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.

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-Hückel 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.  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.