These notes cover the physical chemistry governing molecular behavior in biological systems. It is meant as a resource for those that want to educate themselves or others in biophysics for chemists. This is a work in progress, with new topics and updated material being added, and therefore only select topics are covered so far. I would like to thank Peter Giunta for his assistance preparing the notes, and Tanya Shpigel for her help preparing the notes, and creating this website.
BPC Notes
INTRODUCTION
Background and Reference Material
WATER AND AQUEOUS SOLUTIONS
1. Fluids
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1. What is a Fluid?
2. Radial Distribution Function
3. Excluded Volume
2. Lattice Model of a Fluid
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1. Lattice Models
2. Ideal Lattice Gas
3. Binary Fluid
3. Water's Physical Properties
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1. Water Structure
2. Water Dynamics
3. Electrical Properties of Pure Water
4. Solvation
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1. Solvation
2. Solvation Thermodynamics
3. Solvation Dynamics and Reorganization Energy
5. Hydrophobicity
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1. Hydrophobic Solvation: Thermodynamics
2. Hydrophobic Solvation: Solute Size Effect
3. Hydrophobic Collapse
6. Electrical Properties of Water and Aqueous Solutions
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1. Electrostatics
2. Dielectric Constant and Screening
3. Free Energy of Ions in Solution
4. Ion Distributions in Electrolyte Solution
5. Poisson–Boltzmann Equation
6. Debye–Hückel Theory
7. Ion Distributions Near a Charged Interface
8. Ion Distributions Near a Charged Sphere
MACROMOLECULES
7. Statistical Description of Macromolecular Structure
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1. Segment Models
2. Excluded Volume Effects
3. Polymer Loops
8. Polymer Lattice Models
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1. Entropy of Single Polymer Chain
2. Self-Avoiding Walks
3. Conformational Changes with Temperature
4. Flory–Huggins Model of Polymer Solutions
5. Polymer–Solvent Interactions
9. Macromolecular Mechanics
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1. Force and Work
2. Worm-like Chain
3. Polymer Elasticity and Force–Extension Behavior
DIFFUSION
10. Diffusion
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1. Continuum Diffusion
2. Solving the Diffusion Equation
3. Steady-State Solutions
11. Brownian Motion
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1. Random Walk and Diffusion
2. Markov Chain and Stochastic Processes
3. Fluorescence Correlation Spectroscopy
4. Orientational Diffusion
12. Diffusion in a Potential
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1. Diffusion with Drift
2. Biased Random Walk
3. Diffusion in a Potential
13. Friction and the Langevin Equation
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1. Langevin Equation
2. Brownian Dynamics
TRANSPORT
14. Hydrodynamics
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1. Newtonian Fluids
2. Stokes’ Law
3. Laminar and Turbulent Flow
15. Passive Transport
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1. Dimensionality Reduction
2. Facilitated Diffusion
3. Search Times in Facilitated Diffusion
16. Targeted Diffusion
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1. Diffusion to Capture
2. Diffusion to Capture with Interactions
3. Mean First Passage Time
17. Directed and Active Transport
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1. Motor Proteins
2. Passive vs Active Transport
3. Brownian Ratchet
COOPERATIVITY
18. Cooperativity
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1. Helix–Coil Transition
2. Two-State Thermodynamics
19. Self-Assembly
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1. Micelle Formation
2. Classical Nucleation Theory
3. Why Are Micelles Uniform in Size?
4. Shape of Self-Assembled Amphiphiles
MACROMOLECULAR PROCESSES
20. Protein Folding
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1. Helix–Coil Transition
2. Two-State Thermodynamics
21. Binding and Association
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1. Thermodynamics and Biomolecular Reactions
2. Statistical Thermodynamics of Biomolecular Reactions
3. DNA Hybridization
4. Biomolecular Kinetics
5. Diffusion-Limited Reactions
6. Protein Recognition and Binding
7. Forces Guiding Binding
8. Specificity in Recognition and Binding
DYNAMICS AND KINETICS
22. Biophysical Reaction Dynamics
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1. Concepts and Definitions
2. Computing Dynamics
3. Representations of Dynamics
4. Analyzing Trajectories
5. Time-Correlation Functions
23. Barrier Crossing and Activated Processes
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1. Transition State Theory
2. Kramers’ Theory