Rugged Free Energy Landscapes

This collection of lectures and tutorial reviews focuses on the common computational approaches in use to unravel the static and dynamical behaviour of complex physical systems at the interface of physics, chemistry and biology. Prominent consideration is given to rugged free-energy landscapes. The authors aim to provide a common basis and technical language for the (computational) technology transfer between the fields and systems considered.

This book covers the broad subject of equilibrium statistical mechanics along with many advanced and modern topics such as nucleation, spinodal decomposition, inherent structures of liquids and liquid crystals. Unlike other books on the market, this comprehensive text not only deals with the primary fundamental ideas of statistical mechanics but also covers contemporary topics in this broad and rapidly developing area of chemistry and materials science.

This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase. The book concentrates on RNA polymerases because they play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms. They have also been the subject of spectacular advances in their structural understanding in recent years, as testified by the attribution of the Nobel prize in chemistry in 2006 to Roger Kornberg. The book focuses on two aspects of the transcription cycle that have been more intensively studied thanks to this increased scientific cooperation - the recognition of the promoter by the enzyme, and the achievement of consecutive translocation steps during elongation of the RNA product. Each of these two topics is introduced by an overview, and is then presented by worldwide experts in the field, taking the viewpoint of their specialty. The overview chapters focus on the mechanism-structure interface and the structure-machine interface while the individual chapters within each section concentrate more specifically on particular processes-kinetic analysis, single-molecule spectroscopy, and termination of transcription, amongst others. Specific attention has been paid to the newcomers in the field, with careful descriptions of new emerging techniques and the constitution of an atlas of three-dimensional pictures of the enzymes involved.

Quantitative methods are revolutionizing modern molecular and cellular biology. Groundbreaking technical advances are fueling the rapid expansion in our ability to observe, as seen in multidisciplinary studies that integrate theory, computation, experimental assays, and the control of microenvironments. Integrating new experimental and theoretical methods, Quantitative Biology: From Molecular to Cellular Systems gives both new and established researchers a solid foundation for starting work in this field. The book is organized into three sections: Fundamental Concepts covers bold ideas that inspire novel approaches in modern quantitative biology. It offers perspectives on evolutionary dynamics, system design principles, chance and memory, and information processing in biology. Methods describes recently developed or improved techniques that are transforming biological research. It covers experimental methods for studying single-molecule biochemistry, small-angle scattering from biomolecules, subcellular localization of proteins, and single-cell behavior. It also describes theoretical methods for synthetic biology and modeling random variations among cells. Molecular and Cellular Systems focuses on specific biological systems where modern quantitative biology methods are making an impact. It incorporates case studies of biological systems for which new concepts or methods are increasing our understanding. Examples include protein kinase at the molecular level, the genetic switch of phage lambda at the regulatory system level, and Escherichia coli chemotaxis at the cellular level. In short, Quantitative Biology presents practical tools for the observation, modeling, design, and manipulation of biological systems from the molecular to the cellular levels.

Monte Carlo Simulation in Statistical Physics deals with the computer simulation of many-body systems in condensed-matter physics and related fields of physics, chemistry and beyond, to traffic flows, stock market fluctuations, etc.). Using random numbers generated by a computer, probability distributions are calculated, allowing the estimation of the thermodynamic properties of various systems. This book describes the theoretical background to several variants of these Monte Carlo methodsand gives a systematic presentation from which newcomers can learn to perform such simulations and to analyze their results. The fifth edition covers Classical as well as Quantum Monte Carlo methods. Furthermore a new chapter on the sampling of free energy landscapes has been added. To help students in their work a special web server has been installed to host programs and discussion groups (http://wwwcp.tphys.uni-heidelberg.de). Prof. Binder was the winner of the Berni J. Alder CECAM Award for Computational Physics 2001 as well as the Boltzmann Medal in 2007.

The aim of the workshop was to bring together specialists in various fields where non-exponential relaxation is observed in order to compare models and experimental results and to examine the general physical principles governing this type of behaviour. Non-exponential relaxation is found in extremely diverse physical systems all of which can be classified as complex. The form of the relaxation is generally parametrized using logarithmic, algebraic or stretched exponential decay forms. The conceptually simplest mechanism for the non-exponential decay is a spectrum of relaxation rates due to non-interacting units each of which relaxes with a different intrinsic time constant. Clear experimental examples can be given where for instance the relaxation of a collection of isolated polymer molecules leads to an overall stretched exponential decay. Non-exponential relaxation is observed in all strongly interacting complex systems (structural glasses, spin glasses, etc ... ) where each elementary unit is in interaction with many other units.

Nonequilibrium statistical mechanics (NESM), practically synonymous with time-dependent statistical mechanics (TDSM), is a beautiful and profound subject, vast in scope, diverse in applications, and indispensable in understanding the changing natural phenomena we encounter in the physical, chemical and biological world. Although time dependent phenomena have been studied from antiquity, the modern subject, the nonequilibrium statistical mechanics, has its genesis in Boltzmann’s 1872 classic paper that aimed at extending Maxwell’s kinetic theory of gases by including intermolecular interactions. Subsequent development of the subject drew upon the seminal work of Einstein and Langevin on Brownian motion, Rayleigh and Stokes on hydrodynamics, and on the works of Onsager, Prigogine, Kramers, Kubo, Mori, and Zwanzig. One major goal of this book is to develop and present NESM in an organized fashion so that students can appreciate and understand the flow of the subject from postulates to practical uses. This book takes the students on a journey from fundamentals to applications, mostly using simple mathematics, and fundamental concepts. With the advent of computers and computational packages and techniques, a deep intuitive understanding can allow the students to tackle fairly complex problems, like proteins in lipid membranes or solvation of ions in electrolytes used in batteries. The subject is still evolving rapidly, with forays into complex biological events, and materials science. Nonequilibrium Statistical Mechanics: An Introduction with Applications is, thus, an introductory text that aims to provide students with a background and skill essential to study and understand time-dependent (relaxation) phenomena. It will allow students to calculate transport properties like diffusion and conductivity. The book also teaches the methods to calculate reaction rate on a multi-dimensional energy surface, in another such application. For a beginner in the field, especially for one with an aim to study chemistry and biology, and also physics, one major difficulty faced is a lack of organization of the available study material. Since NESM is a vast subject with many different theoretical tools, the above poses a problem. This book lays the foundations towards understanding time- dependent phenomena in a simple and systematic fashion. It is accessible to students and researchers who have basic training in physics and mathematics. The book can be used to teach advanced undergraduates. Some involved topics, like the projection operator technique and mode coupling theory, are more suitable for Ph.D. level.

This book provides a unique insight into the latest breakthroughs in a consistent manner, at a level accessible to undergraduates, yet with enough attention to the theory and computation to satisfy the professional researcher Statistical physics addresses the study and understanding of systems with many degrees of freedom. As such it has a rich and varied history, with applications to thermodynamics, magnetic phase transitions, and order/disorder transformations, to name just a few. However, the tools of statistical physics can be profitably used to investigate any system with a large number of components. Thus, recent years have seen these methods applied in many unexpected directions, three of which are the main focus of this volume. These applications have been remarkably successful and have enriched the financial, biological, and engineering literature. Although reported in the physics literature, the results tend to be scattered and the underlying unity of the field overlooked.