Computational BiophysicsNovember 28 - December 1, 2005 |
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APPLICATION DEADLINE: October 24, 2005 -- Applications are no longer being accepted DESCRIPTION: The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. Enrollment is limited. |
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TOPICS TENTATIVE AGENDA INSTRUCTORS READINGS |
PROGRAMS FINANCIAL INFORMATION PHOTOS |
08:30-08:45 | Workshop Registration |
08:45-09:00 | Opening Remarks -- Ralph Roskies |
09:00-09:30 | Overview of National Resource for Biomedical Supercomputing (NRBSC) |
09:30-10:30 | Molecular Graphics Perspective of Protein Structure and Function |
10:30-10:50 | Coffee Break |
10:50-12:00 | Molecular Dynamics Method |
12:00-12:30 | Daily Q & A |
12:30-1:30 | Lunch Break |
1:30-1:45 | Overview of Hands-on Sessions |
1:50-2:30 | Molecular Graphics Tutorial |
2:30-2:45 | Coffee Break |
2:45-5:00 | Molecular Graphics Tutorial (continued) |
09:00-10:00 | Molecular Dynamics with NAMD |
10:00-11:00 | Equilibrium Properties of Proteins |
11:00-11:15 | Coffee Break |
11:15-12:15 | Nonequilibrium Properties of Proteins |
12:15-12:30 |
Daily Q & A Group photo |
12:30-1:30 | Lunch Break |
1:30-3:30 | Molecular Dynamics Tutorial |
3:30-3:45 | Coffee Break |
3:45-5:00 | Molecular Dynamics Tutorial (continued) |
09:00-10:00 | Introduction to Classical Force Fields |
10:00-11:00 | Force Fields Parameterization |
11:00-11:15 | Coffee Break |
11:15-12:15 | Applications |
12:15-12:30 | Daily Q&A |
12:30-1:30 | Lunch Break |
1:30-3:00 | Paramaterizing a Novel Residue |
3:00-3:15 | Coffee Break |
3:15-5:00 | Topology File Tutorial |
09:00-10:00 | Transport in Membrane Chanels |
10:00-10:30 | Nanotubes |
10:30-10:40 | Daily Q&A |
10:40-10:50 | Coffee Break /Evaluations |
10:50-12:30 | Nanotubes/IMD |
12:30-1:30 | Lunch Break |
1:30- | Open tutorial work time |
Instructors
Dr. Klaus Schulten
3147 Beckman Institute
University of Illinois
405 N. Mathews
Urbana, IL 61801
Dr. Emad Tajkhorshid
3143 Beckman Institute
University of Illinois
405 N. Mathews
Urbana, IL 61801
Readings
Slides from a previous workshop can be reviewed at:
http://www.ks.uiuc.edu/Training/Workshop/SanFrancisco/lectures.html
Programs
NAMD -- recipient of a 2002 Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.
VMD -- is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
Financial Information
This workshop is funded by grants from the NIH National Center for Research Resources. These grants provide tuition, hotel, supercomputing time, and workshop materials for US academic participants.
ALL participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop.
A few positions may be available for US government employees and corporate and industrial researchers. These participants are responsible for their own hotel accommodations.
Tuition for US government employees is $350 in advance to cover the workshop materials and supercomputing time. (Contract government employees, if they submit a letter from their department head explaining their status as a contract employee, will be considered an academic participant.)
Tuition for corporate and industrial participants is $975 in advance to cover the workshop materials and supercomputing time.
Photos
Group Photo (5 x 7) --8.3 MB
Group Photo (8 x 10) --16 MB