Lecture Notes in Computational Science and Engineering 68 Editors Timothy J. Barth Michael Griebel David E. Keyes Risto M. Nieminen Dirk Roose Tamar Schlick
Sidney Yip Tomás Diaz de la Rubia Editors Scientific Modeling and Simulations Previously published in Scientific Modeling and Simulations, Volume 15, Issues 1 3, 2008 123
Editors Sidney Yip Department of Nuclear Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge, MA 02139-4307 USA syip@mit.edu Tomás Diaz de la Rubia Lawrence Livermore National Laboratory University of California 7000 East Avenue P.O. Box 808 Livermore, CA 94551 USA delarubia@llnl.gov ISBN: 978-1-4020-9740-9 e-isbn: 978-1-4020-9741-6 Lecture Notes in Computational Science and Engineering ISSN 1439-7358 Library of Congress Control Number: 2009922358 Mathematics Subject Classification (2000): 65-01, 65P99, 35B27, 65R20, 70-08, 42C40, 76S05, 76T20 2009 Springer-Verlag Berlin Heidelberg 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, reuse of illustrations, recitation, broadcasting, reproduction on microfilm 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. Violations are liable for prosecution under the German Copyright Law. Cover illustration: cytoskeletal dynamics simulation of human red blood cell, 2007, reproduced with kind permission of Prof. Ju Li, University of Pennsylvania, USA. The use of general descriptive names, registered names, trademarks, 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. Cover design: deblik, Berlin Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com
Contents Advocacy of computational science (Editors preface) T.D. de la Rubia & S. Yip..................................... A retrospective on the journal of computer-aided materials design (JCAD), 1993 2007 S. Yip..................................................... Extrapolative procedures in modelling and simulations: the role of instabilities Characteristic quantities and dimensional analysis Accuracy of models Multiscale simulations of complex systems: computation meets reality E. Kaxiras & S. Succi........................................ Chemomechanics of complex materials: challenges and opportunities in predictive kinetic timescales K.J. Van Vliet.............................................. Tight-binding Hamiltonian from first-principles calculations C.-Z. Wang, W.-C. Lu, Y.-X. Yao, J. Li, S. Yip & K.-M. Ho.......... Atomistic simulation studies of complex carbon and silicon systems using environment-dependent tight-binding potentials C.-Z. Wang, G.-D. Lee, J. Li, S. Yip & K.-M. Ho.................. First-principles modeling of lattice defects: advancing our insight into the structure-properties relationship of ice M. de Koning.............................................. Direct comparison between experiments and computations at the atomic length scale: a case study of graphene J.W. Kysar................................................ 1 2 3 4 5 20 21 39 41 57 59 65 67 80 81 95 97 121 123 141 143 157
vi Shocked materials at the intersection of experiment and simulation H.E. Lorenzana, J.F. Belak, K.S. Bradley, E.M. Bringa, K.S. Budil, J.U. Cazamias, B. El-Dasher, J.A. Hawreliak, J. Hessler, K. Kadau, D.H. Kalantar, J.M. McNaney, D. Milathianaki, K. Rosolankova, D.C. Swift, M. Taravillo, T.W. Van Buuren, J.S. Wark & T.D. de la Rubia............................................ Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates M. Monteferrante, S. Bonella, S. Meloni, E. Vanden-Eijnden & G. Ciccotti................................................. Concurrent design of hierarchical materials and structures D.L. McDowell & G.B. Olson................................. Enthalpy landscapes and the glass transition J.C. Mauro, R.J. Loucks, A.K. Varshneya & P.K. Gupta............ Advanced modulation formats for fiber optic communication systems J.C. Mauro & S. Raghavan................................... Computational challenges in the search for and production of hydrocarbons J. Ullo.................................................... Microscopic mechanics of biomolecules in living cells F. Cleri................................................... Enveloped viruses understood via multiscale simulation: computer-aided vaccine design Z. Shreif, P. Adhangale, S. Cheluvaraja, R. Perera, R. Kuhn & P. Ortoleva................................................ Computational modeling of brain tumors: discrete, continuum or hybrid? Z. Wang & T.S. Deisboeck.................................... Contents 159 186 187 206 207 240 241 281 283 312 313 337 339 362 363 380 381 393