ALL LECTURES

  1. Introduction
  2. Molecular Architecture I
  3. Molecular Architecture II
  4. Bioinformatics I
  5. Bioinformatics II
  6. Molecular Simulation I

CONCEPTS IN THIS LECTURE

Molecular Simulation I

  1. Underlying Principles
  2. Simulation Methods
  3. Molecular Dynamics
  4. Simulating Solutions
  5. Simulating alpha-Helix
  6. Simulating Folded Protein
  7. History of Simulation

4. Molecular Simulation I

4.1. Underlying Principles

4.2. Simulation Methods

  1. SB228 Lecture 4 Lecture4
  2. Lecture 4 Contents
  3. Underlying Principles. Concept 4.1
  4. Underlying Principles
  5. Boltzmanns Distribution
  6. Entropy and Free Energy1
  7. Absolute Probabilities
  8. Dynamic Properties
  9. Types of Motion
  10. Crossing Energy Barriers
  11. Rates of Motion
  1. Simulation Methods. Concept 4.2
  2. Simulation Methods
  3. Moving Over Energy Surface
  4. Reaction Coordinates
  5. Protein Folding Landscape
  6. Levinthals Paradox
  7. Resolve Paradox
  8. Simple Energy Minimization
  9. Convergent Energy Minimization
  10. Monte Carlo Methods
  11. Simulated annealing

4.3. Molecular Dynamics

4.4. Simulating Solutions

  1. Molecular Dynamics. Concept 4.3
  2. Molecular Dynamics
  3. Molecular Potential Energy
  4. Molecular Dynamics theory
  5. Molecular Dynamics Procedure
  6. Molecular Dynamics Procedure 1
  7. Molecular Dynamics Procedure 2
  8. Molecular Dynamics Procedure 3
  9. Units in Force Fields
  1. Simulating Solutions. Concept 4.4
  2. Simulating Liquids.
  3. Water is a Very Simple Molecule
  4. Simulating Liquids
  5. Liquids argon and Water
  6. Pure Water Dynamics
  7. Properties of Liquid Water
  8. Hydrophobic Effect
  9. Simulating Hydrophobic Effect
  10. Voronoi Decomposition
  11. Voronoi analysis of Contacts
  12. Hydrophobic Clusters Cross Box
  13. Methane Solution Dynamics
  14. Butane Solution Dynamics
  15. Benzene Solution Dynamics
  16. Hydrophobic Energy and Contact Surface
  17. Hydrophobic Solutes Perturb Water Density
  18. Large Density Changes

4.5. Simulating alpha-Helix

4.6. Simulating Folded Protein

  1. Simulating alpha-Helix. Concept 4.5
  2. Dynamics of the alpha-Helix
  3. Alpha-Helix Dynamics
  4. Water allows Hydrogen Bonds to Break
  1. Simulating Folded Protein. Concept 4.6
  2. Dynamics of Folded Protein
  3. Protein in Water1
  4. Protein Dynamics
  5. RMS Deviation from X-Ray
  6. Hydrogen Bond Stability
  7. Four Classes of Water Molecules
  8. Density of Surface Water
  9. Orientation of Surface Water
  10. Properties of Water Molecules

4.7. History of Simulation

  1. History of Simulation. Concept 4.7
  2. Los alamos 1943-45
  3. Levinthal 1966
  4. Levinthal Movies
  5. 50 Years of Simulation