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
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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 Microsoft Research Cambridge UK Peng Yin Wyss Institute Boston, MA 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 biomolecular 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 submission 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 (Co-chair) Peng Yin (Co-chair) Luca Cardelli Hendrik Dietz David Doty Shawn Douglas Andrew Ellington Elisa Franco Cody Geary Kurt Gothelf Natasha Jonoska Lila Kari Ken Komiya Marta Kwiatkowska Tim Liedl Chengde Mao Pekka Orponen Jennifer Padilla Matthew Patitz Lulu Qian John Reif Alfonso Rodríguez-Patón Yannick Rondelez Rebecca Schulman David Soloveichik Darko Stefanovic Chris Thachuk Andrew Turberfield Erik Winfree Damien Woods Microsoft Research, UK Harvard University, USA Microsoft Research, UK Technical University of Munich, Germany University of California, San Francisco, USA University of Texas at Austin, USA University of California, Riverside and California Institute of Technology, USA Aarhus University, Denmark Aarhus University, Denmark University of South Florida, USA University of Western Ontario, Canada Tokyo Institute of Technology, Japan University of Oxford, UK Ludwig Maximilian University of Munich, Germany Purdue University, USA Aalto University, Finland Boise State University, USA University of Arkansas, USA Duke University, USA Universidad Politécnica de Madrid, Spain University of Tokyo, Japan Johns Hopkins University, USA University of California, San Francisco University of New Mexico, USA University of Oxford, UK
VIII Organization Organizing Committee William Shih (Co-chair) Peng Yin (Co-chair) Sungwook Woo Elena Chen Harvard University, USA Harvard University, USA Harvard University, USA Harvard University, USA Steering Committee Natasha Jonoska (Chair) Luca Cardelli Anne Condon Masami Hagiya Lila Kari Satoshi Kobayashi Chengde Mao Satoshi Murata John Reif Grzegorz Rozenberg Nadrian Seeman Friedrich Simmel Andrew Turberfield Hao Yan Erik Winfree University of South Florida, USA Microsoft Research, UK University of British Columbia, Canada University of Tokyo, Japan University of Western Ontario, Canada University of Electro-Communications, Japan Purdue University, USA Tohoku University, Japan Duke University, USA University of Leiden, The Netherlands New York University, USA Technical University of Munich, Germany University of Oxford, UK Arizona State University, 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 Barbot, Benoit Beliveau, Brian Boemo, Michael Ceska, Milan Chen, Xi Clamons, Samuel Condon, Anne Dai, Mingjie Dannenberg, Frits de Los Santos, Emmanuel Lorenzo Ellis-Monaghan, Joanna Enaganti, Srujan Kumar Evans, Constantine Gopalkrishnan, Nikhil Gopinath, Ashwin Hendricks, Jacob Johnson, Robert F. Karamichalis, Rallis Karpenko, Daria Kim, Jin-Woo Kim, Jongmin Kopecki, Steffen Kulkarni, Manasi Lakin, Matthew R. Liu, Ninning Manuch, Jan McQuillan, Ian Mohammed, Abdul Majeed Murphy, Niall Myhrvold, Cameron Oishi, Kevin Ong, Luvena Paoletti, Nicola Petersen, Rasmus Lerchedahl Rogers, Trent Sainz de Murieta, Iñaki Schiefer, Nicholas Seki, Shinnosuke Srinivas, Niranjan Subramanian, Hari Summers, Scott Zandron, Claudio
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. Patitz, and Trent A. Rogers Optimal Program-Size Complexity for Self-Assembly at Temperature 1 in3d... 71 David Furcy, Samuel Micka, and Scott M. Summers FlippingTiles:ConcentrationIndependentCoinFlipsinTileSelf-Assembly... 87 Cameron T. Chalk, Bin Fu, Alejandro Huerta, Mario A. Maldonado, Eric Martinez, Robert T. Schweller, and Tim Wylie New Geometric Algorithms for Fully Connected Staged Self-Assembly..... 104 Erik D. Demaine, Sándor P. Fekete, Christian Scheffer, and Arne Schmidt Leader Election and Shape Formation with Self-organizing Programmable Matter....................................... 117 Zahra Derakhshandeh, Robert Gmyr, Thim Strothmann, Rida Bazzi, Andréa W. Richa, and Christian Scheideler Leakless DNA Strand Displacement Systems....................... 133 Chris Thachuk, Erik Winfree, and David Soloveichik Supervised Learning in an Adaptive DNA Strand Displacement Circuit..... 154 Matthew R. Lakin and Darko Stefanovic Automated Design and Verification of Localized DNA Computation Circuits........................................ 168 Michael A. Boemo, Andrew J. Turberfield, and Luca Cardelli
XII Contents On Low Energy Barrier Folding Pathways for Nucleic Acid Sequences..... 181 Leigh-Anne Mathieson and Anne Condon Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands.............................................. 194 Joseph Malcolm Schaeffer, Chris Thachuk, and Erik Winfree Author Index... 213