Table Of ContentForces, Growth and Form in Soft Condensed
Matter: At the Interface between Physics and
Biology
NATO Science Series
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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
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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
