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

Winter 1997

IMA Workshop

Molecular Structure: Dynamics, Geometry and
Topology

January 20-23, 1997

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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Winter 1997 IMA Workshop

Molecular Structure: Dynamics, Geometry and Topology

Winter 1997

IMA Workshop

Molecular Structure: Dynamics, Geometry and
Topology