The Physical Basis of Biochemistry

Contents:
Section 1:
The Science and Philosophy of Biophysical Study, featureing: An
Introduction to Modeling and Statistical Methods
Section 2:
Physical Foundations, featuring: The Potential Energy Surface,
Classical and Quantum Mechanics, Electromagnetics, and Biochemical
Bonding
Section 3:
Measuring a System: Tools for Exploring Natural State Space,
featuring: Thermodynamic Theory and Applications, Spectroscopy,
and Microscopy
Section 4:
The Structure of Biological State Space: Building a Model of Aqueous
Biochemistry, featuring: A Model-Buidling Exploration of Water,
Ionic Solutions, Lipid-Water and Macromlecular Systems, Molecular
Modeling, and the Electrified Interphase
Section 5:
Function and Action in State Space, featuring: Transport, Kinetics
Enzymes, and Electron Transport

Grounds students in the basic principles of biochemistry and molecular biophysics

PREFACEPART I: Principles of Biophysical InquiryChapter 1Introduction: "To the Student"Chapter 2Philosophy and Practice of Biophysical StudyChapter 3Overview of the Biological System Under Study - Descriptive ModelsChapter 4Physical Thoughts, Biological Systems - The application of modeling principles to understanding biological systemsChapter 5Probability and StatisticsPART II: FoundationsChapter 6Physical Principles: Energy - The Prime ObservableChapter 7Biophysical Forces in Molecular SystemsChapter 8An Introduction to Quantum MechanicsChapter 9Chemical PrinciplesChapter 10Measuring the Energy of a System: Energetics and the First Law of ThermodynamicsChapter 11Entropy and the Second Law of ThermodynamicsChapter 12Which Way Did That System Go? The Gibbs Free EnergyChapter 13The Thermodynamics of Phase EquilibriaPART III: Building a Model of Biomolecular StructureChapter 14Water: A Unique Structure, A Unique SolventChapter 15Ion-Solvent InteractionsChapter 16Ion-Ion InteractionsChapter 17Lipids in Aqueous SolutionChapter 18Macromolecules in SolutionChapter 19Molecular Modeling - Mapping Biochemical State SpaceChapter 20The Electrified InterphasePART IV: Function and Action Biological State SpaceChapter 21Transport and Kinetics: Processes Not at EquilibriumChapter 22Flow in a Chemical Potential Field: DiffusionChapter 23Flow in an Electrical Field: ConductionChapter 24Forces Across MembranesChapter 25Kinetics - Chemical KineticsChapter 26Bioelectrochemistry - Charge Transfer in Biological SystemsPART V: Methods for the Measuring Structure and FunctionChapter 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: ScatteringPhenomenaChapter 30Analysis of Structure - MicroscopyChapter 31EpilogueChapter 32Physical ConstantsPART VI: APPENDICESAppendix AReview of Mathematical MethodsAppendix BQuantum ElectrodynamicsAppendix CThe Pre-Socratic Roots of Modern ScienceAppendix DThe Poisson FunctionAppendix EAssumptions of a Kinetic Theory of Ideal Gas BehaviorAppendix FDetermination of a Field from the PotentialAppendix GGeometric OpticsAppendix HThe Compton EffectAppendix IHamilton's Principle of Least Action/Fermat's Principle of Least TimeAppendix JEnergy of Interaction between ionsAppendix KDerivation of the Statement, Qrev > QirrevAppendix LDerivation of the Clausius-Clapeyron EquationAppendix MDerivation of the van't Hoff Equation for Osmotic PressureAppendix NPseudoforcesAppendix OWork of charging and discharging a rigid sphereAppendix PReview of Electrical CircuitsAppendix QFermi's Golden RuleAppendix RAdiabatic vs non-Adiabatic processes