Computational Challenges in Biophysics: Two Applications in
Hydrodynamics.  

by Borries Demeler, Ph.D. The University of Texas Health
Science Center at San Antonio

Date: 10/01 M      
Time: 4:00 pm - 5:15 pm   
SB 3.02.02

Abstract:
 
Application 1: 
Modeling of Macromolecules using Analytical Ultracentrifugation.
 
In this application, an ultracentrifuge is used to collect the
sedimentation and diffusion profile from mixtures of macromolecules
dissolved in a solution and exposed to a large centrifugal force
field. The resulting data are modeled and fitted to a finite
element solution of the differential equation that describes the
sedimentation-diffusion transport in the sample cell. I will discuss
the optimization approaches developed in my laboratory, and how
existing parallelisms are exploited for parallel processing using MPI. 
I will also discuss a Texas-wide supercomputing grid (TIGRE = Texas
Internet Grid for Research and Education) capable of load balancing
multiple analyses over multiple clusters.
 
Application 2:
Hydrodynamic bead-modeling of dynamic biopolymers.
 
A well developed framework exists to predict the hydrodynamic properties
such as sedimentation and diffusion of assemblies of spheres. In an
attempt to model X-ray or NMR atomic resolution structures with this
approach, the atoms of each molecule could be represented as individual
spheres.  However, most molecules of interest are too large to be
suitable for this framework - simplification is required, So, given a
molecular structure with atomic resolution, we wish to replace groups
of atoms with spheres of known density, center of gravity and radius to
create a slightly less detailed model of a molecule that can be analyzed
as an assembly of spheres. This approach is called bead modeling. We
want to go to the next level, which involves treating the model not
as a representation of rigidly connected spheres, but to introduce
constrained flexibility between the beads, and use Monte Carlo analysis
to predict conformational isomers of static bead models, and indeed,
to model Brownian motion and predict rotational diffusion coefficients.
 
I currently have positions open for PHD or Masters students interested in 
developing applications related to either project. An interest in
high performance computing, parallel processing, MPI, C++, mathematical
modeling, physics, and algorithm design is welcome.