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Introduction, Approach, And Tools | |
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Introduction to a New World | |
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Biological and Nonliving Worlds Contrasted | |
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Hierarchical Structure and Function | |
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Some Important Quantities to Get Started | |
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Biophysics and Biochemistry Operate in Water (Water 1) | |
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Important or "Hot" Issues in Biophysics, or How to Be Out-of-Date Quickly | |
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Is There a Career Here Somewhere? | |
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Read Appendix A | |
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How (Most) Physicists Approach Biophysics | |
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Dealing with Nonspherical Cows: Drive for Simplicity | |
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Two Approaches to Biosystems | |
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Comparison of "Physics" and "Biology" Approaches to Organisms | |
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Memorization: Its Advantages and Dangers | |
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Math Tools: First Pass | |
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What Math Do We Need? | |
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Notation: Mathematics vs. Physics Notations | |
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Approximations | |
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Vectors | |
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Two- and Three-Dimensional Geometry | |
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Calculus | |
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Differential Equations | |
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Distributions | |
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Structure And function Water | |
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Introduction | |
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Structure | |
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Unusual Physical Properties | |
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Summary of Important Physical Properties | |
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Bulk vs. Local Structures | |
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Diffusion and Chemical Reactions in Water | |
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Solutes and the Solvent Power of Water | |
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Points to Remember | |
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Structures: From 0.1 to 10 nm and Larger | |
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Software to Display and Analyze Biological Structures | |
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Solvents | |
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Small Molecules | |
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Medium-Sized Molecules: Components of Large Biomolecules | |
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Forces and Free Energies | |
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Biopolymers | |
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Macromolecules: When Does a Molecule Become a Macroscopic Object? | |
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Points to Remember | |
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First Pass at Supramolecular Structures: Assemblies of Biomolecules | |
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Measuring Properties of Three-Dimensional Aggregates | |
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Small Aggregates | |
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Large Aggregates | |
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Two-Dimensional Aggregates: Membranes | |
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Points to Remember | |
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Putting a Cell Together: Physical Sketch | |
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Minimal, Prokaryotic, and Eukaryotic Cells | |
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Physiology: Selective Overview | |
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Reproduction, DNA, and the Cell Nucleus | |
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Sensors and Recognition: Responding to the Outside World without Eyes | |
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Biological Activity: Quantum Microworld | |
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Quantum Primer | |
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Quantum Glossary | |
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Schr�dinger Equation and Other Tools of Quantum Mechanics | |
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Pauli Exclusion Principle | |
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From Atoms to Molecules | |
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Collisions of Atoms and Molecules | |
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Classical vs. Quantum: Is a 1-mm-Long Molecule of DNA a Quantum Object? | |
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Points to Remember | |
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Light and Life | |
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Light: Our Energy Source | |
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Crucial Differences between One 5-eV and Two 2.5-eV Photons | |
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Properties of Photons | |
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Scattering and Refraction | |
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Absorption Spectra | |
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Emission Spectra | |
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Einstein Relations between Absorption and Emission of Atoms (Graduate Section) | |
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Intersystem Crossing: Singlets (S = 0) to Triplets (S = 1) | |
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Energy Transfer (FRET) | |
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Points to Remember | |
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Photosynthesis | |
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Global Numbers | |
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Overall Process | |
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Structural Organization of Photosynthetic Units | |
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Light-Harvesting (Antenna) Proteins: Arrays of Absorbers | |
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Reaction Centers and Charge Separation: Purple Bacteria and Cyanobacteria | |
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Artificial Models and Nonpolluting Energy Production | |
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Points to Remember | |
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Direct Ultraviolet Effects on Biological Systems | |
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Types and Sources of UV Light | |
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Divisions of the UV for Health Purposes: UV-A, UV-B, and UV-C | |
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UV Damage to Organisms: "Action Spectra" | |
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Wavelength-Dependent Photochemical Yields and Protein Damage | |
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UV Damage to DNA | |
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Optical Properties of the Skin | |
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Sunscreens | |
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Points to Remember | |
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Biological Activity: (Classical) Microworld | |
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Mechanics and Dynamics | |
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Conservation Laws, Newton's Laws, Forces, and Torques | |
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Friction: Familiar and Less Familiar Examples of Motion | |
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Gravitational Forces | |
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Volume Changes and Compressibility | |
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Stress and Strain | |
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Force of Friction, Dissipation, Inertia, and Disorder | |
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Fluids and Turbulence | |
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Points to Remember | |
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Random Walks, Diffusion, and Polymer Conformation | |
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Review of Kinetic Theory of Gases: Implications for Biomolecular Averaging | |
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One-Dimensional Random Walk: Probabilities and Distributions | |
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Spreadsheet Model for a One-Dimensional Random Walk | |
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Three-Dimensional Random Walk | |
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Diffusion in the Bulk | |
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Reprise of Photosynthetic Light Harvesting | |
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Biopolymers-A Random Reprise | |
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Points to Remember | |
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Statistical Physics and Thermodynamics Primer | |
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Important Quantities: Temperature, Pressure, Density, and Number | |
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Statistical Mechanical View and Distributions | |
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Equipartition of Energy | |
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"Internal" Energy: Kinetic (K) and Potential (U) | |
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Heat, Internal Energy, Work, and Enthalpy | |
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Conservative and Nonconservative Forces: DNA Example | |
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Ideal Gas Law | |
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Entropy: Gases and Polymers | |
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Free Energy (Gibbs) | |
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Energy Diagrams | |
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Boltzmann Distribution if Numbers Vary: Gibbs Distribution | |
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Equilibrium Constants in Ideal, Uniform Solutions | |
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Free Energy: Enthalpy, Entropy, Mixing, Gradients, Potential, and ATP | |
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Points to Remember | |
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Reactions: Physical View | |
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Energy, Entropy, and Free Energy Diagrams | |
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Rate Theory I: Activation-Energy Model | |
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Diffusion-Controlled Rates (Bimolecular) | |
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Effects of Temperature on Rate Constants | |
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Quantum Tunneling | |
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A B: Unimolecular Reactions | |
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A + B → C Binding Reactions: Free-Solution Reactions | |
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Complex Reactions: Rate-Determining Steps and Michaelis-Menten Analysis | |
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Driving Forces | |
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Reversibility and Detailed Balance | |
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Single-Molecule Behavior | |
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Points to Remember | |
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Molecular Machines: Introduction | |
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Basic Considerations for Motors | |
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DNA-Manipulating Motors | |
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Points to Remember | |
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Assembly | |
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Overview of Assembly Issues | |
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Kinetics and Equilibrium | |
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Restricted Space for Assembly | |
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Entropic Drive: Ordered Structures Can Be Driven by Random Processes | |
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Nucleosomes and Nucleosome-Like Structures | |
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Points to Remember | |
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Reading Skills and Information Sources | |
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Snapshot of the Supporting CD | |
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Glossary | |
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Further Resources | |
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Index | |
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Problem Solving and References appear at the end of each chapter | |