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Concepts in Biophysical Chemistry

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Concepts in Biophysical Chemistry

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.

Biological ChemistryChemistry
Author
Andrei Tokmakoff
Publisher
University of Chicago
Source
LibreTexts
License
CC BY-NC-SA
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 111 sections
  1. 01: Water and Aqueous Solutions
  2. 01: Fluids
  3. 1.01: What is a Fluid
  4. 1.02: Radial Distribution Function
  5. 1.03: Excluded Volume
  6. 02: Lattice Model of a Fluid
  7. 2.01: Lattice Models
  8. 2.02: Ideal Lattice Gas
  9. 2.03: Binary Fluid
  10. 03: Water's Physical Properties
  11. 3.01: Water Structure
  12. 3.02: Water Dynamics
  13. 3.03: Electrical Properties of Pure Water
  14. 04: Solvation
  15. 4.01: Solvation
  16. 4.02: Solvation Thermodynamics
  17. 4.03: Solvation Dynamics and Reorganization Energy
  18. 05: Hydrophobicity
  19. 5.01: Hydrophobic Solvation- Thermodynamics
  20. 5.02: Hydrophobic Solvation- Solute Size Effect
  21. 5.03: Hydrophobic Collapse
  22. 06: Electrical Properties of Water and Aqueous Solutions
  23. 6.01: Electrostatics
  24. 6.02: Dielectric Constant and Screening
  25. 6.03: Free Energy of Ions in Solution
  26. 6.04: Ion Distributions in Electrolyte Solution
  27. 6.05: PoissonBoltzmann Equation
  28. 6.06: DebyeHuckel Theory
  29. 6.07: Ion Distributions Near a Charged Interface
  30. 6.08: Ion Distributions Near a Charged Sphere
  31. 02: Macromolecules
  32. 07: Statistical Description of Macromolecular Structure
  33. 7.01: Segment Models
  34. 7.02: Excluded Volume Effects
  35. 7.03: Polymer Loops
  36. 08: Polymer Lattice Models
  37. 8.01: Entropy of Single Polymer Chain
  38. 8.02: Self-Avoiding Walks
  39. 8.03: Conformational Changes with Temperature
  40. 8.04: FloryHuggins Model of Polymer Solutions
  41. 8.05: PolymerSolvent Interactions
  42. 09: Macromolecular Mechanics
  43. 9.01: Force and Work
  44. 9.02: Worm-like Chain
  45. 9.03: Polymer Elasticity and ForceExtension Behavior
  46. 03: Diffusion
  47. 10: Diffusion
  48. 10.01: Continuum Diffusion
  49. 10.02: Solving the Diffusion Equation
  50. 10.03: Steady-State Solutions
  51. 11: Brownian Motion
  52. 11.01: Random Walk and Diffusion
  53. 11.02: Markov Chain and Stochastic Processes
  54. 11.03: Fluorescence Correlation Spectroscopy
  55. 11.04: Orientational Diffusion
  56. 12: Diffusion in a Potential
  57. 12.01: Diffusion with Drift
  58. 12.02: Biased Random Walk
  59. 12.03: Diffusion in a Potential
  60. 13: Friction and the Langevin Equation
  61. 13.01: Langevin Equation
  62. 13.02: Brownian Dynamics
  63. 04: Transport
  64. 14: Hydrodynamics
  65. 14.01: Newtonian Fluids
  66. 14.02: Stokes Law
  67. 14.03: Laminar and Turbulent Flow
  68. 15: Passive Transport
  69. 15.01: Dimensionality Reduction
  70. 15.02: Facilitated Diffusion
  71. 15.03: Search Times in Facilitated Diffusion
  72. 16: Targeted Diffusion
  73. 16.01: Diffusion to Capture
  74. 16.02: Diffusion to Capture with Interactions
  75. 16.03: Mean First Passage Time
  76. 17: Directed and Active Transport
  77. 17.01: Motor Proteins
  78. 17.02: Passive vs Active Transport
  79. 17.03: Brownian Ratchet
  80. 17.4: Polymerization Ratchet and Translocation Ratchet
  81. 05: Cooperativity
  82. 18: Cooperativity
  83. 18.01: HelixCoil Transition
  84. 18.02: Two-State Thermodynamics
  85. 19: Self-Assembly
  86. 19.01: Micelle Formation
  87. 19.02: Classical Nucleation Theory
  88. 19.03: Why Are Micelles Uniform in Size
  89. 19.04: Shape of Self-Assembled Amphiphiles
  90. 06: Dynamics and Kinetics
  91. 20: Protein Folding
  92. 20.01: HelixCoil Transition
  93. 20.02: Two-State Thermodynamics
  94. 21: Binding and Association
  95. 21.01: Thermodynamics and Biomolecular Reactions
  96. 21.02: Statistical Thermodynamics of Biomolecular Reactions
  97. 21.03: DNA Hybridization
  98. 21.04: Biomolecular Kinetics
  99. 21.05: Diffusion-Limited Reactions
  100. 21.06: Protein Recognition and Binding
  101. 21.07: Forces Guiding Binding
  102. 21.08: Specificity in Recognition and Binding
  103. 22: Biophysical Reaction Dynamics
  104. 22.01: Concepts and Definitions
  105. 22.02: Computing Dynamics
  106. 22.03: Representations of Dynamics
  107. 22.04: Analyzing Trajectories
  108. 22.05: Time-Correlation Functions
  109. 23: Barrier Crossing and Activated Processes
  110. 23.01: Transition State Theory
  111. 23.02: Kramers Theory