DNA Computing 9th International Workshop on DNA Based Computers, DNA

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Junghuei Chen John Reif (Eds.)

DNA Computing 9th International Workshop on DNA Based Computers, DNA9 Madison, WI, USA, June 1-3, 2003 Revised Papers

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Series Editors Gerhard Goos, Karlsruhe University, Germany Juris Hartmanis, Cornell University, NY, USA Jan van Leeuwen, Utrecht University, The Netherlands Volume Editors Junghuei Chen University of Delaware, Department of Chemistry and Biochemistry Newark, DE 19716, USA E-mail: [email protected] John Reif Duke University, Department of Computer Science Durham, NC 27708, USA E-mail: [email protected]

Cataloging-in-Publication Data applied for A catalog record for this book is available from the Library of Congress. Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the Internet at .

CR Subject Classification (1998): F.1, F.2.2, I.2.9, J.3 ISSN 0302-9743 ISBN 3-540-20930-1 Springer-Verlag Berlin Heidelberg New York This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer-Verlag. Violations are liable for prosecution under the German Copyright Law. Springer-Verlag is a part of Springer Science+Business Media springeronline.com c Springer-Verlag Berlin Heidelberg 2004  Printed in Germany Typesetting: Camera-ready by author, data conversion by DA-TeX Gerd Blumenstein Printed on acid-free paper SPIN: 10985632 06/3142 543210

Preface

Biomolecular computing is an interdisciplinary field that draws together molecular biology, DNA nanotechnology, chemistry, physics, computer science and mathematics. The annual international meeting on DNA-based computation has been an exciting forum where scientists of different backgrounds who share a common interest in biomolecular computing can meet and discuss their latest results. The central goal of this conference is to bring together experimentalists and theoreticians whose insights can calibrate each others’ approaches. The 9th Annual International Meeting on DNA Based Computers was held during June 1–4, 2003 in the University of Wisconsin, Madison, USA. The meeting had 106 registered participants from 12 countries around the world. On the first day of the meeting, we had three tutorials: the first was on self-assembly of DNA nano structures which focused on the basic techniques of using designed DNA nano molecules to be self-assembled onto larger structures for computational purposes. This tutorial was given by Hao Yan of Duke University. The second tutorial was given