DNA Computing: 15th International Meeting on DNA Computing, DNA 15, Fayetteville, AR, USA, June 8-11, 2009. Revised Selected Papers PDF
Preview DNA Computing: 15th International Meeting on DNA Computing, DNA 15, Fayetteville, AR, USA, June 8-11, 2009. Revised Selected Papers
Lecture Notes in Computer Science 5877 CommencedPublicationin1973 FoundingandFormerSeriesEditors: GerhardGoos,JurisHartmanis,andJanvanLeeuwen EditorialBoard DavidHutchison LancasterUniversity,UK TakeoKanade CarnegieMellonUniversity,Pittsburgh,PA,USA JosefKittler UniversityofSurrey,Guildford,UK JonM.Kleinberg CornellUniversity,Ithaca,NY,USA AlfredKobsa UniversityofCalifornia,Irvine,CA,USA FriedemannMattern ETHZurich,Switzerland JohnC.Mitchell StanfordUniversity,CA,USA MoniNaor WeizmannInstituteofScience,Rehovot,Israel OscarNierstrasz UniversityofBern,Switzerland C.PanduRangan IndianInstituteofTechnology,Madras,India BernhardSteffen TUDortmundUniversity,Germany MadhuSudan MicrosoftResearch,Cambridge,MA,USA DemetriTerzopoulos UniversityofCalifornia,LosAngeles,CA,USA DougTygar UniversityofCalifornia,Berkeley,CA,USA GerhardWeikum Max-PlanckInstituteofComputerScience,Saarbruecken,Germany Russell Deaton Akira Suyama (Eds.) DNA Computing and Molecular Programming 15th International Conference, DNA 15 Fayetteville,AR, USA, June 8-11, 2009 Revised Selected Papers 1 3 VolumeEditors RussellDeaton Dept.ofComputerScienceandComputerEngineering,JBHT-CSCE504 1UniversityofArkansas Fayetteville,AR72701,USA E-mail:[email protected] AkiraSuyama DepartmentofLifeScienceandInstituteofPhysics GraduateSchoolofArtsandSciences,TheUniversityofTokyo 3-8-1Komaba,Meguro-ku,Tokyo,153-8902,Japan E-mail:[email protected] LibraryofCongressControlNumber:2009939331 CRSubjectClassification(1998):F.1,F.2.2,I.2.9,J.3 LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues ISSN 0302-9743 ISBN-10 3-642-10603-XSpringerBerlinHeidelbergNewYork ISBN-13 978-3-642-10603-3SpringerBerlinHeidelbergNewYork Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. springer.com ©Springer-VerlagBerlinHeidelberg2009 PrintedinGermany Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SPIN:12798117 06/3180 543210 Preface The 15th International Conference on DNA Computing and Molecular Pro- gramming was held during June 8-11, 2009 on the campus of the University of Arkansas in Fayetteville, AR. The conference attracts researchers from dis- parate disciplines in science and technology to foster interdisciplinary research into the molecular-scale manipulation of matter. In particular, implementation ofnanoscalecomputationandprogrammedassemblyofmaterialsareofinterest. Papersattheconferencetypicallyareamixofexperimentalandtheoreticalpre- sentations.TheconferenceisheldundertheauspicesoftheInternationalSociety for Nanoscale Science, Computation, and Engineering (ISNSCE). The DNA15 Program Committee received 38 paper submissions, of which 20 were accepted for oral presentation and 10 for poster presentation. The meeting was attended by 68 registeredparticipants,which included 36 students. This volume contains 16 papers selected from contributed oral presentations. Thisyear“MolecularProgramming”wasaddedtothetitleoftheconference, which reflects a broader scope beyond DNA-based nanotechnology and compu- tation. This was evident in the range of invited talks at the conference. Tuto- rials on“Computer Science for (not only) Molecular Biologists” by Wing-Ning Li (University of Arkansas), “Structural DNA Nanotechnology” by John Reif (Duke University), and “Autonomous Molecular Computing and Robotics” by MilanStojanovic(ColumbiaUniversity)werepresentedonthefirstday.Onsub- sequentdays,inadditiontothecontributedtalksandposters,plenarytalkswere given by James Aspnes (Yale University) on “Population Protocols,” Reinhard Laubenbacher (Virginia Tech) on “Discrete Model of Gene Regulation in Net- works,” David Leigh (University of Edinburgh) on “Synthetic Motors and Ma- chines,” Kenichi Morita (Hiroshima University) on “Computation in Reversible Cellular Automata,” and Itamar Willner on “Programmed DNA assemblies for Machinery, Logic Gates, and Computing Applications.” The editors would like to thank the members of the Program Committee and the reviewers for all their hard work reviewing papers and providing con- structivecommentstoauthors.TheyalsothankallthemembersoftheOrganiz- ing Committee, and particularly, Jin-Woo Kim, the Co-chair of the Organizing Committee.CindyPickneyoftheComputerScienceandComputerEngineering and Linda Pate of the Biological Engineering Departments at the University of Arkansasdeservespecialmentionforalloftheirwork.ShellyWaltersattheCity of Fayetteville Visitor’s Bureau was an invaluable resource. They also thank all the sponsors of the conference. The editors would also like to thank the confer- enceSteeringCommittee,andinparticular,NatashaJonoska,thecurrentChair, and Lila Kari,the previousChair for valuable advice.Finally, the editors thank the authors, attendees, and additional staff that helped make the conference successful. September 2009 Russell Deaton Akira Suyama Organization DNA15 was organized by the Department of Computer Science and Computer Engineeering,University of Arkansas,in cooperationwith the InternationalSo- ciety for Nanoscale Science, Computation, and Engineering (ISNSCE). Steering Committee Natasha Jonoska University of South Florida, USA Leonard Adleman University of Southern California (honorary), USA Anne Condon University of British Columbia, Canada Masami Hagiya University of Tokyo, Japan Lika Kari University of Western Ontario, Canada Chengde Mao Purdue University, USA Giancarlo Mauri University of Milan-Bicocca, Italy Satoshi Murata Tokyo Institute of Technology, Japan John Reif Duke University, USA Grzegorz Rozenberg Leiden University, The Netherlands Nadrian Seeman New York University, USA Andrew Tuberfield Oxford University, UK Erik Winfree California Institute of Technology, USA Program Committee Matteo Cavaliere CoSBi, Trento, Italy Anne Condon University of British Columbia, Canada Russell Deaton (chair) University of Arkansas, USA Ashish Goel Stanford University, USA Hendrik Jan Hoogeboom Leiden University, The Netherlands Lika Kari University of Western Ontario, Canada Ehud Keinan Technion-Israel Institute of Technology, Israel Thom LaBean Duke University, USA Giancarlo Mauri University of Milan-Bicocca, Italy Yongli Mi Hong Kong University of Science and Technology Satoshi Murata Tokyo Institute of Technology, Japan Andrei Paun Louisiana Tech University, USA Paul Rothemund California Institute of Technology, USA Yasu Sakakibara Keio University, Japan Ned Seeman New York University, USA Friedrich Simmel Technische Universita¨t Mu¨nchen, Germany VIII Organization Petr Sosik Silesian University in Opava, Czech Republic Akira Suyama (co-chair) University of Tokyo, Japan Andrew Turberfield Oxford University, UK Ron Weiss Princeton University, USA Masayuki Yamamura Tokyo Institute of Technology, Japan Hao Yan Arizona State University, USA Bernie Yurke Boise State University, USA Organizing Committee Russell Deaton (Chair) University of Arkansas Jin-Woo Kim (Co-chair) University of Arkansas George Holmes University of Arkansas Chaim Goodman-Strauss University of Arkansas Wing-Ning Li University of Arkansas Referees Cheng, Qi Ibrahimi, Morteza Masson, Benoit Davidsohn, Noah Iaccarino, Gennaro Saurabh, Gupta Gupta, Saurabh Jack, John Seki, Shinnosuke Sponsoring Institutions Air Force Office of Scientific Research Arkansas Biosciences Institute Arkansas Science and Technology Authority University of Arkansas College of Engineering University of Arkansas Graduate School University of Arkansas Department of Computer Science and Computer Engineering University of Arkansas Department of BiologicalEngineering Division of Agriculture, University of Arkansas Table of Contents Filter Position in Networks of Evolutionary Processors Does Not Matter: A Direct Proof ........................................... 1 Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, and Jose M. Sempere Strand Algebras for DNA Computing............................... 12 Luca Cardelli A Domain-Specific Language for Programming in the Tile Assembly Model .......................................................... 25 David Doty and Matthew J. Patitz Limitations of Self-assembly at Temperature One .................... 35 David Doty, Matthew J. Patitz, and Scott M. Summers Advancing the Deoxyribozyme-BasedLogic Gate Design Process....... 45 M. Leigh Fanning, Joanne Macdonald, and Darko Stefanovic DNA Chips for Species Identification and BiologicalPhylogenies ....... 55 Max H. Garzon, Tit-Yee Wong, and Vinhthuy Phan Renewable, Time-Responsive DNA Logic Gates for Scalable Digital Circuits......................................................... 67 Ashish Goel and Morteza Ibrahimi Self-assembly of the Discrete Sierpinski Carpet and Related Fractals.... 78 Steven M. Kautz and James I. Lathrop Automatic Design of DNA Logic Gates Based on Kinetic Simulation ... 88 Ibuki Kawamata, Fumiaki Tanaka, and Masami Hagiya Design of a Biomolecular Device That Executes Process Algebra ....... 97 Urmi Majumder and John H. Reif NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots..................................................... 106 J´an Manˇuch, Chris Thachuk, Ladislav Stacho, and Anne Condon The Effect of Malformed Tiles on Tile Assemblies within kTAM ....... 116 Ya Meng and Navin Kashyap PositionalState RepresentationandIts TransitionControlforPhotonic DNA Automaton ................................................ 126 Hiroto Sakai, Yusuke Ogura, and Jun Tanida X Table of Contents Construction of AND Gate for RTRACS with the Capacity of Extension to NAND Gate......................................... 137 Yoko Sakai, Yoriko Mawatari, Kiyonari Yamasaki, Koh-ichiroh Shohda, and Akira Suyama Time-Complexity of Multilayered DNA Strand Displacement Circuits... 144 Georg Seelig and David Soloveichik Distributed Agreement in Tile Self-assembly......................... 154 Aaron Sterling Author Index.................................................. 165 Filter Position in Networks of Evolutionary Processors Does Not Matter: A Direct Proof Paolo Bottoni1, Anna Labella1, Florin Manea2,(cid:1), Victor Mitrana2,3,(cid:1), and Jose M. Sempere3,(cid:1)(cid:1) 1 Department of Computer Science, “Sapienza” Universityof Rome Via Salaria 113, 00198 Rome, Italy {bottoni,labella}@di.uniroma1.it 2 Faculty of Mathematics, Universityof Bucharest Str. Academiei 14, 70109 Bucharest, Romania {flmanea,mitrana}@fmi.unibuc.ro 3 Department of Information Systemsand Computation Technical University of Valencia, Camino deVera s/n. 46022 Valencia, Spain [email protected] Abstract. In this paper we give a direct proof of the fact that the computational power ofnetworks ofevolutionary processors and that of networksofevolutionaryprocessorswithfilteredconnectionsisthesame. ItisknownthatbothareequivalenttoTuringmachines.Weproposehere a direct simulation of onedevice bytheother. Each computational step in one model is simulated in a constant number of computational steps intheotheronewhileatranslationviaTuringmachinessquaresthetime complexity. 1 Introduction The origin of accepting networks of evolutionary processors (ANEP for short) is a basic architecture for parallel and distributed symbolic processing, related to the Connection Machine [5] as well as the Logic Flow paradigm [4], which consists of several very simple processors (called evolutionary processors), each of them being placed in a node of a virtual complete graph. By an evolutionary processor we mean an abstract processor which is able to perform very simple operations, namely point mutations in a DNA sequence (insertion, deletion or substitution of a pair of nucleotides). More generally, each node may be viewed asacellhavinggeneticinformationencodedinDNAsequenceswhichmayevolve by local evolutionary events, that is point mutations. Each node is specialized just for one of these evolutionary operations. Furthermore, the data in each (cid:1) WorksupportedbythePN-IIPrograms 11052 (GlobalComp) and 11056 (CellSim). Victor Mitrana acknowledges support from Academy of Finland, project 132727. (cid:1)(cid:1) Work supported by the Spanish Ministerio de Educaci´on y Ciencia under project TIN2007-60769. R.DeatonandA.Suyama(Eds.):DNA15,LNCS5877,pp.1–11,2009. (cid:1)c Springer-VerlagBerlinHeidelberg2009 2 P. Bottoni et al. node is organized in the form of multisets of words (each word may appear in an arbitrarily large number of copies), and all copies are processed in parallel such that all the possible events that can take place do actually take place. Further, all the nodes send simultaneously their data and the receiving nodes handlealsosimultaneouslyallthearrivingmessages,accordingtosomestrategies modelled as permitting and forbidding filters and filtering criteria, see [7]. The reader interested in a more detailed discussion about the model is referred to [7,6]. In[7] one showsthat this model is computationally complete and presents a characterization of the complexity class NP based on accepting networks of evolutionary processors (ANEP for short). It is clear that filters associated with each node of an ANEP allow a strong control of the computation. Indeed, every node has an input and output filter; two nodes can exchange data if it passes the output filter of the sender and the input filter of the receiver.Moreover,if some data is sent outby some node and not able to enter any node, then it is lost. The ANEP model considered in [7] is simplified in [2] by moving the filters from the nodes to the edges. Each edge is viewed as a two-way channel such that the input and output filters, respec- tively, of the two nodes connected by the edge coincide. Clearly, the possibility of controlling the computation in such networks seems to be diminished. For instance, there is no possibility to lose data during the communicationsteps. In spite ofthis fact,inthe aforementionedworkone provesthat thesenew devices, called accepting networks of evolutionary processors with filtered connections (ANEPFC) are still computationally complete. This means that moving the fil- ters from the nodes to the edges does not decrease the computational power of the model. Although the two variants are equivalent from the computational power point of view, no direct proof for this equivalence has been proposed so far.Itis the aimofthis papertofillthis gap.We mentionthatbothsimulations presented here are time efficient, namely each computational step in one model is simulated in a constant number of computational steps in the other. This is particularly useful when one wants to translate a solution from one model into the other. A translation via a Turing machine squares the time complexity of the new solution. 2 Basic Definitions We startbysummarizingthe notionsusedthroughoutthe paper.Analphabet is afinite andnonemptysetofsymbols.The cardinalityofafinite setAis written card(A). Any finite sequence of symbols from analphabet V is called word over V.The set ofallwordsoverV is denoted by V∗ andthe empty wordis denoted byε.Thelengthofawordxisdenotedby|x|whilealph(x)denotestheminimal alphabet W such that x∈W∗. We saythata rulea→b,witha,b∈V ∪{ε}andab(cid:4)=εis a substitution rule ifbothaandbarenotε;itisadeletion ruleifa(cid:4)=εandb=ε;itisaninsertion rule if a=ε and b(cid:4)=ε. The set of all substitution, deletion, and insertion rules over an alphabet V are denoted by SubV, DelV, and InsV, respectively.
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