TCBG Summer School - Urbana, Jun. 2-13, 2003
Lectures
All lectures of the 2003 Theoretical and Computational Biophysics Summer School are available on video. The summer school tutorials have proven to be valuable for self-study of the practical use of VMD and NAMD. Now together with the lectures it becomes even easier to learn modeling using VMD, NAMD, and BioCoRE through the internet.
- 6/2: Introduction to Protein Structure and Dynamics (K. Schulten)
- Welcome, Opening Remarks, and Overview (pdf, 8.5M ) (Video)
- Molecular Graphics Perspective of Protein Structure and Function (pdf, 4.3M ) (Video)
- Molecular Dynamics Methods (Part 1) (pdf, 3.0M ) (Video)
- Molecular Dynamics Methods (Part 2) (pdf, 3.2M ) (Video)
- Equilibrium Properties of Proteins (pdf, 5.6M ) (Video)
- 6/3: Statistical Mechanics of Proteins (I. Kosztin)
- Equilibrium and Nonequilibrium Properties of Proteins (pdf, 796K ) (Video)
- Coherent Motion in Proteins: Temperature Echoes (pdf, 134K ) (Video)
- Simulated Cooling of Proteins (pdf, 881K ) (Video)
- 6/4: Steered Molecular Dynamics of Proteins (K. Schulten)
- Introduction and Examples (pdf, 7.0M ) (Video)
- Mechanical Proteins (pdf, 9.5M ) (Video)
- Determining Potentials (pdf, 1.2M ) (Video)
- 6/5: Simulating Membrane Channels (E. Tajkhorshid)
- Introduction and Examples (pdf, 4.3M ) (Video)
- Transport in Aquaporins (pdf, 29M ) (Video)
- Nanotubes (pdf, 4.7M ) (Video)
- 6/6: Quantum Chemistry of Proteins (T. Martinez)
- Introduction and Examples (pdf, 6.8M ) (Video)
- Ab Initio and Semiempirical Quantum Chemistry (pdf, 3.5M ) (Video)
- QM/MM Methods and Direct Dynamics (pdf, 1.3M ) (Video)
- 6/9: Parameters for Classical Force Fields (Z. Schulten)
- Introduction and Examples (pdf, 1.3M ) (Video)
- Introduction to Classical Force Fields (pdf, 1.3M ) (Video)
- Methods of Parameterization (pdf, 1.7M ) (Video)
- 6/10: Bioinformatics of Proteins (Z. Schulten)
- Introduction and Examples (pdf, 19M ) (Video)
- Sequence and Structure Alignment Algorithms (pdf, 19M ) (Video)
- Sequence and Structural Analysis Tools on the Web (pdf, 19M ) (Video)
- 6/11: Simulation of Lipids (M. Klein); Parallel Computing (L. Kale)
- Atomic Level Simulation of Membranes (pdf, 12M ) (Video)
- Coarse Grained Modeling of Lipid Phases (pdf, 12M ) (Video)
- Introduction to Parallel Computing Issues (pdf, 1.9M ) (Video)
- Cluster Building (pdf, 897K ) (Video)
- 6/12: Numerical Algorithms (T. Schlick, R. Skeel)
- Force Evaluation, Integrators, and Propagators (pdf, 473K) (Notes (pdf, 207K) ), (Video)
- Optimization Techniques (pdf, 17M) (Homework 1: Biphenyl Minimization (pdf, 161K ) ) (Video)
- Monte Carlo Methods (pdf, 17M) (Homework 2: Global Optimization (pdf, 161K ) ) (Video)
- 6/13: Modeling Large Systems (K. Schulten)
- Molecular Machines of the Living Cell (pdf, 10M ) (Video)
- Light Harvesting in Photosynthesis (pdf, 24M ) (Video)
- ATP Synthase (pdf, 23M ) (Video)
* archive of prior realmedia versions of lectures available here.
