the DNA-based molecular data flow logic gates. Some experimental results demonstrating implementation of a single logic NAND gate and only in one vessel calculation of a tree-like Boolean function with the help of the PCR are provided. These techniques may be utilized in massively parallel computers and on DNA chips.
• WMRL - WMRL01
  P. Wasiewicz, J. J. Mulawka, W. R. Rudnicki, and B. Lesyng. Arithmetic operations on DNA-subtraction. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• Wol - Wol00
  Stuart Wolpert. UCLA chemists report significant progress toward molecular computers; research ahead of schedule, http://www.uclanews.ucla.edu/docs/LSSW358.html. Only on the net.
• Woo03 - Wood03
  D. H. Wood. DNA computing capabilities for game theory. Natural Computing, 2(1):85--108, 2003.
• WRML00
  P. Wasiewicz, R. Rudnicki, J.J. Mulawka, and B. Lesyng. Adding numbers with DNA. In -, pages 265--270, 2000. In Proceedings 2000 IEEE International Conference on Systems, Man \& Cybernetics - SMC2000.
  Abstract: The new algorithm of DNA computing for adding binary integer numbers is presented. It requires the unique representation of bits placed in test tubes treated as registers. Amplification step used for the carry operation allows in theory to add numbers at the same quantity of elementary operations, regardless of a number of bits used for representation. New notation proposed in this paper allows for efficient and abstract description of the technical operations on DNA.
  Nashville, USA
• WTFK00 - WKJ00
  R. Weiss and Jr. T. F. Knight. Engineered communications for microbial robotics. In Condon and Rozenberg [P6], pages 1--16.
  Abstract: Multicellular organisms create complex patterned structures from identical, unreliable components. Learning how to engineer such robust behavior is important to both an improved understanding of computer science and to a better understanding of the natural developmental process. Earlier work by our colleagues and ourselves on amorphous computing demonstrates in simulation how one might build complex patterned behavior in this way. This work reports on our first efforts to engineer microbial cells to exhibit this kind of multicellular pattern directed behavior. We describe a specific natural system, the Lux operon of Vibrio fischeri, which exhibits sensity dependent behavior using a well characterized set of genetic components. We have isolated, sequenced, and used these components to engineer intercellular communications mechanisms between living bacteria cells. In combination with digitally controlled intracellular genetic circuits, we believe this work allows us to begin the more difficult process of using these communication mechanisms to perform directed engineering of multicellular structures, using techniques such as chemical diffusion dependent behavior. These same techniques form as essential part of our toolkit for engineering with life, and are widely applicable in the field of microbial robotics, with potential applications in medicine, environmental monitoring and control, engineered crop cultivation, and molecular scale fabrication.
• WW96 - WilliamsWood96
  R. M. Williams and D. H. Wood. Exascale computer algebra problems interconnect with molecular reactions and complexity theory. In Landweber and Baum [2AWDBC].
  Abstract: In discussing exascale (exa = 10¹⁸) computer algebra problems we interconnect three themes. First, DNA is an attractive medium for computation because of its density and parallelism. Second, computer algebra is similar to DNA laboratory reactions. Both rearrange identical subunits. Third, determinant and/or permanent expansions exemplify many levels of complexity. These three issues are combined in a planned experiment using a DNA algorithm to evaluate or approximate the permanent of a matrix of zeros and ones, a well-known problem in the class \#P-Complete. Such problems are harder than those previously addressed by DNA techniques in the pioneering articles of Adleman and Lipton. This points the way to DNA methods for expanding a symbolic determinant given its zero pattern, which is of still higher complexity. We begin to approach interesting problem sizes because we reduce scale-up difficulties by alternating intermediate steps of building and filtering. The example algorithm suggests directions toward the general problem of expanding symbolic determinants and permanents given their zero entries.
• WY - WY03
  K. Wakabayashi and M. Yamamura. Bacterial evolution based on genomic algorithm in vitro. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• WY01
  K. Wakabayashi and M. Yamamura. A realization of information gate by using enterococcus faecalis pheromone system. In Jonoska and Seeman [P7], pages 269--278.
  Abstract: In this paper, we introduce a novel signal element by using bacterial pheromones. In multicellular organism, every call can communicate and exchange information with other cells. Bacteria also have such mechanism. Enterococcus faecalis, one of the gram-positive bacteria, has a unique pheromone system. Male cells are stimulated by pheromones from female cells, and they give their plasmide to female cells through conjugation phenomenon. The variety of pheromones and they inducible activities of plasmid transfer inspire us that Enterococcus faecalis can serve as a pheromone-dependent DNA transporter. We show a design to realize logically controlled information gates by using Enterococcus faecalis and show an experimental plan. It is still on going project, but we can show the feasibility that bacterial pheromone system would provide alternative methodologies in molecular computing research.
• WYS96 - Winf96
  E. Winfree, X. Yang, and N. C. Seeman. Universal computation via self-assembly of DNA: some theory and experiments. In Landweber and Baum [2AWDBC], ftp://hope.caltech.edu/pub/winfree/DIMACS/self-assem.ps.
  Abstract: In this paper we examine the computational capabilities inherit in the hybridization of DNA molecules. First we consider theoretical models, and show that the self-assembly of oligonucleotides into linear duplex DNA can only generate sets of sequences equivalent to regular languages. If branched DNA is used for self-assembly of dendrimer structures, only sets equivalent to context-free languages can be achieved. In contrast, we show that the self-assembly of double crossover molecules into two dimensional sheets or three dimensional solids is theoretically capable of universal computation. The proof relies on a very direct simulation of a universal class of cellular automata. In the second part of this paper, we present results from preliminary experiments which investigate the critical computational step in a two-dimensional self-assembly process.
• YA - YA01
  Takaneka Yoichi and Hashimoto Akhiro. A proposal of DNA computing on beads and its application to SAT problems. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• YA02
  T. Yoichi and H. Akihiro. Shortening the computational time of the fluorescent DNA computing. In Hagiya and Ohuchi [PP8], pages 85--94.
  The volume contains [RTS02], [AJS02], [LRB02], [LSeo02], [YA02], [Torre02], [BKW02], [ADeo02], [DCeo02], [KKA02], [HCH02], [TY02], [IMVeo02], [FJ02], [BFMZ02], [Head02], [Reif02].
  Poster papers presented at the conference [BM02], [DCBR02], [HS02], [KYeo02], [KSLZ02], [LPeo02], [LYeo02], [MRV02], [MY02], [SI02], [TBW02], [THC02].
• YFLR03 - YFeo03
  H. Yan, L. Feng, T. LaBean, and J. H. Reif. Parallel molecular computation of pair-wise XOR using DNA "string tile" self-assembly. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 97, 2003.
• YHM01
  M. Yamamura, Y. Hiroto, and T. Matoba. Another realization of aqueous computing with peptide nucleic acid. In Jonoska and Seeman [P7], pages 213--222.
  Abstract: Head proposed a framework of aqueous computing as a code design free molecular computing. Aqueous computing handles an aqueous solution of general-purpose memory molecules with a small set of elementary laboratory operations. It fits to solve a certain pattern of NP complete problems. We focus upon scaling the address space up and propose another biomolecular realization. Peptide nucleic acid (PNA) is an artificial analogue of DNA. Since PNA-DNA hybrid has higher melting temperature than DNA-DNA case, PNA will take over hydrogen bonds and displace itself into a double strand DNA. This phenomenon can be regarded as an irreversible write-once operation on a memory molecule. PNA brings a much larger address space than natural enzymes can provide. In this paper, we propose elementary operations for aqueous computing with PNAand realize one bit memory for a feasibility study to confirm strand displacement by PNA. We also propose an idea to copy a memory state upon a DNA sequence by using whiplash PCR.
• YK97
  T. Yokomori and S. Kobayashi. DNA-EC : A model of DNA-computing based on equality checking. In Rubin and Wood [P3], pages 334--347, http://ylab-gw.cs.uec.ac.jp/Papers/yokomori/dimacs97.ps.gz.
  Abstract: This paper proposes new models for DNA computation based on a simple principle called equality checking. The advantages of the proposed models may include ( i) the universal computability of the general models, ( ii) the clarity and simplicity of molecular biological operations employed, and therefore ( iii) the high feasibility in molecular biological implementation of the models.
• YKF95
  T. Yokomori, S. Kobayashi, and C. Ferretti. On the power of circular splicing systems and DNA computability. Technical Report Report CSIM 95-01, University of Electro-Communications, Department of Computer Science and Information Mathematics, Chofu, Tokyo 182, Japan, July 1995.
  Abstract: A new type of generative mechanisms was recently introduced under the name of extended H-systems, and it has been shown that extended H-systems with finite sets of axioms and finite sets of rules exactly characterize the recursively enumerable languages, thus having the full power of Turing machines. Also, it was shown that there is a universal extended H system analogous to a universal Turing machine. In this paper, we propose a new type of splicing models called circular H-systems, and show that they have the same computational power as Turing machines. Proposed new models are based on circular splicings which come from biological motivations of interactions between linear and circular DNA sequences, and hence, the models seem to have some advantages over other existing models dealing with only linear strings. We also show that there effectively exists a universal circular H system which can simulate any circular H system with the same terminal alphabet, which naturally leads us to a feasible design for a DNA computer based on circular splicing. Surprisingly, all these results are obtained without considering multiplicity constraints, which is in marked contrast to the previous results for linear H systems.
• YKF97 - Yokomori97
  T. Yokomori, S. Kobayashi, and C. Ferretti. On the power of circular splicing systems and DNA computability. In IEEE International Conference on Evolutionary Computation, 1997, http://ylab-gw.cs.uec.ac.jp/../Papers/yokomori/cssfinal.ps.gz.
  Abstract: From a biological motivation of interactions between linear and circular DNA sequences, we propose a new type of splicing models called circular H systems and show that they have the same computational power as Turing machines. It is also shown that there effectively exists a universal circular H system which can simulate any circular H system with the same terminal alphabet, which strongly suggests a feasible design for a DNA computer based on circular splicing.
• YL - YL01
  Ilya Yvanov and Jerzy Leszczynski. Ab initio and molecular dynamics study on the nanomechanical properties of DNA fragments. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• YLFR - YLBeo03
  H. Yan, T. H. LaBean, L. Feng, and J. H. Reif. Directed nucleation assembly of barcode patterned DNA lattices. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• YMC99 - YurkeEA98
  B. Yurke, A. P. Mills, and S. L. Cheng. DNA implementation of addition in which the input strands are separate from the operator strand. In Kari et al. [P4], pages 165--174.
  Abstract: A DNA representation of Boolean logic for which the input strands are separated from the operator strand is described and used to construct a two-bit DNA adder. The successful operation of the adder for several test inputs demonstrates that digital molecular computation with a complexity of order 30 gates is feasible.
  The proceedings contain [LandKari98], [KleinEA98], [LiuEA98], [CukrEA98], [MancaEA98], [ZLi98-1], [GarzJon98], [MargRo98], [SakaEA98], [KhoGif98], [Conrad98], [Kazic98], [Ji98], [Eng98], [JonosEA98], [FuBei98], [YurkeEA98], [MillsEA98], [YoshiEA98], [WangEA98], [FaulhEA98], [GehaReif98], [FBZ98], [HGK98]
• Yok99 - Y99
  T. Yokomori. YAC: Yet another computation model of self-assembly. In Winfree and Gifford [P5], pages 155--169.
  Abstract: This paper proposes a new model for DNA computation termed YAC based on self-assembly principle. The model has three advantages: (i) It has the universal computability of Turing machines. (ii) It requires only simple and basic molecular biological operations. Besides annealing and melting in a one-pot reaction, only the detection of a completely hybridized double stranded molecule is used. (iii) Therefore, a molecular biological implementation of the model seems highly feasible. In order to make YAC computation more resource efficient, we introduce an incremental computation method.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• Yok02
  T. Yokomori. Molecular computing paradigm toward freedom from Turing's charm. Natural Computing, 1(4):333--390, 2002.
• YPF+03 - YHeo03
  H Yan, S. H. Park, L. Feng, G. Finkelstein, J. H. Reif, and T. LaBean. 4x4 DNA tile and lattices: characterization, self-assembly and metallization of a novel DNA nanostructure motif. In Preliminary Proceedings of DNA Computing, 9th international Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1-4 June 2003, page 98, 2003.
• YS99
  H. Yoshida and A. Suyama. Solution to 3-SAT by breadth first search. In Winfree and Gifford [P5], pages 9--22.
  Abstract: We have actually solved a very simple instance of 4-variable-10-clause 3-SAT problem with DNA molecules using experimental protocols amenable to automation. The algorithm is based on breadth first search, as can be seen in Ogihara and Ray's [OR97], whereby we have succeeded in drastic decrease of the number of DNA molecules that must be present in a test tube. Computer simulations demonstrated that the necessary number of DNA molecules for solving n-variable 3-SAT problems was around 2^0.5n. Hence, compared with the conventional brute force method, our algorithm and implementation can be extended to a larger-scale 3-SAT problem with ease.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• YYS+99 - YYSHTSMO99
  Masahito Yamamoto, Jin Yamashita, Toshikazu Shiba, Takuo Hirayama, Shigeharu Takiya, Keiji Suzuki, Masanobu Munekata, and Azuma Ohuchi. A study on the hybridization process in DNA computing. In Winfree and Gifford [P5], pages 101--110.
  Abstract: A hybridization process is a basic and significant process in DNA computing. Therefore, in order to clarify the problems that may be occurred in the process, we have to analyze the process in detail. In this paper, we focus on the hybridization process. First, we introduce a simulation model of the process and then discuss the usefulness of the simulator. Next, we propose a new encoding method for avoiding miss-annealings (errors). In order to show the validity of the simulator and the effectiveness of our encoding method, we introduce a Hamiltonian path problem with 4 vertices and discuss the results of laboratory experiments.
  The proceedings contain [WCAeo99],[RHeo99],[FCLL99],[GDRF99],[HMG99],[MYP99],[MCC99],[LL99],[YS99],[Y99],[YYSHTSMO99],[TYM99],[PY99-1],[GLR99],[LWR99],[CW99],[BB99],[KL99],[EHRV99]
• ZC96 - ZaunerConrad96
  Klaus-Peter Zauner and Michael Conrad. Parallel computing with DNA: toward the anti-universal machine. In Hans-Michael Voigt, Werner Ebeling, Ingo Rechenberg, and Hans-Paul Schwefel, editors, Parallel Problem Solving from Nature---PPSN IV, Proceedings, volume 1141 of Lecture Notes in Computer Science, pages 696--705, Berlin, 1996. Springer Verlag, Berlin, Heidelberg, New York, ISBN 3-540-61723-X.
  Summary Provides a simple, step by step, introduction to Adleman's original experiment. Introduces the notion of an instance machine, i.e., a computer that represents a problem instance, not in its state, but in its structure.
  Abstract: A DNA-based biomolecular string processing scheme demonstrated by Adleman has attracted wide attention. While it is not known to what degree the scheme can scale up, it nevertheless introduces a new and interesting concept which seems so far to have been overlooked. The key point is that the Adleman scheme involves building specific hardware for a single problem instance. This opens a design degree of freedom that is not limited to biomolecular architectures.
• ZC00
  K.-P. Zauner and M. Conrad. Enzymatic pattern processing. Naturwissenschaften, 87(8):360--362, 2000, http://www.cs.wayne.edu/~kjz/KPZ/PublicationsOnline/NatWissV87P360/NatWissV87P360.html.
  Abstract: A table-top prototype has been constructed that uses the enzyme malate dehydrogenase to recognize input signal patterns. The device is controlled by the enzyme in response to injection of Mg²⁺ used as a signaling substance. Output is monitored spectroscopically. If Mg²⁺ is injected along either of two signal lines (i.e., if the input signal pattern is 10 or 01) the device emits an output of 1. Injection along neither or both lines results in an output of 0. The enzyme in effect is used as a transform that converts the linearly inseparable exclusive-or problem into a linearly separable problem.
• ZC01
  K.-P. Zauner and M. Conrad. Molecular approach to informal computing. Soft Computing, 5(1):39--44, 2001, http://www.cs.wayne.edu/~kjz/KPZ/PublicationsOnline/SoftCompV5P39/SoftCompV5P39.html.
  Abstract: Cells and organisms are natural molecular computers. The problem domains effectively addressed by these systems are complementary to, and in fundamental respects far exceed, the domains addressable by current computing devices. The vast majority of information processing problems do not have sufficiently compact formal specifications to fall within the reach of programmable machines. Our working hypothesis is that the unique properties of molecular materials are the key to extending information processing technology beyond the narrow limits of formal computing.
• ZCL - ZCL01
  Xichun Zhou, Lan Cao, and Sam Fong Yau Li. Large improvements of the lower detection limit of microgravimetric DNA biosensor using oligonucleotide-functionalized au nenoparticle or biotin-functionalized au nanoparticle. Poster at 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A, 10-13 June 2001.
• ZFM97 - ZandronEA97
  C. Zandron, C. Ferretti, and G. Mauri. A reduced distributed splicing system for RE languages. In G. Paun and A. Salomaa, editors, New trends in Formal Language. Control, cooperatio, and conbinatorics, volume 1218 of Lecture Notes in Computer Science, pages 346--366. Springer Verlag, Berlin, Heidelberg, New York, 1997.
  Abstract: In this paper we prove that each recursively enumerable language can be generated using a distributed splicing system with a fixed number of test tubes. This improves a recent result by Csuhaj-Varjú, Kari, Paun, proving computational completeness only for a system with a number of tubes depending on the cardinality of the used alphabet.
• ZFM00a - ZFM00_1
  C. Zandron, C. Ferretti, and G. Mauri. Priorities and variable thickness of membranes in rewriting P systems. manuscript, 2000.
• ZFM00b - ZFM00-2
  C. Zandron, C. Ferretti, and G. Mauri. Solving NP-complete problems using P systems with active membranes, chapter 289-301. Unconventional Models of Computation. Springer Verlag, Berlin, Heidelberg, New York, 2000. I. Antoniou and C.S. Calude and M.J. Dinneen eds.
• ZFM00c - ZFM00-3
  C. Zandron, C. Ferretti, and G. Mauri. Solving NP-complete problems using P systems with active membranes. In Antoniou et al. [UMC2K], pages 289--301.
  Abstract: A recently introduced variant of P-systems considers membranes which can multiply by division. These systems use two types of division: division for elementary membranes (i.e. membranes not containing other membranes inside) and division for non-elementary membranes. In two recent papers it is shown how to solve the Satisfiability problem and the Hamiltonian Path problem (two well known NP complete problems) in linear time with respect to the input length, using both types of division. We show in this paper that P-systems with only division for elementary membranes suffice to solve these two problems in linear time. It is possible to solve NP complete problems in polynomial time using P-systems without membrane division? We show, moreover, that (if P \neq NP) deterministic P-systems without membrane division are not able to solve NP complete problems in polynomial time.
• ZFM00d - ZFM00-1
  C. Zandron, C. Ferretti, and G. Mauri. Using membrane features in P systems. In Calude et al. [WMP2000], pages 296--311.
  Abstract: In the basic variant of P systems, membranes are used as separators and as channels of communications. Other variants, introduced to obtain more "realistic" models, consider membranes with different features: membranes of variable thickness, electrically charged membranes and active membranes (membranes can be divided in two or more membranes). These features are not only useful to obtain "realistic" models: we show how we can use them to get simpler and faster models.
  TR140, CDMTCS, Univ. Auckland
• Zin - Zingel03
  T. Zingel. On matrix representation of slicing languages of extended multiset H systems. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• Ziz02 - ZIZZA02
  R. Zizza. On the power of classes of splicing systems. PhD thesis, University of Milan, 2002.
  Abstract: My thesis provides an overview and investigations on Molecular Computing and Splicing Systems. Molecular Computing is a novel branch connecting Computer Science, Mathematics and Biology: computation is carried on by DNA molecules and the operations are performed by using enzymes and other biological processes. Splicing Systems are formal models of a recombinant generative process among molecules which are cut and pasted by a simultaneous action of restriction and ligase enzymes. Splicing operation is introduced as an operator on strings and systems generating languages are defined, whose generating power is compared with classical results in Formal Languages. My thesis concerns particular (finite) splicing systems for linear and circular splicing in a perspective which has never been explored so far. Decidability and descriptional complexity questions are answered, various results are provided by using combinatorics on words, classical issues in Formal Languages and novel ideas on automata. Deep connections with Theory of (variable length) Codes have been discovered. Problems and conjectures for future work are also proposed. A flash of biochemical background, thought out of our scope, is provided together with an extensive bibliography.
• ZJH+ - ZZeo03
  Z. Zhang, Z. Jian, Z. Huang, Y. Shi, and L. He. Sensitive detection of DNA molecular derivatives by liquid-massspectrometry during DNA computing. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.
• ZMF00
  C. Zandron, G. Mauri, and C. Ferretti. Universality and normal forms on membrane systems. In International Workshop Grammar Systems 2000 (R. Freund, A. Kelemenova), Bad Ischl, Austria, July 2000, pages 61--74, 2000.
  Abstract: The work presents techniques and details for some improvements and new results concerning membrane systems. These system can be defined following several variations in their formalism, and every model starts a race to the simplest possible universal set of features. We try to outline our results on universality and previous ones in a common framework, following our understanding of the essentials shared by all the techniques based on simulation between grammar systems. Moreover, we contrast the approach to further results we obtained with techniques based on normal forms, which we define on some membrane systems.
• ZSC+ - ZS03
  T. Zheng, M. Shortreed, Y. Chen, M. Lu, and L. Smith. Increasing capture efficiency in surface-based DNA computing with a multiple-probe. Poster paper at 9th International Workshop on DNA-Based Computers, DNA 2003, Madison, Wisconsin, USA, 1--4 June 2003.