Concepts in Biophysical Chemistry

by Andrei Tokmakoff

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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.

Description from LibreTexts.

Publisher
University of Chicago
Subjects
Chemistry, Biological Chemistry
Licence
CC BY-NC-SA 4.0, as LibreTexts states it. Non-commercial use only.
Who can read
Tweens profiles and older, judged from its title and subjects

Contents

LibreTexts writes equations in TeX, and here they show as TeX; the PDF has them typeset.

  1. Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. 1: Water and Aqueous Solutions
  7. 1: Fluids
  8. 1.1: What is a Fluid?
  9. 1.2: Radial Distribution Function
  10. 1.3: Excluded Volume
  11. 2: Lattice Model of a Fluid
  12. 2.1: Lattice Models
  13. 2.2: Ideal Lattice Gas
  14. 2.3: Binary Fluid
  15. 3: Water's Physical Properties
  16. 3.1: Water Structure
  17. 3.2: Water Dynamics
  18. 3.3: Electrical Properties of Pure Water
  19. 4: Solvation
  20. 4.1: Solvation
  21. 4.2: Solvation Thermodynamics
  22. 4.3: Solvation Dynamics and Reorganization Energy
  23. 5: Hydrophobicity
  24. 5.1: Hydrophobic Solvation - Thermodynamics
  25. 5.2: Hydrophobic Solvation- Solute Size Effect
  26. 5.3: Hydrophobic Collapse
  27. 6: Electrical Properties of Water and Aqueous Solutions
  28. 6.1: Electrostatics
  29. 6.2: Dielectric Constant and Screening
  30. 6.3: Free Energy of Ions in Solution
  31. 6.4: Ion Distributions in Electrolyte Solution
  32. 6.5: Poisson–Boltzmann Equation
  33. 6.6: Debye–Hückel Theory
  34. 6.7: Ion Distributions Near a Charged Interface
  35. 6.8: Ion Distributions Near a Charged Sphere
  36. 2: Macromolecules
  37. 7: Statistical Description of Macromolecular Structure
  38. 7.1: Segment Models
  39. 7.2: Excluded Volume Effects
  40. 7.3: Polymer Loops
  41. 8: Polymer Lattice Models
  42. 8.1: Entropy of Single Polymer Chain
  43. 8.2: Self-Avoiding Walks
  44. 8.3: Conformational Changes with Temperature
  45. 8.4: Flory–Huggins Model of Polymer Solutions
  46. 8.5: Polymer–Solvent Interactions
  47. 9: Macromolecular Mechanics
  48. 9.1: Force and Work
  49. 9.2: Worm-like Chain
  50. 9.3: Polymer Elasticity and Force–Extension Behavior
  51. 3: Diffusion
  52. 10: Diffusion
  53. 10.1: Continuum Diffusion
  54. 10.2: Solving the Diffusion Equation
  55. 10.3: Steady-State Solutions
  56. 11: Brownian Motion
  57. 11.1: Random Walk and Diffusion
  58. 11.2: Markov Chain and Stochastic Processes
  59. 11.3: Fluorescence Correlation Spectroscopy
  60. 11.4: Orientational Diffusion
  61. 12: Diffusion in a Potential
  62. 12.1: Diffusion with Drift
  63. 12.2: Biased Random Walk
  64. 12.3: Diffusion in a Potential
  65. 13: Friction and the Langevin Equation
  66. 13.1: Langevin Equation
  67. 13.2: Brownian Dynamics
  68. 4: Transport
  69. 14: Hydrodynamics
  70. 14.1: Newtonian Fluids
  71. 14.2: Stokes’ Law
  72. 14.3: Laminar and Turbulent Flow
  73. 15: Passive Transport
  74. 15.1: Dimensionality Reduction
  75. 15.2: Facilitated Diffusion
  76. 15.3: Search Times in Facilitated Diffusion
  77. 16: Targeted Diffusion
  78. 16.1: Diffusion to Capture
  79. 16.2: Diffusion to Capture with Interactions
  80. 16.3: Mean First Passage Time
  81. 17: Directed and Active Transport
  82. 17.1: Motor Proteins
  83. 17.2: Passive vs Active Transport
  84. 17.3: Brownian Ratchet
  85. 17.4: Polymerization Ratchet and Translocation Ratchet
  86. 5: Cooperativity
  87. 18: Cooperativity
  88. 18.1: Helix–Coil Transition
  89. 18.2: Two-State Thermodynamics
  90. 19: Self-Assembly
  91. 19.1: Micelle Formation
  92. 19.2: Classical Nucleation Theory
  93. 19.3: Why Are Micelles Uniform in Size?
  94. 19.4: Shape of Self-Assembled Amphiphiles
  95. 6: Dynamics and Kinetics
  96. 20: Protein Folding
  97. 20.1: Models for Simulating Folding
  98. 20.2: Perspectives on Protein Folding Dynamics
  99. 21: Binding and Association
  100. 21.1: Thermodynamics and Biomolecular Reactions
  101. 21.2: Statistical Thermodynamics of Biomolecular Reactions
  102. 21.3: DNA Hybridization
  103. 21.4: Biomolecular Kinetics
  104. 21.5: Diffusion-Limited Reactions
  105. 21.6: Protein Recognition and Binding
  106. 21.7: Forces Guiding Binding
  107. 21.8: Specificity in Recognition and Binding
  108. 22: Biophysical Reaction Dynamics
  109. 22.1: Concepts and Definitions
  110. 22.2: Computing Dynamics
  111. 22.3: Representations of Dynamics
  112. 22.4: Analyzing Trajectories
  113. 22.5: Time-Correlation Functions
  114. 23: Barrier Crossing and Activated Processes
  115. 23.1: Transition State Theory
  116. 23.2: Kramers’ Theory
  117. Back Matter
  118. Index
  119. Glossary
  120. Detailed Licensing