David Soloveichik Bernard Yurke (Eds.) DNA Computing and LNCS 8141 Molecular Programming 19th International Conference, DNA 19 Tempe, AZ, USA, September 2013 Proceedings 123 Lecture Notes in Computer Science 8141 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Alfred Kobsa University of California, Irvine, CA, USA Friedemann Mattern ETH Zurich, Switzerland John C. Mitchell Stanford University, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel Oscar Nierstrasz University of Bern, Switzerland C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Germany Madhu Sudan Microsoft Research, Cambridge, MA, USA Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbruecken, Germany David Soloveichik Bernard Yurke (Eds.) DNA Computing and Molecular Programming 19th International Conference, DNA 19 Tempe, AZ, USA, September 22-27, 2013 Proceedings 13 Volume Editors David Soloveichik University of California, San Francisco Center for Systems and Synthetic Biology 1700 4th Street San Francisco, CA 94158, USA E-mail: [email protected] Bernard Yurke Boise State University Materials Science and Engineering Department 1910 University Drive Boise, ID 83725, USA E-mail: [email protected] ISSN 0302-9743 e-ISSN 1611-3349 ISBN 978-3-319-01927-7 e-ISBN 978-3-319-01928-4 DOI 10.1007/978-3-319-01928-4 Springer Cham Heidelberg New York Dordrecht London Library of Congress Control Number: 2013946048 CR Subject Classification (1998): F.1, F.2.2, J.3, E.1, I.2, G.2, F.4 LNCS Sublibrary: SL 1 – Theoretical Computer Science and General Issues © Springer International Publishing Switzerland 2013 This work is subject to copyright. 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Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface This volume contains the refereed proceedings of DNA19: the 19th International Conference on DNA Computing and Molecular Programming, held September 22–27, 2013, at Arizona State University, Arizona, USA. Research in DNA computing and molecular programming draws together many disciplines (including mathematics, computer science, physics, chemistry, materials science, and biology) to address the analysis, design, and synthesis of information-based molecular systems. This annual meeting is the premier forum where scientists with diverse backgrounds come together with the common pur- pose of applying principles and tools of computer science, physics, chemistry and mathematics to advance molecular-scale computation and nanoengineer- ing. Continuing this tradition, the 19th International Conference on DNA Com- puting and Molecular Programming (DNA19), organized under the auspices of the International Society for Nanoscale Science, Computation, and Engineering (ISNSCE), focused on important recent experimental and theoretical results. This year the Program Committee received 29 full paper submissions and 30 one-page abstracts. The Committee selected 14 full papers for oral presenta- tion and inclusion in these proceedings, and 14 abstracts were selected for oral presentation only. Many of the remaining submissions were selected for poster presentation, along with posters chosen from 51 additional poster-only submis- sions. The topics were well-balanced between theoretical and experimental work, with submissions from 18 countries, reflecting the diversity of the community. The scientific program also included six invited speakers: Alessandra Carbone (Pierre and Marie Curie University), Hendrik Dietz (Technical Uni- versity of Munich), Eric Goles (Adolfo Ib´a˜nez University), Chengde Mao (Pur- due University), Lulu Qian (California Institute of Technology), and Yannick Rondelez (University of Tokyo). Following the conference, a one-day workshop, Nanoday 2013, was held fea- turing current topics in nanotechnology. The speakers included Nadrian Seeman (New York University), Friedrich Simmel (Technical University Munich), John Spence (Arizona State University), Kurt Gothelf (Aarhus University), Tim Liedl (Ludwig Maximilians University of Munich), William Shih (Harvard Medical School), John Chaput (Arizona State University), Paul Steinhardt (Princeton University), Hanadi Sleiman (McGill University), Peng Yin (Harvard Medical School), and Dongsheng Liu (Tsinghua University). The editors would like to thank the members of the Program Committee and the external referees for their hard work in reviewing submissions and of- fering constructive suggestions to the authors. They also thank the Organizing VI Preface and Steering Committees, and particularly Hao Yan and Natasha Jonoska, the respective Committee Chairs, for their invaluable help and advice. Finally, the editors would like to thank all the sponsors, authors, and attendees for support- ing the DNA computing and molecular programming community, and helping to make the conference a success. July 2013 David Soloveichik Bernard Yurke Organization DNA19 was organized by Arizona State University in cooperation with the Inter- national Society for Nanoscale Science, Computation, and Engineering (ISNSCE). Steering Committee Natasha Jonoska (Chair) University of South Florida, USA Luca Cardelli Microsoft Research Cambridge, UK Anne Condon University of British Columbia, Canada Masami Hagiya University of Tokyo, Japan Lila Kari University of Western Ontario, Canada Satoshi Kobayashi University of Electro-Communication, Japan Chengde Mao Purdue University, USA Satoshi Murata Tohoku University, Japan John Reif Duke University, USA Grzegorz Rozenberg University of Leiden, The Netherlands Nadrian Seeman New York University, USA Friedrich Simmel Technische Universit¨at M¨unchen, Germany Andrew J. Turberfield Oxford University, UK Hao Yan Arizona State University, USA Erik Winfree California Institute of Technology, USA Organizing Committee Hao Yan (Chair) Arizona State University, USA Jeanette Nangreave Arizona State University, USA Yan Liu Arizona State University, USA Program Committee David Soloveichik (Co-chair) University of California, San Francisco, USA Bernard Yurke (Co-chair) Boise State University, USA Robert Brijder Hasselt University, Belgium Luca Cardelli Microsoft Research Cambridge, UK Andrew Ellington University of Texas at Austin, USA Elisa Franco University of California, Riverside, USA Kurt Gothelf Aarhus University, Denmark Natasha Jonoska University of South Florida, USA Lila Kari University of Western Ontario, Canada Satoshi Kobayashi University of Electro-Communications, Japan VIII Organization Dongsheng Liu Tsinghua University, China Chengde Mao Purdue University, USA Yongli Mi Hong Kong University of Science and Technology, China Satoshi Murata Tohoku University, Japan Jennifer E. Padilla New York University, USA Matthew J. Patitz University of Arkansas, USA Andrew Phillips Microsoft Research Cambridge, UK John Reif Duke University, USA Alfonso Rodr´ıguez-Pat´on Universidad Polit´ecnica de Madrid, Spain Yannick Rondelez University of Tokyo, Japan Robert Schweller University of Texas-Pan American, USA Shinnosuke Seki Aalto University, Finland Friedrich Simmel Technical University of Munich, Germany Darko Stefanovic University of New Mexico, USA Chris Thachuk University of British Columbia, Canada Andrew J. Turberfield University of Oxford, UK Erik Winfree California Institute of Technology, USA Damien Woods California Institute