Friday, September 22

Methods for Biomolecular Dynamics

10:30 AM-12:30 PM
New Hampshire 3

For "Biomolecular Simulation Applications", see MS12.

Computer simulations of biomolecular dynamics typically require vast amounts of computer time, due both to the extreme range of time scales and to the problem of sampling a high dimensional configuration space. Although molecular dynamics (MD) is most often employed as a means to sample phase space according to a prescribed probability distribution, it is also used in the case of macromolecules to study the statistics of conformational changes. Computational challenges involve the fast evaluation of forces, the overcoming of time step limitations arising from high frequency motions, and the problem of sampling regions of configuration space separated by high energy barriers.

Organizers: Robert Skeel
University of Illinois, Urbana-Champaign, USA
Tamar Schlick
Courant Institute of Mathematical Sciences, New York University, USA
10:30-10:45 Using Molecular Simulation to Probe the Structural Basis of Regulation in the Tyrosine Kinase Enzyme Hck
Matthew Young, The Rockefeller University, USA
10:45-11:00 Langevin Stabilization for Molecular Dynamics
Jesús Izaguirre, University of Notre Dame, USA
11:00-11:25 Long Time Dynamics of Biomolecules
Ron Elber and Veaceslav Zaloj, Cornell University, USA
11:30-11:55 Examining Complex Processes and Reactions
Bernard R. Brooks, National Institutes of Health, USA
12:00-12:25 An Ewald Summation Based Multipole Method
Zhong-Hui Duan and Robert Krasny, University of Michigan, Ann Arbor, USA

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