Molecular Modeling and Simulation An Interdisciplinary Guide

Science is a way of looking, reverencing. And the purpose of all science, like living, which amounts to the same thing, is not the ac­ cumulation of gnostic power, the fixing of formulas for the name of God, the stockpiling of brutal efficiency, accomplis

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S.S. Antman J .E. Marsden L. Sirovich S. Wiggins Geophysics and Planetary Seiences Mathematical Biology L. Glass, J.D. Murray Mechanics and Materials R.V. Kohn Systems and Control S.S. Sastry, P.S. Krishnaprasad

Problems in engineering, computational science, and the physical and biological sciences are using increasingly sophisticated mathematical techniques. Thus, the bridge between the mathematical sciences and other disciplines is heavily traveled. The correspondingly increased dialog between the disciplines has led to the establishment of the series: Interdisciplinary Applied Mathematics. The purpose of this series is to meet the current and future needs for the interaction between various science and technology areas on the one band and mathematics on the other. This is done, firstly, by encouraging the ways that mathematics may be applied in traditional areas, as well as point towards new and innovative areas of applications; and, secondly, by encouraging other scientific disciplines to engage in a dialog with mathematicians outlining their problems to both access new methods and suggest innovative developments within mathematics itself. The series will consist of monographs and high-level texts from researchers working on the interplay between mathematics and other fields of science and technology.

Interdisciplinary Applied Mathematics Volumes published are listed at the end of this book.

Springer Science+Business Media, LLC

Tamar Schlick

Molecular Modeling and Simulation An Interdisciplinary Guide

With 147 Full-Color Illustrations

Springer

Tamar Schlick Department of Mathematics and Chemistry Courant Institute of Mathematical Sciences New York University New York, NY 10012 USA [email protected] Editors J.E. Marsden L. Sirovich Control and Dynarnical Systems Division of Applied Mathematics Brown University Mail Code 107-81 Providence, RI 02912 California Institute of Technology USA Pasadena, CA 91125 chico @camelot.mssm.edu USA marsden @cds.caltech.edu S. Wiggins S.S. Antman Department of Mathematics School of Mathematics University of Bristol and Bristol, BS8 1TW Institute for Physical Science and Technology United Kingdom University of Maryland [email protected] College Park, MD 20742-4015 USA [email protected] Cover illustration: © Wayne Thiebaud/Licensed by VAGA, New York, NY. Courtesy of the Alian Stone Gallery, NYC.

Mathematics Subject Classification (2000): 92-01, 92Exx, 92C40 Library of Congress Cataloging-in-Publication Data Schlick, Tamar. Molecular modeling and simulation: an interdisciplinary guide 1 Tamar Schlick. p. cm.- (lnterdisciplinary applied mathematics ; 21) lncludes bibliographical references and index. ISBN 978-1-4757-5893-1 ISBN 978-0-387-22464-0 (eBook) DOI 10.1007/978-0-387-22464-0 1. Biomo1ecules-Models. 2. Biomolecules-Models-Computer simulation. 1. Title. Il. Interdisciplinary applied mathematics ; v. 21. QD480 .S37 2002 572'.33'015118-dc21 2002016003 ISBN 978-1-4757-5893-1 Printed on acid-free paper. © 2002 Springer Science+Business Media New York Originally publ