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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| Important or "Hot" Issues in Biophysics, or How to Be Out-of-Date Quickly | |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 | |