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Computational biology has developed rapidly during the last two
decades following the genomic revolution which culminated in the
sequencing of the human genome. More than ever it has developed
into a field which embraces computational methods from different
branches of the exact sciences: pure and applied mathematics,
computer science, theoretical physics. This Second Edition provides
a solid introduction to the techniques of statistical mechanics for
graduate students and researchers in computational biology and
biophysics. Material has been reorganized to clarify equilbrium and
nonequilibrium aspects of biomolecular systems Content has been
expanded, in particular in the treatment of the electrostatic
interactions of biomolecules and the application of non-equilibrium
statistical mechanics to biomolecules New network-based approaches
for the study of proteins are presented. All treated topics are put
firmly in the context of the current research literature, allowing
the reader to easily follow an individual path into a specific
research field. Exercises and Tasks accompany the presentations of
the topics with the intention of enabling the readers to test their
comprehension of the developed basic concepts.
An invaluable resource for computational biologists and researchers
from other fields seeking an introduction to the topic, Chromatin:
Structure, Dynamics, Regulation offers comprehensive coverage of
this dynamic interdisciplinary field, from the basics to the latest
research. Computational methods from statistical physics and
bioinformatics are detailed whenever possible without lengthy
recourse to specialized techniques.
This book is a treatise on the thermodynamic and dynamic properties
of thin liquid films at solid surfaces and, in particular, their
rupture instabilities. For the quantitative study of these
phenomena, polymer thin films (sometimes referred to as
"ultrathin") have proven to be an invaluable experimental model
system. What is it that makes thin film instabilities special and
interesting? First, thin polymeric films have an important range of
applications. An understanding of their instabilities is therefore
of practical relevance for the design of such films. The first
chapter of the book intends to give a snapshot of current
applications, and an outlook on promising future ones. Second, thin
liquid films are an interdisciplinary research topic, which leads
to a fairly heterogeneous community working on the topic. It
justifies attempting to write a text which gives a coherent
presentation of the field which researchers across their
specialized communities might be interested in. Finally, thin
liquid films are an interesting laboratory for a theorist to
confront a well-established theory, hydrodynamics, with its limits.
Thin films are therefore a field in which a highly fruitful
exchange and collaboration exists between experimentalists and
theorists. The book stretches from the more concrete to more
abstract levels of study: we roughly progress from applications via
theory and experiment to rigorous mathematical theory. For an
experimental scientist, the book should serve as a reference and
guide to what is the current consensus of the theoretical
underpinnings of the field of thin film dynamics. Controversial
problems on which such a consensus has not yet been reached are
clearly indicated in the text, as well as discussed in a final
chapter. From a theoretical point of view, the field of dewetting
has mainly been treated in a mathematically 'light' yet elegant
fashion, often making use of scaling arguments. For the untrained
researcher, this approach is not always easy to follow. The present
book attempts to bridge between the 'light' and the 'rigorous',
always with the ambition to enhance insight and understanding - and
to not let go the elegance of the theory.
Quantitative methods have a particular knack for improving any
field they touch. For biology, computational techniques have led to
enormous strides in our understanding of biological systems, but
there is still vast territory to cover. Statistical physics
especially holds great potential for elucidating the
structural-functional relationships in biomolecules, as well as
their static and dynamic properties. Breaking New Ground
Computational Biology: A Statistical Mechanics Perspective is the
first book dedicated to the interface between statistical physics
and bioinformatics. Introducing both equilibrium and nonequilibrium
statistical mechanics in a manner tailored to computational
biologists, the author applies these methods to understand and
model the properties of various biomolecules and biological
networks at the systems level. Unique Vision, Novel Approach
Blossey combines his enthusiasm for uniting the fields of physics
and computational biology with his considerable experience,
knowledge, and gift for teaching. He uses numerous examples and
tasks to illustrate and test understanding of the concepts, and he
supplies a detailed keyword list for easy navigation and
comprehension. His approach takes full advantage of the latest
tools in statistical physics and computer science to build a strong
set of tools for confronting new challenges in computational
biology. Making the concepts crystal clear without sacrificing
mathematical rigor, Computational Biology: A Statistical Mechanics
Perspective is the perfect tool to broaden your skills in
computational biology.
Computational biology has developed rapidly during the last two
decades following the genomic revolution which culminated in the
sequencing of the human genome. More than ever it has developed
into a field which embraces computational methods from different
branches of the exact sciences: pure and applied mathematics,
computer science, theoretical physics. This Second Edition provides
a solid introduction to the techniques of statistical mechanics for
graduate students and researchers in computational biology and
biophysics. Material has been reorganized to clarify equilbrium and
nonequilibrium aspects of biomolecular systems Content has been
expanded, in particular in the treatment of the electrostatic
interactions of biomolecules and the application of non-equilibrium
statistical mechanics to biomolecules New network-based approaches
for the study of proteins are presented. All treated topics are put
firmly in the context of the current research literature, allowing
the reader to easily follow an individual path into a specific
research field. Exercises and Tasks accompany the presentations of
the topics with the intention of enabling the readers to test their
comprehension of the developed basic concepts.
An invaluable resource for computational biologists and researchers
from other fields seeking an introduction to the topic, Chromatin:
Structure, Dynamics, Regulation offers comprehensive coverage of
this dynamic interdisciplinary field, from the basics to the latest
research. Computational methods from statistical physics and
bioinformatics are detailed whenever possible without lengthy
recourse to specialized techniques.
This brief book introduces the Poisson-Boltzmann equation in three
chapters that build upon one another, offering a systematic entry
to advanced students and researchers. Chapter one formulates the
equation and develops the linearized version of Debye-HĂźckel
theory as well as exact solutions to the nonlinear equation in
simple geometries and generalizations to higher-order
equations.   Chapter two introduces the
statistical physics approach to the Poisson-Boltzmann equation. It
allows the treatment of fluctuation effects, treated in the loop
expansion, and in a variational approach. First applications are
treated in detail: the problem of the surface tension under the
addition of salt, a classic problem discussed by Onsager and
Samaras in the 1930s, which is developed in modern terms within the
loop expansion, and the adsorption of a charged polymer on a
like-charged surface within the variational approach.Â
Chapter three finally discusses the extension of Poisson-Boltzmann
theory to explicit solvent. This is done in two ways: on the
phenomenological level of nonlocal electrostatics and with a
statistical physics model that treats the solvent molecules as
molecular dipoles. This model is then treated in the mean-field
approximation and with the variational method introduced in Chapter
two, rounding up the development of the mathematical approaches of
Poisson-Boltzmann theory. After studying this book, a
graduate student will be able to access the research literature on
the Poisson-Boltzmann equation with a solid background.Â
This book is a treatise on the thermodynamic and dynamic properties
of thin liquid films at solid surfaces and, in particular, their
rupture instabilities. For the quantitative study of these
phenomena, polymer thin films (sometimes referred to as ultrathin )
have proven to be an invaluable experimental model system.
What is it that makes thin film instabilities special and
interesting? First, thin polymeric films have an important range of
applications. An understanding of their instabilities is therefore
of practical relevance for the design of such films. The first
chapter of the book intends to give a snapshot of current
applications, and an outlook on promising future ones. Second, thin
liquid films are an interdisciplinary research topic, which leads
to a fairly heterogeneous community working on the topic. It
justifies attempting to write a text which gives a coherent
presentation of the field which researchers across their
specialized communities might be interested in. Finally, thin
liquid films are an interesting laboratory for a theorist to
confront a well-established theory, hydrodynamics, with its limits.
Thin films are therefore a field in which a highly fruitful
exchange and collaboration exists between experimentalists and
theorists. The book stretches from the more concrete to more
abstract levels of study: we roughly progress from applications via
theory and experiment to rigorous mathematical theory. For an
experimental scientist, the book should serve as a reference and
guide to what is the current consensus of the theoretical
underpinnings of the field of thin film dynamics. Controversial
problems on which such a consensus has not yet been reached are
clearly indicated in the text, as well as discussed in a final
chapter. From a theoretical point of view, the field of dewetting
has mainly been treated in a mathematically light yet elegant
fashion, often making use of scaling arguments. For the untrained
researcher, this approach is not always easy to follow. The present
book attempts to bridge between the light and the rigorous, always
with the ambition to enhance insight and understanding - and to not
let go the elegance of the theory.
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