Modern methods for theoretical physical chemistry of biopolymers evgeni starikov et al (elsevier, 2006)

Modern Methods for Theoretical Physical Chemistry of Biopolymers by Evgeni Starikov (Editor), James P Lewis (Editor), Shigenori Tanaka (Editor) • • • Pub Date: August 2006 ISBN: 0444522204 Publisher: Elsevier Science & Technology Books List of Contributors Shinji Amari Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan J F R Archilla Group of Nonlinear Physics, Departamento de Física Aplicada I, ETSI Informática, University of Sevilla, Avda Reina Mercedes, s/n 41012, Sevilla, Spain David N Beratan Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708, U.S.A F Matthias Bickelhaupt Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands Johan Bredenberg Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry, Hälsovägen 7, SE-141 57 Huddinge, Sweden Ralf Bulla Theoretische Physik III, Universität Augsburg, D-86135, Augsburg, Germany Arrigo Calzolari National Centre on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, c/o Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy Hiroshi Chuman Institute of Health Biosciences, University of Tokushima, Tokushima, 770-8505, Japan Peter Claiden Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ, UK Daniel L Cox Department of Physics, University of California, Davis, CA 95616, U.S.A v vi List of Contributors Tobias Cramer Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany Jane Crawshaw Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ, UK Gianaurelio Cuniberti Institut für Theoretische Physik Korrelationen und Magnetismus, Universität Regensburg, D-93040, Regensburg, Germany Martin Dahlberg Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91, Stockholm, Sweden Owen R Davies School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3YB, UK James Elliott Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ, UK Robert G Endres Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, U.S.A; and NEC Laboratories America, Inc., Princeton, NJ 08540 U.S.A Dmitri G Fedorov National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, 305-8568 Ibaraki, Japan Rosa Di Felice National Centre on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, c/o Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy B Fischer Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany Kaori Fukuzawa Division of Science and Technology, Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan; and CREST, Japan Science and Technology Agency (JST), Japan List of Contributors vii Yi Qin Gao Department of Chemistry, Texas A&M University, College Station, TX 77845, U.S.A Heather L Gordon Department of Chemistry and Centre for Biotechnology, Brock University, St Catharines, Ontario, L2S 3A1, Canada Hitoshi Goto Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan Célia Fonseca Guerra Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands Rafael Gutierrez Institut für Theoretische Physik Korrelationen und Magnetismus, Universität Regensburg, D-93040, Regensburg, Germany Michiaki Hamada Mizuho Information and Research Institute, Inc., Tokyo, 101-8443, Japan D Hennig Freie Universität Berlin, Fachbereich Physik, Institut für Theoretische Physik, Arnimallee 14, 14195 Berlin, Germany Arnd Hübsch Department of Physics, University of California, Davis, CA 95616, U.S.A Yuichi Inadomi Grid Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan Yuichiro Inagaki Mizuho Information and Research Institute, Inc., Tokyo, 101-8443, Japan John E Inglesfield School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3YB, UK Masakatsu Ito Grid Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan viii List of Contributors Toshiyuki Kamakura Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan Martin Karplus Deparment of Chemistry and Chemical Biology, Harvard University, MA 02138, U.S.A; and Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000 Strasbourg, France Kazuo Kitaura National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, 305-8568 Ibaraki, Japan Thorsten Koslowski Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany Petras J Kundrotas Department of Biosciences at Novum Research Park, Karolinska Institutet, SE-141 57 Huddinge, Sweden Noriyuki Kurita Department of Knowledge-Based Information Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan Aatto Laaksonen Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91, Stockholm, Sweden Victor D Lakhno Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation K H Lee Korean Institute for Science and Technology, Supercomputing Materials Laboratory, P.O Box 131, Cheongryang, Seoul 130-650, Korea J P Lewis Department of Physics and Astronomy, Brigham Young University, Provo, UT 846024658, U.S.A Jianping Lin Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708, U.S.A List of Contributors ix Raimo A Lohikoski University of Jyväskylä, Department of Physics, FIN - 40014 University of Jyväskylä, Finland Pekka Mark Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry, Hälsovägen 7, SE-141 57 Huddinge, Sweden R Marsh Department of Physics and Astronomy, Brigham Young University, Provo, UT 846024658, U.S.A H Merlitz Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany Yuji Mochizuki Advancesoft and Institute of Industrial Science, Center for Collaborative Research, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; and CREST, Japan Science and Technology Agency (JST), Japan; Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan Umpei Nagashima Grid Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan Yoshihiro Nakajima Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan Tatsuya Nakano Division of Safety Information on Drug, Food and Chemicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 1538904, Japan; and CREST, Japan Science and Technology Agency (JST), Japan Naofumi Nakayama Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan Takayuki Natsume Department of Knowledge-Based Information Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan x List of Contributors Lennart Nilsson Department of Biosciences at NOVUM, Center for Structural Biochemistry, Karolinska Institutet, S-141 57 Huddinge, Sweden; Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry, Hälsovägen 7, SE-141 57 Huddinge, Sweden Takeshi Nishikawa Grid Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8561, Japan Sigeaki Obata Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Toyohashi, 441-8580, Japan Miroslav Pinak Japan Atomic Energy Agency, Shirakata, Shirane 2-4, 319-1195 Tokai, Japan Dragan M Popovic Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, U.S.A Jason Quenneville Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, U.S.A Aina Quintilla Research Center Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe, Germany R A Römer Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, U.K Stuart M Rothstein Departments of Chemistry and Physics, Brock University, St Catharines, Ontario, L2S 3A1, Canada Mitsuhisa Sato Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan Matthias Schmitz Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstraße 67, 80538 München, Germany List of Contributors xi A Schug Forschungszentrum Karlsruhe, Institute for Nanotechnology, P.O Box 3640, D-76021 Karlsruhe, Germany Yasuo Sengoku Department of Knowledge-Based Information Engineering, Toyohashi University of Technology, Toyohashi, Aichi 441-8580, Japan Rajiv R P Singh Department of Physics, University of California, Davis, CA 95616, U.S.A Spiros S Skourtis Department of Physics, University of Cyprus, Nicosia 1678, Cyprus Evgeni B Starikov Department of Chemistry, Freie Universität Berlin, Germany; Department of Structural Biology at NOVUM, Karolinkska Institute, Huddinge, Sweden; and Research Center Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe, Germany Alexei A Stuchebrukhov Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, U.S.A Shigenori Tanaka Graduate School of Science and Technology, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan; and CREST, Japan Science and Technology Agency (JST), Japan Paul Tavan Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstraße 67, 80538 München, Germany Nadine Utz Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany A Verma Forschungszentrum Karlsruhe, Institute for Scientific Computing, P.O Box 3640, D-76021 Karlsruhe, Germany Alexander A Voityuk Instituciú Catalana de Recerca i Estudis Avanỗats, Institute of Computational Chemistry, Universitat de Girona, 17071 Girona, Spain xii List of Contributors H Wang Department of Physics and Astronomy, Brigham Young University, Provo, UT 846024658, U.S.A Toshio Watanabe Grid Technology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan Wolfgang Wenzel Research Center Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe, Germany; Forschungszentrum Karlsruhe, Institute for Nanotechnology, P.O Box 3640, D-76021 Karlsruhe, Germany Alan Windle Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ, UK Wei Yang Deparment of Chemistry and Chemical Biology, Harvard University, MA 02138, U.S.A ... results Ewgeni B Starikov Shigenori Tanaka James P Lewis © 2006 Elsevier B.V All rights reserved Modern Methods for Theoretical Physical Chemistry of Biopolymers Edited by E.B Starikov, J.P Lewis... currently available theoretical methods Bengt Nordén President of the Fourth Class (Chemistry) of the Royal Swedish Academy of Sciences and former Chairman of its Nobel Committee for Chemistry Preface.. .Modern Methods for Theoretical Physical Chemistry of Biopolymers by Evgeni Starikov (Editor), James P Lewis (Editor), Shigenori Tanaka