SCIENCE AT THE EDGE SEMINAR

Friday, December 1 at 11:30am

Room 1400 Biomedical and Physical Sciences Bldg.

Refreshments at 11:15


Speaker: Steve Plimpton
         Sandia National Laboratories

Title:   Modeling Biological Cells Via Simulations of Diffusing
         Reactive Particles

Abstract:

Cells interact with their environment via a cascade of biochemical
reactions that invoke a signaling, metabolic, or regulatory response.
The properties of these reaction networks can be modeled at various
levels of detail from continuum to stochastic, and steady-state
to kinetic. Our group (and others) have been developing tools that
attempt to simulate how such networks execute in cellular geometries with
spatio-temporal detail. In our model a single particle represents a
protein, complex, or other biomolecule. Cellular compartment boundaries
are idealized or triangulated surfaces. Particles diffuse via 3d Brownian
motion within the cytoplasm, or in 2d on membrane surfaces. When
particles are near each other, they interact in accord with Monte Carlo
rules to perform biochemical reactions which can represent complex
formation, dissociation events, ligand binding, etc.


In this talk, I'll describe the methods used to perform reactions, and
compare them to Gillespie's original Stochastic Simulation Algorithm.
I'll illustrate the effects stochasticity and spatial organization have
on biochemical networks at the cellular scale and show examples of how
such models can address biological questions. I'll also highlight some
of the interesting computational and algorithmic issues. This is an
emerging field of simulation with many open questions, but the eventual
goal is to enable whole-cell models of protein networks with realistic
numbers of biomolecules.


Support: This work has been partially funded by the US Department of
Energy's Genomics: GTL program (www.doegenomestolife.org) under project
"Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling" (www.genomes-to-life.org).