Computational Biophysics Workshop

Program

Locations:
  • Lectures: Room 3269 of the Beckman Institute
  • Tutorials: Room 3269 and TCBG Innovation Areas I & II at Beckman

Mon, July 15: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:30-09:00 Registration
09:00-09:10 Opening Remarks
09:10-10:40 Structure and Sequence Analysis with VMD
Coffee Break  
11:00-12:00 Introduction to Molecular Dynamics with NAMD
12:00-12:20 Q & A; Group picture
Lunch Break  
14:00-16:00 VMD Tutorial - Using VMD
NAMD Tutorial
Coffee Break  
16:15-18:00 VMD Tutorial - Using VMD
NAMD Tutorial

 

Tue, July 16: Introduction to Bioinformatics - Zaida Luthey-Schulten

09:00-10:30 Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
Coffee Break  
10:50-12:00 Application of MultiSeq to Evolution of Translation Machinery
12:00-12:30 Q & A; Group picture
Lunch Break  
14:00-16:00

Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) Expert Sequence Analysis
     - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
     - Evolution of Translation EF-Tu: tRNA
     - Evolution of Translation: The Ribosome; or
4) Participants work on their own projects

Coffee Break  
16:15-18:00

Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) Expert Sequence Analysis
     - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes
     - Evolution of Translation EF-Tu: tRNA
     - Evolution of Translation: The Ribosome; or
4) Participants work on their own projects

 

Wed, July 17: Computational Nano-Bio - Alek Aksimentiev

09:00-10:30 Modeling the Interface between Biological and Synthetic Materials
Coffee Break  
10:50-12:00 Sequencing DNA Using Nanopores
12:00-12:20 Q & A
Lunch Break  
14:00-16:30

Visualizing MD Results: Stretching dsDNA Mini Tutorial
Modeling Synthetic Ion Channels with Coarse-Grained Molecular Dynamics
Coffee Break  
16:45-18:00 User-Defined Forces in NAMD
Introduction to MD Simulation of DNA-protein systems

 

Thu, July 18: Statistical Mechanics of Proteins - Klaus Schulten

09:00-10:00 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
10:00-10:45 Applications of VMD / NAMD in Modern Research
Coffee Break  
11:00-12:00 Introduction to GPU Accelerated NAMD Simulation - K. Schulten, R. McGreevy
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Shape-Based Coarse Graining or Free Energy Set Tutorials
Coffee Break  
16:15-18:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Shape-Based Coarse Graining or Free Energy Set Tutorials

 

Fri, July 19: Introduction to Cellular Processes - Zaida Luthey-Schulten

09:00-10:30 Whole Cell Simulations
Coffee Break  
10:50-12:00 Introduction to Systems Biology
12:00-12:20 Q & A
Lunch Break  
14:00 -16:00 Lattice Microbes
Coffee Break  
16:15-18:00 Dynamical Network Analysis

 

Tutorial Options (not printed, but supported at the workshop):
Shape-Based Coarse Graining
Free Energy Set Tutorials:
     - A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD
     - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD

Click here to see descriptions of tutorials listed in program.

Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Resource for Macromolecular Modeling and Bioinformatics".