Campuses:

Molecular

Saturday, May 16, 2009 - 2:45pm - 3:30pm
Robert Krasny (University of Michigan)
No Abstract
Saturday, May 16, 2009 - 9:00am - 9:45am
Benedict Leimkuhler (University of Edinburgh)
No Abstract
Friday, May 15, 2009 - 9:00am - 9:45am
Berend Smit (University of California, Berkeley)
No Abstract
Friday, May 15, 2009 - 11:00am - 11:45am
Benedict Leimkuhler (University of Edinburgh)
No Abstract
Friday, May 22, 2009 - 10:30am - 11:10am
Benedict Leimkuhler (University of Edinburgh)
For molecular dynamics to be useful for recovering macroscopically-relevant information (e.g. thermodynamic averages), it must be regulated by auxiliary control laws. Typically these would represent thermal or pressure controls. In this talk I will discuss a general family of stochastic-dynamic methods, including gentle thermostats which mildly perturb averaged dynamics and some very aggressive thermostats intended to enhance sampling of the canonical ensemble.
Tuesday, May 19, 2009 - 10:00am - 10:40am
Giovanni Ciccotti (Università di Roma La Sapienza)
We present the need (especially critical for multiscale simulations) of extending standard equilibrium Molecular Dynamics to nonequilibrium situations. We show how this is possible in full rigor by use of the nonlinear Kubo-Onsager relation, connecting dynamical nonequilibrium averages to equilibrium (more genarally, initial distribution) averages over suitable time-evolved variables.
Friday, May 8, 2009 - 9:00am - 9:30am
Roland Lindh (Lund University)
No Abstract
Thursday, January 15, 2009 - 2:00pm - 2:30pm
Jiali Gao (University of Minnesota, Twin Cities)
Molecular dynamics simulation has become a powerful tool for studying biochemical properties. At the heart of these calculations is the potential energy function that describes intermolecular interactions in the system, and often it is the accuracy of the potential energy surface that determines the reliability of simulation results. The current generation of force fields was essentially established in the 1960s; while the accuracy has been improved tremendously by systematic parameterization, little has changed in the formalism.
Friday, January 16, 2009 - 9:30am - 10:00am
Vitaly Rassolov (University of South Carolina)
Joint work with Sophya Garashchuk (Universit of South Carolina).
Tuesday, January 13, 2009 - 5:10pm - 5:40pm
Marcus Weber (Konrad-Zuse-Zentrum für Informationstechnik (ZIB))
Conformation dynamics aims at an identification of dynamically metastable subsets of the position space of molecular systems.
A time-discretized molecular simulation of such a system leads to a Markov operator. A space discretization of this operator leads to a
stochastic transition matrix. In the talk, a cluster algorithm is presented which identifies metastable subsets of the position space by
a spectral analysis of the transition matrix. This analysis was originally valid for reversible Markov chains, but can be extended to the

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