Computational Biophysics Workshop - Urbana, April 6-10, 2015

Program

Locations:
  • Lectures and tutorials: 3269 Beckman Institute

Monday, April 6: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:00-08:30 Registration & Coffee
08:30-09:00 Welcome, Brief Overview, and Opening Remarks
09:00-10:30 Introduction to Molecular Dynamics with NAMD
10:30-10:50 Coffee Break
10:50-12:00 Exemplary Applications of VMD / NAMD in Modern Research
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: VMD Tutorial, NAMD Tutorial, VMD Images and Movies Tutorial

Tuesday, April 7: Force Field Parameterization - Emad Tajkhorshid

08:30-09:00 Coffee Break
09:00-10:30 Introduction to Classical Force Fields - Topology, Parameters, and Structure Files
10:30-10:50 Coffee Break
10:50-12:00 Examples and Applications / Force Field Toolkit
12:00-12:20 Q & A; Group picture
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Topology File Tutorial, Parametrizing a Novel Residue, NAMD Tutorial

Wednesday, April 8: Introductions to Evolutionary Concepts, Network Analysis, and Cell Simulations - Zan Luthey-Schulten

08:30-09:00 Coffee Break
09:00-10:30 Applications of Evolutionary Algorithms and Network Analysis in MultiSeq/VMD to Translation
10:30-10:50 Coffee Break
10:50-12:00 Introduction to Simulations of Bacterial Cells
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Aquaporins with the VMD MultiSeq Tool, Evolution of Translation: Class-I aminoacyl-tRNA synthetases, Evolution of Translation: EF-Tu, Evolution of Translation: Ribosome, Dynamical Network Analysis, Lattice Microbe Simulations

Thursday, April 9: Computational Nano-Bio - Alek Aksimentiev

08:30-09:00 Coffee Break
09:00-10:30 Introduction to Modeling and Simulations of Nucleic Acid Systems
10:30-10:50 Coffee Break
10:50-12:00 Modeling the Interface Between Biological and Synthetic Materials
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Tutorials
16:00-16:20 Coffee Break
16:20-18:00 Tutorials
Recommended tutorials: Modeling Nanopores for Sequencing DNA, User-defined forces in NAMD, Introduction to MD simulations of DNA-protein systems,

Friday, April 10: Free Energy Calculations - Chris Chipot

08:30-09:00 Coffee Break
09:00-10:30 Introduction to Free-energy Calculations (part 1)
10:30-10:50 Coffee Break
10:50-12:00 Introduction to Free-energy Calculations (part 2)
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-18:00 Tutorials (held in Innovation Courtyard)
Recommended tutorials: Free Energy Tutorial; Adaptive Biasing Force Tutorial; Protein-Ligand Binding Tutorial


Click here to see descriptions of tutorials listed in program.

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