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IMA Workshop
Molecular Structure: Dynamics, Geometry and Topology
January 20-23, 1997

Mathematics of High Performance Computing
Molecular Modeling and HPC

Organizers:

Tamar Schlick (Courant Institute) and Ridgway Scott (Univ. of Houston)

The design or redesign of macromolecules to perform biological or industrial functions requires quantum mechanical models to be solved. Various approximate models are currently being refined and further developed as the power of available computers increases. Monte Carlo techniques are also becoming feasible for this class of problem. The workshop will combine researchers involved in the development of these diverse techniques and identify mathematical problems for further study.

The structure of macromolecules can often be described as a linear sequence of bonded atoms (e.g. a DNA nucleotide sequence) yet the three-dimensional structure (and resulting function) remain elusive. The ``protein folding problem'' is one of the simplest to state and yet impossible to solve for molecules of substantial size. Different approaches are being proposed for attacking this problem, ranging from topology, geometry, mechanics, and even artificial intelligence. The workshop will focus on the various mathematical approaches available. Fundamental to the three dimensional structure is the quantum-mechanically determined local bond structure.

Workshop Schedule

All Talks are held in Vincent Hall Room 570, unless otherwise noted. To view abstracts, click on the talk's title.

Text-only version of schedule

SCHEDULE for MONDAY, JANUARY 20
1/20/97 is Martin Kuther King Day, and a University of Minnesota holiday. IMA offices may be closed, although staff will be on hand for the workshop
9:00 am Registration and Coffee IMA Lounge, Vincent Hall 502
10:00 am A.Friedman, R.Gulliver, R. Scott Welcome and Orientation
10:15 am Tamar Schlick,
Courant Institute
Molecular Dynamics: An Overview and Recent Work
10:30 am Coffee Break IMA Lounge, Vincent Hall 502
11:15 am Tamar Schlick,
Courant Institute
Molecular Dynamics: An Overview and Recent Work (cont.)
2:00 pm Jan Hermans,
University of North Carolina
Simulations of protein dynamics: Investigations of conformation change and interactions with small molecules
4:00 pm IMA Tea (and more!) Vincent Hall 502 (The IMA Lounge)
SCHEDULE for TUESDAY, JANUARY 21
9:00 am Coffee IMA Lounge, Vincent Hall 502
10:00 am Randy Paffenroth,
University of Maryland
Software Demonstration: the Autovisualization Application (AVA)
10:30 am Coffee Break IMA Lounge, Vincent Hall 502
11:00 am Robert D. Skeel,
University of Illinois
Difficulties with Multiple Time Stepping and the Fast Multipole Algorithm in Molecular Dynamics
2:00 pm Ben Leimkuhler,
University of Kansas
New Geometric Integrators for Molecular Simulation
3:30 pm Steve Plimpton
Sandia National Labs
Parallel Algorithms for Molecular Dynamics Simulations:Particle-Mesh Ewald and rRESPA
SCHEDULE for WEDNESDAY, JANUARY 22
9:00 am Registration and Coffee IMA Lounge, Vincent Hall 502
9:30 am Jorge J. Moré,
Argonne National Laboratory
Distance Geometry Problems: Global Solutions
10:30 am Coffee Break IMA Lounge, Vincent Hall 502
11:00 am Zhijun Wu,
Argonne National Laboratory
Geometrical Structures of Large, Confined Ionic Systems
2:00 pm Richard A. Friesner,
Columbia University
A Computational Approach to the Determination of Protein Tertiary Structure Assuming Knowledge of Secondary Structure
3:00 pm Coffee IMA Lounge, Vincent Hall 502
6:00 pm Workshop Dinner Radisson Hotel, Alumni Room, 2nd Floor
SCHEDULE for THURSDAY, JANUARY 23
9:00 am Coffee IMA Lounge, Vincent Hall 502
9:30 pm L. Ridgway Scott,
University of Houston
High-Performance Computation in Biomolecular Modeling
10:30 am Coffee Break IMA Lounge, Vincent Hall 502
11:00 am De Witt Sumners,
Florida State University
Topological approaches to molecular structure
2:00 pm Craig J. Benham,
Mount Sinai School of Medicine
Sites of Superhelical DNA Duplex Destabilization Occur at Specific Regulatory Regions
3:00 pm Coffee Break IMA Lounge, Vincent Hall 502
3:30 pm Robert Manning
University of Maryland
Continuum Mechanics Computations of DNA Cyclization

 

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1996-1997 Mathematics in High Performance Computing

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