The Physical Basis of Biochemistry

PREFACE

PART I: Principles of Biophysical Inquiry
Chapter 1Introduction: “To the Student”
Chapter 2Philosophy and Practice of Biophysical Study
Chapter 3Overview of the Biological System Under Study – Descriptive Models
Chapter 4Physical Thoughts, Biological Systems - The application of modeling principles to understanding biological systems
Chapter 5Probability and Statistics

PART II: Foundations
Chapter 6Physical Principles: Energy - The Prime Observable
Chapter 7Biophysical Forces in Molecular Systems
Chapter 8An Introduction to Quantum Mechanics
Chapter 9Chemical Principles
Chapter 10Measuring the Energy of a System: Energetics and the First Law of Thermodynamics
Chapter 11Entropy and the Second Law of Thermodynamics
Chapter 12Which Way Did That System Go? The Gibbs Free Energy
Chapter 13The Thermodynamics of Phase Equilibria

PART III: Building a Model of Biomolecular Structure
Chapter 14Water: A Unique Structure, A Unique Solvent
Chapter 15Ion-Solvent Interactions
Chapter 16Ion-Ion Interactions
Chapter 17Lipids in Aqueous Solution
Chapter 18Macromolecules in Solution
Chapter 19Molecular Modeling - Mapping Biochemical State Space
Chapter 20The Electrified Interphase

PART IV: Function and Action Biological State Space
Chapter 21Transport and Kinetics: Processes Not at Equilibrium
Chapter 22Flow in a Chemical Potential Field: Diffusion
Chapter 23Flow in an Electrical Field: Conduction
Chapter 24Forces Across Membranes
Chapter 25Kinetics - Chemical Kinetics
Chapter 26Bioelectrochemistry – Charge Transfer in Biological Systems

PART V: Methods for the Measuring Structure and Function
Chapter 27Separation and Characterization of Biomolecules Based on Macroscopic Properties (with Kristin E. Bergethon)
Chapter 28Determining Structure by molecular interactions with photons: Electronic Spectroscopy (with Kristin Bergethon)
Chapter 29Determining Structure by molecular interactions with photons: ScatteringPhenomena
Chapter 30Analysis of Structure – Microscopy
Chapter 31Epilogue
Chapter 32Physical Constants

PART VI: APPENDICES
Appendix AReview of Mathematical Methods
Appendix BQuantum Electrodynamics
Appendix CThe Pre-Socratic Roots of Modern Science
Appendix DThe Poisson Function
Appendix EAssumptions of a Kinetic Theory of Ideal Gas Behavior
Appendix FDetermination of a Field from the Potential
Appendix GGeometric Optics
Appendix HThe Compton Effect
Appendix IHamilton's Principle of Least Action/Fermat's Principle of Least Time
Appendix JEnergy of Interaction between ions
Appendix KDerivation of the Statement, Qrev > Qirrev
Appendix LDerivation of the Clausius-Clapeyron Equation
Appendix MDerivation of the van't Hoff Equation for Osmotic Pressure
Appendix NPseudoforces
Appendix OWork of charging and discharging a rigid sphere
Appendix PReview of Electrical Circuits
Appendix QFermi's Golden Rule
Appendix RAdiabatic vs non-Adiabatic processes