The Physical Basis of Biochemistry The Foundations of Molecular Biophysics

Grounds students in the basic principles of biochemistry and molecular biophysics Delves into the explosive developments in the area of genomics, and in turn, proteomics, bioinformatics, and computational and visualization technologies Emphasizes the interdisciplinary nature of biophysical chemistry Contains numerous problem sets and examples, and clear illustrations
The Physical Basis of Biochemistry is an introduction to the philosophy and practice of an interdisciplinary field in which biological systems are explored using the quantitative perspective of the physical scientist. As with the first edition, the idea that a fundamental understanding of the basic physical principles underlying chemical biological systems is vital remains the focus of this second edition. This new edition of The Physical Basis of Biochemistry has substantial new material added with respect to models at the simple molecular level (including van der Waals gases and virial treatments) which is tied to coverage of models of polymer thermo-dynamics. The second edition is partitioned into five sections: the central concept that science is a way of looking at the world; the physical under-pinnings of biophysical chemistry with an emphasis first on energy, work and forces of biological importance; exploring how models applicable to molecular biophysics are constructed; the three-dimensional potential energy surface put into motion; and a succinct discussion of the bio-physical methods used to evaluate structure and function in biological systems. Additionally, a section of appendices continues to serve the pur¬pose of presenting some review information and certain topics in detail. The Physical Basis of Biochemistry will be of interest to quantitatively-oriented biologists as well as aspiring chemists, physicists, and engineers with an interest in biological systems.

Table of contents

PREFACE PART I: Principles of Biophysical Inquiry Chapter 1 Introduction: “To the Student” Chapter 2 Philosophy and Practice of Biophysical Study Chapter 3 Overview of the Biological System Under Study – Descriptive Models Chapter 4 Physical Thoughts, Biological Systems - The application of modeling principles to understanding biological systems Chapter 5 Probability and Statistics PART II: Foundations Chapter 6 Physical Principles: Energy - The Prime Observable Chapter 7 Biophysical Forces in Molecular Systems Chapter 8 An Introduction to Quantum Mechanics Chapter 9 Chemical Principles Chapter 10 Measuring the Energy of a System: Energetics and the First Law of Thermodynamics Chapter 11 Entropy and the Second Law of Thermodynamics Chapter 12 Which Way Did That System Go? The Gibbs Free Energy Chapter 13 The Thermodynamics of Phase Equilibria PART III: Building a Model of Biomolecular Structure Chapter 14 Water: A Unique Structure, A Unique Solvent Chapter 15 Ion-Solvent Interactions Chapter 16 Ion-Ion Interactions Chapter 17 Lipids in Aqueous Solution Chapter 18 Macromolecules in Solution Chapter 19 Molecular Modeling - Mapping Biochemical State Space Chapter 20 The Electrified Interphase PART IV: Function and Action Biological State Space Chapter 21 Transport and Kinetics: Processes Not at Equilibrium Chapter 22 Flow in a Chemical Potential Field: Diffusion Chapter 23 Flow in an Electrical Field: Conduction Chapter 24 Forces Across Membranes Chapter 25 Kinetics - Chemical Kinetics Chapter 26 Bioelectrochemistry – Charge Transfer in Biological Systems PART V: Methods for the Measuring Structure and Function Chapter 27 Separation and Characterization of Biomolecules Based on Macroscopic Properties (with Kristin E. Bergethon) Chapter 28 Determining Structure by molecular interactions with photons: Electronic Spectroscopy (with Kristin Bergethon) Chapter 29 Determining Structure by molecular interactions with photons: Scattering Phenomena Chapter 30 Analysis of Structure – Microscopy Chapter 31 Epilogue Chapter 32 Physical Constants PART VI: APPENDICES Appendix A Review of Mathematical Methods Appendix B Quantum Electrodynamics Appendix C The Pre-Socratic Roots of Modern Science Appendix D The Poisson Function Appendix E Assumptions of a Kinetic Theory of Ideal Gas Behavior Appendix F Determination of a Field from the Potential Appendix G Geometric Optics Appendix H The Compton Effect Appendix I Hamilton's Principle of Least Action/Fermat's Principle of Least Time Appendix J Energy of Interaction between ions Appendix K Derivation of the Statement, Qrev > Qirrev Appendix L Derivation of the Clausius-Clapeyron Equation Appendix M Derivation of the van't Hoff Equation for Osmotic Pressure Appendix N Pseudoforces Appendix O Work of charging and discharging a rigid sphere Appendix P Review of Electrical Circuits Appendix Q Fermi's Golden Rule Appendix R Adiabatic vs non-Adiabatic processes

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