Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge Texts in Biomedical Engineering) [Hardcover]

Daniel A. Beard (Author), Hong Qian (Author)

Book Description

ISBN-10: 0521870704 | ISBN-13: 978-0521870702 | Publication Date: July 7, 2008 | Edition: 1

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.

Editorial Reviews

Review

"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 quantitatively 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 marvelously 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 modeling, 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 modelings 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

"This work will help shift a reader's focus from a reductionist perspective to the broader approach of systems biology and the dynamic behavior that allows components of cells and organisms to come together to function properly."
J.A. Kelly, Choice

Book 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 modelling of biochemical systems for an interdisciplinary audience.

See all Editorial Reviews

Product Details

• Hardcover: 330 pages
• Publisher: Cambridge University Press; 1 edition (July 7, 2008)
• Language: English
• ISBN-10: 0521870704
• ISBN-13: 978-0521870702
• Product Dimensions: 9.8 x 6.8 x 0.9 inches
• Shipping Weight: 1.8 pounds (View shipping rates and policies)
• Average Customer Review: 5.0 out of 5 stars  See all reviews (3 customer reviews)
• Amazon Best Sellers Rank: #1,404,475 in Books (See Top 100 in Books)

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Most Helpful Customer Reviews

11 of 11 people found the following review helpful:

5.0 out of 5 stars A book that fills an important gap, November 23, 2008

By 

A. J. Cornish Bowden (Marseilles, France) - See all my reviews
(REAL NAME)   

This review is from: Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge Texts in Biomedical Engineering) (Hardcover)

Almost everybody finds classical thermodynamics difficult, and this has always been so: even the great physicists of the 19th century who created the subject had to struggle to understand it. It is not so much that the mathematics is so difficult: with a proper grounding in calculus, especially partial differentiation, one can understand the equations and their derivation easily enough in mathematical terms. On the other hand the qualitative ideas of statistical thermodynamics are not so difficult either. It is the effort relating these to the mathematics, and to classical thermodynamics (heat engines, Carnot cycles, etc.) that causes the eyes to glaze over.

Unfortunately, however, a training in thermodynamics is absolutely essential to chemistry and to the chemical underpinning of the biophysical analysis of cellular systems. Metabolism, for example, is not just a matter of listing all the chemical reactions; it is also a matter of knowing which ones will readily proceed and in what conditions. Determining all this involved a great deal of measurements in the 20th century on the equilibrium constants and other thermodynamic parameters of biochemical reactions. More than that, it involved understanding how the thermodynamic parameters of whole sequences of reactions depend on those of the individual processes, and how these depend on those of the component reactants.

Until now, however, textbooks that explain the principles of thermodynamics in the biochemical context have been few, a fewer still have been written in a way that students can be expected to understand. The new book of Daniel Beard and Hong Qian fills an important gap, therefore, and should be widely adopted in all departments where physical biochemistry is taught.

The first part of the book covers the basic concepts of thermodynamics, as far as possible using biologically relevant examples. Almost immediately the authors introduce the ideas that "in biology and chemistry we are usually not interested in the study of isolated systems", and that "biochemical processes occur in an aqueous environment". This brings us quite quickly to the idea that the Gibbs energy (not the entropy, and not the Helmholtz energy) is the quantity to consider in determining the thermodynamic driving force in a typical biochemical reaction. Likewise the stress is entirely on reactions in solutions, without the emphasis on gases (whether perfect or not) that tended to characterize textbooks in the past and to mystify raeders who wondered what perfect gases had to do with the sort of processes of primary concern in biology. This part of the book also deals with basic ideas of kinetics and transport.

In the second part the authors move on to the analysis and modelling of biochemical systems, the second part of which barely existed as a research topic twenty years ago but has in recent years become an essential component of systems biology. The relationship between enzyme mechanisms and reaction kinetics is explained briefly (as this is not a kinetics book) but thoroughly, and is followed by a chapter on control mechanisms and signalling, focussing on the properties such as zero-order ultrasensitivity and biochemical oscillations that are not possible for single enzymes but can emerge from interactions between several enzymes.

The last part of the book deals with several of what the authors call special topics, mainly ones that have been mentioned already but require a more profound and detailed treatment. A chapter, for example, is devoted to constraint-based analysis of biochemical systems -- the sort of modelling one can do when there is not enough information to set up an adequate kinetic model.

In summary (as I am quoted on the back cover as saying in my report to the publishers), this is one of the most useful and readable accounts of biochemical thermodynamics that I have seen for a long time, if indeed ever.

4 of 6 people found the following review helpful:

5.0 out of 5 stars A great book, December 22, 2008

By 

Deepak Nagrath (harvard, MA, USa) - See all my reviews
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This review is from: Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge Texts in Biomedical Engineering) (Hardcover)

I loved the book right from its first page to the last. Daniel and Hong have explained biophysics principle quantitatively in an easy to understand manner.

It is really a marvelous book. Essential for graduate students desiring to learn biophysical principles applied in cellular context.

Thank you Daniel and Hong for writing such a great book.

0 of 5 people found the following review helpful:

5.0 out of 5 stars Great, September 26, 2010

By 

Pat - See all my reviews

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This review is from: Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge Texts in Biomedical Engineering) (Hardcover)

The book as in very good or better condition. With the exception of a few very minor marks which were barely visible, the book was in perfect condition.