Seminars & Events

MCS Division Seminar
"Modeling Macromolecular Dynamics from Simulations"

DATE: March 29, 2007
TIME: 2:00pm
SPEAKER: Nina Hinrichs, Stanford University
LOCATION: Building 221 Conference Room A216, Argonne
HOST: Mihai Anitescu

Description:
Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences -- for example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using distributed computing methods such as Folding@Home.

The analysis of these large, high-dimensional, data sets presents new
computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

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