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 Chapman & Hall/CRC
Mathematical and Computational Biology Series

Computational Biology
A Statistical Mechanics Perspective
Second Edition

Ralf Blossey
Computational Biology
A Statistical Mechanics
Perspective
Second Edition
Computational Biology
A Statistical Mechanics
Perspective
Second Edition

Ralf Blossey
CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742

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Library of Congress Cataloging-in-Publication Data

Names: Blossey, Ralf, author.

Title: Computational biology : a statistical mechanics perspective /
Ralf Blossey.
Description: Second edition. | Boca Raton, Florida : CRC Press, [2020] |
Series: Chapman & Hall/CRC mathematical and computational biology |
Includes bibliographical references and index.
Identifiers: LCCN 2019011496| ISBN 9781138587861 (hbk : alk. paper) |
ISBN 9780429503672 (ebk)
Subjects: LCSH: Biomolecules--Mechanical properties. | Statistical
mechanics. | Computational biology.
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To SyMaNi and Mum
Contents

PREFACE TO THE SECOND EDITION ix

PREFACE TO THE FIRST EDITION xi

Part I Equilibrium Statistical Mechanics

Chapter 1  Equilibrium Statistical Mechanics 3

1.1 Z: THE PARTITION FUNCTION 3

1.2 RELATION TO THERMODYNAMICS 7
1.3 COMPUTING Z 13
1.4 THE ISING MODEL 15

Chapter 2  Biomolecular Structure: DNA, RNA, Proteins 39

2.1 DNA, RNA AND PROTEINS: THE BUILDING BLOCKS 39

2.2 REPRESENTING RNA STRUCTURE 47
2.3 COMPUTING RNA SECONDARY STRUCTURE:
COMBINATORICS 51
2.4 THE RNA PARTITION FUNCTION 55
2.5 PROTEIN FOLDING AND DOCKING 61
2.6 PULLING DNA 68

Chapter 3  Phase Transitions in RNA and DNA 83

3.1 RNA PHASE BEHAVIOUR 83

3.2 THE DNA MELTING TRANSITION 86
3.3 THE MELTING PROFILES OF GENOMIC DNA AND
CDNA 98

vii
viii  Contents

Chapter 4  Soft Matter Electrostatics 119

4.1 THE FREE ENERGY OF ELECTROSTATIC SYSTEMS 119

4.2 THE POISSON-BOLTZMANN EQUATION 122
4.3 PROTEIN ELECTROSTATICS 126
4.4 CHROMATIN ELECTROSTATICS 131

Part II Non-equilibrium Statistical Mechanics

Chapter 5  Back to P: Probabilities over Time 151

5.1 STOCHASTIC PROCESSES 152

5.2 THE MASTER EQUATION 155
5.3 THE FOKKER-PLANCK AND LANGEVIN EQUATIONS 163
5.4 SEQUENCE ALIGNMENT: A NON-EQUILIBRIUM PHASE
TRANSITION 176

Chapter 6  Fluctuation Theorems 191

6.1 THE FLUCTUATION-DISSIPATION THEOREM 191

6.2 THE JARZYNSKI EQUALITY AND CROOKS’
THEOREM 193
6.3 APPLICATIONS OF THE FLUCTUATION THEOREMS 195
Chapter 7  Dynamics of Biological Networks 207

7.1 THE λ-REPRESSOR 208

7.2 DYNAMICS OF GENE REGULATORY NETWORKS 216
7.3 INTRINSIC NOISE 226
Chapter 8  Biological Networks: Space 245

8.1 EXTRINSIC VS. INTRINSIC NOISE 245

8.2 THE TURING INSIGHT 249
8.3 NETWORKS AS GRAPHS 256
8.4 STATISTICAL MECHANICS OF NETWORKS 263
8.5 SMALL WORLDS 267

Index 281
Preface to the Second
Edition

I am grateful to the publisher who asked me to renew my book as a second

edition. Indeed, after more than ten years, the field of computational biol-
ogy/statistical physics—the particular interface of two fields I am interested
in—has matured in many ways. Going through the first edition again was a
great pleasure when comparing past views to current insights.

As a consequence, the book has substantially changed while maintaining its

core contents. New material has been added, but in particular I have reworked
its whole architecture. In the second edition, there are only two parts: one on
equilibrium statistical physics and one on non-equilibrium statistical physics.
The theoretical tools in these fields that the book introduces are placed at the
beginning of each part, and then the applications follow. I hope that this new
structure will help the readers to master the material.

As a side effect of following the now classic dichotomy of statistical physics—

equilibrium and non-equilibrium—the focus on universal aspects, those that
statistical physics is most attuned to, has been sharpened. Even more than
before, this makes the book not a biophysics book. Since 2006, when the first
edition went into print, new books on biophysics have appeared, especially
bioinformatics books.

I hope that with its modifications, including updated additional notes to the
literature and references, this book will continue to find its readership and
help to introduce its readers to this exciting field of research.

Lille, February 2019

Ralf Blossey

ix
Preface to the First
Edition

This is not a biophysics book.

The readers of this book will indeed find a number of topics in it which com-
monly classify as biophysics; an example is the discussion of the electrostatic
properties of biomolecules. But the book’s ambition is different from being yet
another introduction into biophysics. I therefore like to explain my motivation
for the selection of topics I made.

The title of the book establishes a link between computational biology on the
one side, and statistical mechanics on the other. Computational biology is
the name of a new discipline. It is probably fair to say that it is, in fact, an
emerging one, since a new name is not sufficient to establish a new discipline.
Quantitative methods have been applied to biological problems since many
years; this has led to a vast number of different subdisciplines of established
fields of science: there is a mathematical biology, a biomathematics, a bio-
statistics, a bioinformatics, a biophysics, a theoretical biology, a quantitative
biology... this list is certainly not exhaustive.

All these subdisciplines emerged out of the existing fields and developed by
an act of transfer: the use of a method or a mathematical approach within a
new context, its application to new problems. One may expect that at some
point in the future all these different subdisciplines may merge into a common
discipline. For the time being and for the lack of a definite name, let us call
this discipline computational biology.

This book wants to contribute a particular element to this field; the use of
statistical mechanics methods for the modelling of the properties of biologi-
cal systems. Statistical physics is the scientific discipline which was developed
in order to understand the properties of matter composed of many particles.
Traditionally, it has been applied to non-living matter: gases, liquids, and
solids. Meanwhile, it is increasingly applied to what is nowadays called “soft

xi
xii  Preface to the First Edition

matter” which encompasses complex objects like colloids, membranes, and

biomolecules, hence objects which do not clearly fall into any one of the clas-
sic categories.

Statistical mechanics methods are therefore indeed essential in their applica-

tion to biophysical problems, since they are needed to understand the static
and dynamic properties of biomolecules, complex molecular machines, and
even whole cell behaviour.

But there is a second aspect for which these methods can prove important,
and this relates to the information content of the biological systems. Biology
is built on recognition processes: DNA strands have to recognize each other,
proteins have to identify DNA binding sites, etc. In bioinformatics, these recog-
nition problems are commonly modelled as pattern recognition problems: this
mapping is the basis of the enormous success of the field of modern genomics.

Moving beyond genomics, however, to the biology of whole systems, it be-

comes increasingly clear that an understanding of the physical properties of
biological systems becomes more and more important for processes involving
biological information content: DNA is not merely a string spelled out in a
four-letter alphabet, but it is also an elastic string. There is biological infor-
mation contained in its structure and its dynamics. Biology employs physical
mechanisms to organize its information processes. This becomes particularly
evident, as we begin to understand, in the properties of chromatin, the DNA-
protein complex making up the chromosomes in the nucleus of eukaryotic cells
(a topic which is discussed in the book), or, in the particle interaction net-
works upon which the cellular machinery relies.

This book is placed at just this interface: between biological recognition on

the one hand, and the statistical physics methods that can be employed to
understand the underlying mechanisms.

The first part of the book gives a concise introduction into the main concepts
of statistical mechanics, equilibrium, and non-equilibrium. The exposition is
introductory in the choice of topics addressed, but still mathematically chal-
lenging. Whenever possible, I have tried to illustrate the methods with simple
examples.

The second part of the book is devoted to biomolecules, to DNA, RNA, pro-
teins, and chromatin, i.e., the progression of topics follows more or less what
is commonly known as the central dogma of molecular biology. In this part,
mostly equilibrium statistical mechanics is needed. The concern here is to
understand and model the processes of base-pair recognition and (supra-)
molecular structure formation.
 Preface to the First Edition  xiii

The third part of the book is devoted to biological networks. Here, both equi-
librium and non-equilibrium concepts introduced in the first part are used.
The presentation covers several of the non-equilibrium statistical physics ap-
proaches described in Chapter 2 of Part I, and illustrates them on biologically
motivated and relevant model systems.

Throughout the book, Exercises and Tasks are scattered, most of them in the
first part. They are intended to motivate the readers to participate actively
in the topics of the book. The distinction between Exercises and Tasks is the
following: Exercises should be done in order to verify that the concept that
was introduced has been understood. Tasks are more ambitious and usually
require either a more involved calculation or an additional idea to obtain the
answer.

A final technical note: the book is complemented by a detailed key word list.
Key words listed are marked in italics throughout the text.

In the course of shaping the idea of this book and writing it, I profited from
discussions with many colleagues. I am especially thankful to Arndt Benecke,
Dennis Bray, Martin Brinkmann, Luca Cardelli, Enrico Carlon, Avi Halperin,
Andreas Hildebrandt, Martin Howard, Oliver Kohlbacher, Hans Meinhardt,
Thomas Lengauer, Hans-Peter Lenhof, Annick Lesne, Ralf Metzler, Johan
Paulsson, Andrew Phillips, Wilson Poon, Helmut Schiessel, Bernard Vanden-
bunder, Jean-Marc Victor, Pieter Rein ten Wolde, Edouard Yeramian.

Finally, I would particularly like to thank Andreas Hildebrandt and Mar-

tin Howard for their detailed and helpful remarks on an early version of the
manuscript.

I gratefully acknowledge the hospitality of the Institut d’Électronique, de Mi-

croélectronique et de Nanotechnologie (IEMN) in Villeneuve d’Ascq and the
Institut des Hautes Études in Bures-sur-Yvette, where parts of this book were
written.

Lille, 2006
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