Chemical Biophysics: Quantitative Analysis of Cellular Systems

Description

Chemical Biophysics provides an engineering-based approach to biochemical system analysis for graduate-level courses on systems biology, computational bioengineering and molecular biophysics. It is the first textbook to apply rigorous physical chemistry principles to mathematical and computational modeling of biochemical systems for an interdisciplinary audience. The book is structured to show the student the basic biophysical concepts before applying this theory to computational modeling and analysis, building up to advanced topics and research. Topics explored include the kinetics of nonequilibrium open biological systems, enzyme mediated reactions, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems. End-of-chapter exercises range from confidence-building calculations to computational simulation projects.

Daniel A. Beard is Associate Professor in the Department of Physiology, Biotechnology and Bioengineering Center, Medical College of Wisconsin. He researches nonequilibrium thermodynamics in biochemical networks. Hong Qian is Professor of Applied Mathematics in the University of Washington. His research interests span computational systems biology, molecular biophysics and mathematical biology and include stochastic analysis and statistical physics of biological systems.

'There are a growing number of physicists, engineers, mathematicians and chemists who are interested in joining the post-genomics party and addressing cutting-edge problems in molecular and cell biology. The barrier to entry can be high and prohibitive. This marvelous new book opens the door for the quantitively inclined. Beard and Qian, in an accessible and clear style, present fundamental methods that can be used to model and analyze an array of biomolecular systems and processes, ranging from enzyme kinetics to gene regulatory networks to cellular transport. This book will appeal to autodidacts as well as professors looking for course texts.' J. J. Collins, Professor of Biomedical Engineering and MacArthur Fellow, Boston University 'This is one of the most useful and readable accounts of biochemical thermodynamics that I have seen for a long time, if indeed ever. It is very definitely a book that I shall want to have on my shelves and to refer others to, because it contains a considerable amount of information not easy to find elsewhere.' Athel Cornish-Bowden, Directeur de Recherche, CNRS, Marseilles 'Dan Beard's and Hong Qian's Chemical Biophysics is a masterful portrayal of a critically important new area of science. The success of genomics now makes it imperative to understand the relationships between proteomics, biochemical systems behavior and the physiology of the intact animal or human. This book provides the path. Its clarity of description, making the complexities seem simple by adhering to fundamental principles, avoiding cluttering detail while painting the broad picture to great depth, makes it a pleasure to read and a treasure to study. It's a must for scientists and scholars working to understand integrative biology.' James B. Bassingthwaighte, Professor of Bioengineering, Biomathematics and Radiology at the University of Washington, Seattle 'This wonderful book will be indispensable to specialists in the fields of systems biology, biochemical kinetics, cell signaling, genetic circuits and quantitative aspects of biology, and also to undergraduate and graduate students. It presents a systematic approach to analyzing biochemical systems. The complex subjects are described in a clear style, with carefully crafted definitions and derivations. This unique book is an important step in the development and dissemination of systems biology approaches.' Aleksander S. Popel, Professor of Biomedical Engineering, Johns Hopkins University 'Chemical Biophysics: Quantitative Analysis of Cellular Systems by Daniel Beard and Hong Qian fills a significant niche. The text is a concise yet clear exposition of the fundamentals of chemical thermodynamics and kinetics, aimed specifically at practitioners of the new science of systems biology. It is marvellously illustrated with biochemical examples that will aid those who aim to analyze and model the workings of biological cells.' David Eisenberg, Director UCLA-DOE Institute for Genomics & Proteomics, University of California, Los Angeles, Investigator, Howard Hughes Medical Institute 'As computational biology moves into a more integrative and multi-scale phase, to provide the quantitative framework for linking the mass of experimental data generated by molecular techniques at the subcellular level to tissue and organ scale physiology, it is vitally important that models are based on quantitative approaches that incorporate, wherever possible, thermodynamically constrained biophysical mechanisms. This new book on the Chemical Biophysics of Cellular Processes by Dan Beard and Hong Qian does a wonderful job of formulating models for metabolic pathways, gene regulatory networks and protein interaction networks on the well-established principles of physical chemistry. Topics include enzyme catalyzed reactions, reaction-diffusion modelling, membrane transport, the chemical master equation and much more. This book will be of lasting value to computational biologists and bioengineers.' Professor Peter J Hunter, Auckland Bioengineering Institute at the University of Auckland 'Metabolic modeling often contain simplified assumptions to achieve convergence of their equations and these sometimes violate principles of solution physical chemistry. Readers of this remarkable monograph will no longer find those approaches satisfactory because Beard and Qian elucidate principles of kinetics and thermodynamics of electrolyte solutions relevant to metabolic modeling and computational biology. They show how these principles are essential for molecular modeling of cellular processes most of which involve ionized molecules and macromolecules in the cytoplasm. Their exposition is rigorous. The chapters have an enormous scope and depth that present clear derivations, explanations and examples. Beard and Qian set the bar very high for future metabolic modeling yet show how the details involved can be managed well and correctly. Analyses at this level of detail are necessary before more complex concepts of molecular crowding and intracellular compartmentalization can be considered. I expect this monograph will become a landmark in computational and systems biology and will be read thoroughly by all scholars in these fields.'Martin J. Kushmerick, Professor of Radiology, Bioengineering, Physiology and Biophysics at the University of Washington, Seattle