[Colloquium] Talk by Nina S. Hinrichs on Friday, March 30, 2007

[Margery Ishmael]

DEPARTMENT OF COMPUTER SCIENCE - TALK

Date: Friday, March 30, 2007
Time: 2:30 p.m.
Place: Ryerson 251 (1100 E. 58th St.)

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Speaker: NINA SINGHAL HINRICHS, Stanford University

Web page:  http://www.stanford.edu/~nsinghal/

Title:  Modeling macromolecular dynamics from simulations

Abstract:

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 at 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.

Bio:  Nina Singhal Hinrichs is a Ph.D. student in Computer Science at
Stanford University.  She received her B.S. degree in Chemical  
Engineering
and Mathematics from MIT in 2001.  Her current research interests  
involve
applying computational and statistical techniques to understand  
molecular
dynamics trajectories.

***The talk will be followed by refreshments in Ryerson 255***

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Hosts:  Stuart A. Kurtz & Ridgway Scott

People in need of assistance should call 773-834-8977 in advance.

For information on future CS talks: http://www.cs.uchicago.edu/events



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