ALL LECTURES
Introduction Molecular Architecture I Molecular Architecture II Molecular Simulation I Molecular Simulation II

CONCEPTS IN THIS LECTURE
Molecular Simulation II
Normal Mode theory Protein Normal Modes Unfolding alpha Helix Unfolding Proteins Folding Simplified Chains Folding Simulations

5. Molecular Simulation II
5.1. Normal Mode theory	5.2. Protein Normal Modes
SB228 Lecture 5 Lecture5 Molecular Simulation II Normal Mode theory. Concept 5.1 Normal Mode Dynamics Basic theory Normal Modes in High Dimensions1 Normal Modes in High Dimensions2 Normal Modes in High Dimensions3 Molecular Potential Energy Potential Energy in torsion Space Theory of Normal Modes I Theory of Normal Modes II	Protein Normal Modes. Concept 5.2 Rates of Vibration Amplitudes of Vibration Trypsin inhibitor Modes BPTI Normal Modes Movie Lysozyme Modes Lysozyme Normal Modes Movie Ribonuclease Modes Ribonuclease Normal Modes Movie
5.3. Unfolding alpha Helix	5.4. Unfolding Proteins
Unfolding alpha Helix. Concept 5.3 Alpha-Helix Unfolding Why Simulate Unfolding Unfold alpha-Helix Effect of Temperature Helix Less Stable in Water Water allows Hydrogen Bonds to Break Helix Unfolding Movie Distributions in Solution	Unfolding Proteins. Concept 5.4 Protein Unfolding What Happens to Secondary Structure Protein Unfolding1 Movie What Happens to aromatic Sidechains Protein Unfolding2 Movie Unfolding Pathway Connection to Experiment1 Connection to Experiment2 Connection to Experiment3
5.5. Folding Simplified Chains	5.6. Folding Simulations
Folding Simplified Chains. Concept 5.5 Fold Simplified Proteins Why is Folding So Difficult Simplified Models for Folding1 Virtual Bonds Simplified Models for Folding2 Cartoon Folding Movie 3x3x3 Cube Protein Folding Lattice Model of Folding	Folding Simulations. Concept 5.6 Folding Simulations Need Massive Computational Resources Villin Folding IBM Blue Gene Project IBM Blue Gene Design Folding at Home Folding at Home Helix Folding Pande Helix Folding Movie Pande Villin Folding Movie Folding at Home Rates