Forces, Growth and Form in Soft Condensed Matter: At the Interface between Physics and Biology NATO Science Series A Series presenting the results of scientific meetings supported under the NATO Science Programme. The Series is published by IOS Press, Amsterdam, and Kluwer Academic Publishers in conjunction with the NATO Scientific Affairs Division Sub-Series I. Life and Behavioural Sciences IOS Press II. Mathematics, Physics and Chemistry Kluwer Academic Publishers III. Computer and Systems Science IOS Press IV. Earth and Environmental Sciences Kluwer Academic Publishers V. Science and Technology Policy IOS Press The NATO Science Series continues the series of books published formerly as the NATO ASI Series. The NATO Science Programme offers support for collaboration in civil science between scientists of countries of the Euro-Atlantic Partnership Council. The types of scientific meeting generally supported are “Advanced Study Institutes” and “Advanced Research Workshops”, although other types of meeting are supported from time to time. The NATO Science Series collects together the results of these meetings. The meetings are co-organized bij scientists from NATO countries and scientists from NATO’s Partner countries – countries of the CIS and Central and Eastern Europe. Advanced Study Institutes are high-level tutorial courses offering in-depth study of latest advances in a field. Advanced Research Workshops are expert meetings aimed at critical assessment of a field, and identification of directions for future action. As a consequence of the restructuring of the NATO Science Programme in 1999, the NATO Science Series has been re-organised and there are currently Five Sub-series as noted above. Please consult the following web sites for information on previous volumes published in the Series, as well as details of earlier Sub-series. http://www.nato.int/science http://www.wkap.nl http://www.iospress.nl http://www.wtv-books.de/nato-pco.htm Series II: Mathematics, Physics and Chemistry–Vol. 160 Forces, Growth and Form in Soft Condensed Matter: At the Interface between Physics and Biology edited by A.T. Skjeltorp Institute for Energy Technology, Kjeller, Norway and Department of Physics, University of Oslo, Norway and A.V. Belushkin Frank Laboratory of Neutron Physics, Dubna, Russia KLUWER ACADEMIC PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW eBook ISBN: 1-4020-2340-5 Print ISBN: 1-4020-2338-3 ©2005 Springer Science + Business Media, Inc. Print ©2004 Kluwer Academic Publishers Dordrecht All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Springer's eBookstore at: http://ebooks.kluweronline.com and the Springer Global Website Online at: http://www.springeronline.com CONTENTS Preface vii Organizing committee and participants ix The physico-chemical basis of self-assembling structures 1 J. Israelachvili (invited) and I. Ladyzinski Supramolecular assembly of biological molecules 29 C.R. Safinya (invited) Simple examples of cell motility 51 J.-F. Joanny (invited) Statistical physics of unzipping DNA 65 D.R. Nelson (invited) Can theory predict two-state protein folding rates? An experimental perspective 93 B. Gillespie and K.W. Plaxco (invited) Copolymers with long-range correlations: Sequence design near a surface 113 N. Yu. Starovoitova, P.G. Khalatur and A.R. Khokhlov (invited) Novel approach to the study of rotational and translational diffusion in crystals 135 A.V. Belushkin (invited) The bacterial flagellar motor 145 R.M. Berry (invited) Self-assembly and dynamics of magnetic holes 165 A.T. Skjeltorp (seminar), J. Akselvoll, K. De Lange Kristiansen, G. Helgesen, R. Toussaint, E.G. Flekkøy and J. Cernak Structures in molecular networks 181 K. Sneppen (invited), S. Maslov and K.A. Eriksen Oscillating gene expressions in regulatory networks 195 M.H. Jensen (invited), K. Sneppen and T. Giana Transport properties of segmented polymers and non-spherical nanoparticles 203 studied by Brownian dynamics simulations S.N. Naess and A. Elgsaeter (invited) Cytokinesis: The initital linear phase crosses over to a multiplicity of non-linear 217 endings D. Biron, P. Libros, D. Sagi, D. Mirelman and E. Moses (invited) v vi Information dynamics in living systems 235 J. Breivik (seminar) Index 243 PREFACE This volume comprises the proceedings of a NATO Advanced Study Institute held at Geilo, Norway, 24 March - 3 April 2003, the seventeenth ASI in a series held every two years since 1971. The objective of this ASI was to identify and discuss areas where synergism between modern physics, soft condensed matter and biology might be most fruitful. The main pedagogical approach was to have lecturers focussing on basic understanding of important aspects of the relative role of the various interactions - electrostatic, hydrophobic, steric, conformational, van der Waals etc. Soft condensed matter and the connection between physics and biology have been the themes of several earlier Geilo Schools. A return to these subjects thus allowed a fresh look and a possibility for defining new directions for research. Examples of soft materials, which were discussed at this ASI, included colloidal dispersions, gels, biopolymers and charged polymer solutions, polyelectrolytes, protein/membrane complexes, nucleic acids and their complexes. Indeed, most forms of condensed matter are soft and these substances are composed of aggregates and macromolecules, with interactions that are too weak and complex to form crystals spontaneously. A characteristic feature is that small external forces, slight perturbations in temperature, pressure or concentration, can all be enough to induce significant structural changes. Thermal fluctuations are almost by definition strong in soft materials and entropy is a predominant determinant of structure, so that disorder, slow dynamics and plastic deformation are the rule. Hence the phrase ‘soft condensed matter’ has been coined. Of sheer necessity, soft materials have interested engineers for ages. They also form the basis of entire fields of science such as biology. However, only recently have physicists taken an interest in such materials, and attempted to implement what is the essence of physics, that is to produce simple models that contain the irreducible minimum information required to explain essential features. One of the reasons physicists has not been able to apply that type of reasoning to biology has been the lack of data of the right sort. Only with the advent of single molecule spectroscopies and techniques such as optical tweezers are we beginning to get quantitative data on things such as DNA elasticity, the motion of molecular motors, electron and proton transfer rates etc. that are sufficiently reliable to test simple models. The availability of new experimental tools and simulation capability is allowing physicists to apply their methods to areas of biology such as the prediction of structure on the basis of known microscopic forces. This is an active area of research in which new insights are constantly emerging. For example, much of the non-specific self-assembly activity in our cells are determined by electrostatics but in a way that cannot be predicted from simple mean field theory. Examples include DNA packaging, DNA transport across membranes, virus self-assembly and some stages of protein folding. A key issue is the fact that the media in which all of this happens have strong spatial variations in dielectric constant -- e.g. water and lipids. The difficulty of this whole area is epitomized by the fact that, until recently, we couldn’t even predict whether two DNA strands would attract or repel each other at close range. The starting point, and the underlying theme throughout the ASI, was a thorough discussion of the relative role of the various fundamental interactions in soft and biological matter systems (electrostatic, hydrophobic, steric, conformational, van der vii viii Waals, etc.). The next focus was on how these competing interactions influenced the form and topology of such systems, like polymers and proteins, leading to hierarchical structures in self-assembling systems and folding patterns sometimes described in terms of chirality, braids and knots. Finally, focus was also on how the competing interactions influence various bioprocesses like genetic regulation and biological evolution taking place in systems like biopolymers, macromolecules and cell membranes. The scientific content of the school was timely and these proceedings should provide a useful definition of the current status. The Institute brought together many lecturers, students and active researchers in the field from a wide range of countries, both NATO and NATO Partner Countries. The lectures fulfilled the aim of the Study Institute in creating a learning environment and a forum for discussion on the topics stated above. They were supplemented by a few contributed seminars and a large number of poster presentations. These seminars and posters were collected in extended abstract form and issued as an open report available at the Institute for Energy Technology, Kjeller, Norway (Report IFE/KR/E-2003/001). Financial support was principally from the NATO Scientific Affairs Division, but also from the Institute for Energy Technology, NORDITA in Copenhagen and the nationally coordinated research team COMPLEX in Norway. The editors are most grateful to J.O. Fossum, J. Hertz, M.H. Jensen, R. Pynn and H. Thomas who helped them plan the programme and G. Helgesen for helping with many practical details. Finally, we would like to express our deep gratitude to Else-Brit Jørgensen of the Institute for Energy Technology, for all her work and care for all the practical organization before, during, and after the school, including the preparation of these proceedings. June 2003 Arne T. Skjeltorp Alexander V. Belushkin LIST OF PARTICIPANTS Organizing Committee: Skjeltorp, Arne T., Director Institute for Energy Technology, POB 40, N-2027 Kjeller, Norway Belushkin, Alexander V., Co-director Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Moscow region, Russia Helgesen, Geir, Technical assistant Institute for Energy Technology, POB 40, N-2027 Kjeller, Norway Jørgensen, Else-Brit, Secretary Institute for Energy Technology, POB 40, N-2027 Kjeller, Norway Participants: Aharony, Amnon School of Physics and Astronomy, Tel Aviv University, 69978 Tel Aviv, Israel Almásy, László KFKI-SzFKI, POB 49, Budapest – 1525, Hungary Alvarez Lacalle, Enrique Departament ECM, Facultat de Fisica., Universitat de Barcelona, c/Marti i Franques 1 08028, Spain Amarie, Dragos Indiana University, Department of Physics, Swain Hall West 117, 727 E. 3rd Street, Bloomington, IN 47405-7105, USA Antunes, Filipe R. Virgílio Correia, lote 7, 3E, 3000 COIMBRA, Portugal Avdeev, Mikhail FLNP, JINR, 141980 Dubna, Moscow Reg., Russia Bakk, Audun Nordita, Blegdamsvej 17, DK-2100 København Ø, Denmark ix x Bergli, Joakim Departement d’Estructura i Constituents de la Materia, Facultat de Fisica, Av. Diagonal, 647, E-08028 Barcelona, Spain Berry, Richard Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom Bock Axelsen, Jacob Niels Bohr Institutet, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark Bogomolova, Eugenia V. Dept. of Botany, Biology & Soil Sciences Faculty, St.Petersburg State University, Universitetskaya emb. 7/9, 199034 St.Petersburg, Russia Bolhuis, Peter Dept of Chemical Engineering, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands Breivik, Jarle Section for Immunotherapy, Department of Immunology, The Norwegian Radium Hospital, 0310 Oslo, Norway Bruinsma, Robijn UCLA Department of Physics & Astronomy, Box 951547, Los Angeles, CA 90095- 1547, USA Bu, Huaitian Department of Chemistry, University of Oslo, P.O.Box 1033 Blindern, 0315 Oslo, Norway Buchanan, Mark Department of Complex Systems, Division of Physics and Astronomy, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands Buyukmurat, Yasemin Istanbul University, Science Faculty, Physics Department, Vezneciler, 34459, Istanbul, Turkey Campas, Otger Dept. Estructura i Constituents de la Materia, Facultat de Fisica, Universitat de Barcelona, Av. Diagonal, n° 647, E-08028, Barcelona, Spain