Free Energy Calculations


Book Description

Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.




Introducing Biological Energetics


Book Description

This novel, interdisciplinary text presents biological understanding in terms of general underlying principles, treating energy as the overarching theme and emphasizing the all-pervading influence of energy transformation in every process, both living and non-living. Key processes and concepts are explained in turn, culminating in a description of the overall functioning and regulation of a living cell. The book rounds off the story of life with a brief account of the endosymbiotic origins of eukaryotic cells, the development of multicellularity, and the emergence of modern plants and animals. Multidisciplinary research in science is becoming commonplace. However, as traditional boundaries start to break down, researchers are increasingly aware of the deficiencies in their knowledge of related disciplines. Introducing Biological Energetics redresses the reciprocal imbalance in the knowledge levels of physical and biological scientists in particular. Its style of presentation and depth of treatment has been carefully designed to unite these two readerships.




Introduction to Biomolecular Energetics


Book Description

Introduction to Biomolecular Energetics Including Ligand-Receptor Interactions focuses on the concepts of energetics and their biological applications, including the study of ligand-receptor interactions. The book provides quantitative calculations and addresses topics that have become more prominent in the biochemical and related sciences in recent years, including the first and second laws of thermodynamics, the concept of entropy, free energy or chemical potential, group-transfer potential, physicochemical behavior, and enzyme kinetics. This volume is organized into 10 chapters, and it begins with an overview of the scope of energetics and two general approaches to the field: the classical or phenomenological approach and the statistical-molecular approach. The chapters that follow explore the concepts of energy and entropy in the context of the first and second laws of thermodynamics, along with the relationships between work, heat, energy and entropy as an index of exhaustion. The discussion then shifts to the free energy function and general procedures for computing standard free energies. The book also introduces the reader to the fundamental relationship between chemical potential (free energy) and concentration; high-energy bond and the concept of group-transfer potential; the use of thermodynamic methods in the analysis of physicochemical behavior; and statistical thermodynamics. The final chapter examines the number of ligands that are bound by the receptor entity, how strongly the ligands are held, and the molecular nature of the forces of ligand-receptor interaction. This book will be of interest to biologists and those who want to understand the principles of energetics governing biochemical changes.




Foundations of Bioenergetics


Book Description

Foundations of Bioenergetics provides an introduction to the physical foundations of bioenergetics and the methods of applying these constructs to biological problems. It combines parts of thermal physics, biochemistry, ecology, and cellular and organismic biology into a single coherent work. Much of the material in this volume comes from ""Entropy for Biologists,"" an introductory thermodynamics book aimed particularly at life scientists. Some of the topics originally appeared in the monograph ""Energy Flow in Biology."" The current volume expands on that material with respect to biological applications and attempts to bridge the gap between physics and biology. The book explains basic concepts such as energy, temperature, the second law of thermodynamics, entropy, information theory, and statistical mechanics. It discusses the relations between thermodynamics and statistical mechanics, free-energy functions, radiant energy, the free energy of cells and tissue, chemical kinetics, and cyclic flows. It examines the relationships between energy flows and biological processes; applications of the concepts of Gibbs free energy, chemical potential, and activity; and measurements of temperature, energy, and thermochemical quantities. The book also includes chapters that deal with irreversible dynamics, irreversible theory, and osmotic flow.




Energy Flow in Biology


Book Description







Principles of Energetics


Book Description

The purpose of this book is to lay the groundwork for the analysis and the design of processes with a view to energetic efficiency. Energetics is used in the original sense of the engineer W. J. M. Rankine (Proc. Roy. Philosoph. Soc. of Glasgow III, 381 [1955]) and the physical chemist J. N. Br\3nsted (Principles and Problems in Energetics, Interscience, New York, 1955), i.e., the macroscopic description of the flows of different forms of energy, and the general laws governing the mutual transforma tions of these flows. The prerequisite for the use of the book is a conventional course in equilibrium thermodynamics as usually taken in the junior (third) col lege year. The author believes that while knowledge about equilibria is essential, most engineers and many scientists are mostly interested in systems in which equilibrium has not yet been reached. In such systems, flow phenomena such as heat, mass and electricity transfer, as well as chemical reactions, can take place, and it is important to know the driv ing forces and laws governing the interactions of these flows.