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DNA Computing and Molecular Programming Andrew Phillips Peng Yin (Eds.) DNA Computing and LNCS 9211 Molecular Programming 21st International Conference, DNA 21 Boston and Cambridge, MA, USA, August 17–21, 2015 Proceedings 123 Lecture Notes in Computer Science 9211 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, Lancaster, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Friedemann Mattern ETH Zurich, Zürich, Switzerland John C. Mitchell Stanford University, Stanford, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Dortmund, Germany Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbrücken, Germany More information about this series at http://www.springer.com/series/7407 Andrew Phillips • Peng Yin (Eds.) DNA Computing and Molecular Programming 21st International Conference, DNA 21 Boston and Cambridge, MA, USA, August 17–21, 2015 Proceedings 123 Editors Andrew Phillips Peng Yin Microsoft Research Wyss Institute Cambridge Boston, MA UK USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Computer Science ISBN 978-3-319-21998-1 ISBN 978-3-319-21999-8 (eBook) DOI 10.1007/978-3-319-21999-8 Library of Congress Control Number: 2015944724 LNCS Sublibrary: SL1 – Theoretical Computer Science and General Issues Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer International Publishing AG Switzerland is part of Springer Science+Business Media (www.springer.com) Preface This volume contains the papers presented at DNA 21: the 21st International Conference on DNA Computing and Molecular Programming. The conference was held at the Wyss Institute for Biologically Inspired Engineering, Harvard University, Massachusetts, USA, during August 17–21, 2015, and organized under the auspices of the International Society for Nanoscale Science, Computation and Engineering (ISNSCE). The DNA conference series aims to draw together mathematics, computer science, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. Presentations were sought in all areas that relate to biomolecular computing, including, but not restricted to: algorithms and models for computation on biomolec- ular systems; computational processes in vitro and in vivo; molecular switches, gates, devices, and circuits; molecular folding and self-assembly of nanostructures; analysis and theoretical models of laboratory techniques; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine. Authors who wished to present their work were asked to select one of two sub- mission tracks: Track A (full paper) or Track B (one-page abstract with supplementary document). Track B is primarily for authors submitting experimental results who plan to submit to a journal rather than publish in the conference proceedings. We received 63 submissions for oral presentations: 26 submissions in Track A and 37 submissions in Track B. Each submission was reviewed by at least three reviewers, with an average of four reviewers per paper. The Program Committee accepted 13 papers in Track A and 15 papers in Track B. This volume contains the papers accepted for Track A. We express our sincere appreciation to our invited speakers: George Church, Sharon Glotzer, Lila Kari, Paul Rothemund, Leslie Valiant, and Chris Voigt. We would also like to thank all of the authors who contributed papers to these proceedings, and who presented papers and posters during the conference. Last but not least, the editors would like to thank the members of the Program Committee and the additional invited reviewers for their hard work in reviewing the papers and providing constructive comments to authors. August 2015 Andrew Phillips Peng Yin Organization DNA 21 was organized at the Wyss Institute for Biologically Inspired Engineering, Harvard University, in cooperation with the International Society for Nanoscale Science, Computation and Engineering (ISNSCE). Program Committee Andrew Phillips Microsoft Research, UK (Co-chair) Peng Yin (Co-chair) Harvard University, USA Luca Cardelli Microsoft Research, UK Hendrik Dietz Technical University of Munich, Germany David Doty California Institute of Technology, USA Shawn Douglas University of California, San Francisco, USA Andrew Ellington University of Texas at Austin, USA Elisa Franco University of California, Riverside and California Institute of Technology, USA Cody Geary Aarhus University, Denmark Kurt Gothelf Aarhus University, Denmark Natasha Jonoska University of South Florida, USA Lila Kari University of Western Ontario, Canada Ken Komiya Tokyo Institute of Technology, Japan Marta Kwiatkowska University of Oxford, UK Tim Liedl Ludwig Maximilian University of Munich, Germany Chengde Mao Purdue University, USA Pekka Orponen Aalto University, Finland Jennifer Padilla Boise State University, USA Matthew Patitz University of Arkansas, USA Lulu Qian California Institute of Technology, USA John Reif Duke University, USA Alfonso Universidad Politécnica de Madrid, Spain Rodríguez-Patón Yannick Rondelez University of Tokyo, Japan Rebecca Schulman Johns Hopkins University, USA David Soloveichik University of California, San Francisco Darko Stefanovic University of New Mexico, USA Chris Thachuk California Institute of Technology, USA Andrew Turberfield University of Oxford, UK Erik Winfree California Institute of Technology, USA Damien Woods California Institute of Technology, USA VIII Organization Organizing Committee William Shih Harvard University, USA (Co-chair) Peng Yin (Co-chair) Harvard University, USA Sungwook Woo Harvard University, USA Elena Chen Harvard University, USA Steering Committee Natasha Jonoska University of South Florida, USA (Chair) Luca Cardelli Microsoft Research, 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-Communications, 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 Technical University of Munich, Germany Andrew Turberfield University of Oxford, UK Hao Yan Arizona State University, USA Erik Winfree California Institute of Technology, USA Sponsoring Institutions Wyss Institute for Biologically Inspired Engineering, Harvard University Air Force Office of Scientific Research Army Research Office National Science Foundation Office of Naval Research Organization IX Additional Reviewers Angeli, David Gopinath, Ashwin Myhrvold, Cameron Barbot, Benoit Hendricks, Jacob Oishi, Kevin Beliveau, Brian Johnson, Robert F. Ong, Luvena Boemo, Michael Karamichalis, Rallis Paoletti, Nicola Ceska, Milan Karpenko, Daria Petersen, Rasmus Chen, Xi Kim, Jin-Woo Lerchedahl Clamons, Samuel Kim, Jongmin Rogers, Trent Condon, Anne Kopecki, Steffen Sainz de Murieta, Iñaki Dai, Mingjie Kulkarni, Manasi Schiefer, Nicholas Dannenberg, Frits Lakin, Matthew R. Seki, Shinnosuke de Los Santos, Liu, Ninning Srinivas, Niranjan Emmanuel Lorenzo Manuch, Jan Subramanian, Hari Ellis-Monaghan, Joanna McQuillan, Ian Summers, Scott Enaganti, Srujan Kumar Mohammed, Zandron, Claudio Evans, Constantine Abdul Majeed Gopalkrishnan, Nikhil Murphy, Niall Contents Dominance and T-Invariants for Petri Nets and Chemical Reaction Networks . 1 Robert Brijder Synthesizing and Tuning Chemical Reaction Networks with Specified Behaviours . 16 Neil Dalchau, Niall Murphy, Rasmus Petersen, and Boyan Yordanov Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model . 34 Nicholas Schiefer and Erik Winfree Reflections on Tiles (in Self-Assembly) . 55 Jacob Hendricks, Matthew J.
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