Friday, September 22

MS19
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.

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