Biological Systems | Materials and Mechanical Properties | Geophysics Research | Network Research | Simulations of Large Complex Networks
Research projects in rational drug design, structural biology, modeling of large biological
assemblies (such as ribosomes and liposomes), micro-array data analysis and biomechanics:
One research group is focusing on the biological targets of phospholipid growth factors
(PLGF) that include receptor proteins in two families, the membrane-bound G protein-coupled
receptor (GPCR) family and the nuclear peroxisome proliferator activated receptor
gamma. They develop structural models of the GPCR family members responsive to PLGF
and use these models to understand, at the molecular level, interactions between PLGF
and their receptors. The group uses several computational methods (homology modeling,
docking, QSAR and pharmacophore) to develop receptor-selective molecules that can
be used by experimental collaborators to probe the physiology of individual PLGF receptors.
Another research group is modeling the domain motion of proteins, RNA and biological
assemblies. They use molecular dynamics, coarse-grained elastic network model, and
normal mode analysis to understand how the enzyme dynamics is related to its function.
The group currently is modeling the mechanics of ribosome.
Other researchers are interested in the structure and dynamics of lipid membranes
from a biophysicist point of view. They use coarse-grained models to study the multi-component
phase separation in lipid membranes. Researchers are also developing algorithms
that can be applied in computational biology and bioinformatics, in micro-array data
analysis and in biomechanics. This latter group uses finite element analysis to study
the influence of the shape of the spacer on the stress distribution in the spine.
Materials and Mechanical Properties
Research projects that study metal oxides at the atomic level, soft condensed matter
at molecular to meso-scale, fluid mechanics, to solid mechanical systems: One group
uses statistical mechanical methods (Monte Carlo and molecular dynamics) to study
how the nanoscale confinement could affect the properties of polymers.
Other groups are interested in computational modeling of the thermodynamic and kinetic
behavior of polymer nanocomposites, the dynamics and transport of polymers in nanopores,
modeling fluid flow, especially those with a highly deformable gas-liquid interface
at which surface tension forces are significant and in dynamic analysis and design
of standard gear transmission systems using computer simulation and modeling.
Research projects that study crustal deformation and earthquake clustering in intra-continental
settings which include multiple earthquake cycles and linear and non-linear viscoelastic
processes is the focus of one group. Other groups study: complex seismic hazard modeling
using more realistic near-surface geology, crustal structure, and fault rupture processes;
probabilistic seismic hazard analyses for estimates of hazard uncertainty using Monte
Carlo modeling; and 3D finite-difference and finite-element ground motion simulations.
Research projects in the design and evaluation of routing protocols for high-speed
networks is the focus of one group. Another group is designing a scalable simulator
that can be run on parallel computers to simulate tens of thousands of networks and
millions of hosts to study the propagation of Internet worms which can infect millions
of computers in a few minutes.
Simulations of Large Complex Networks
Research projects in simulating large complex systems, such as neural and social systems,
using analysis tools from statistical physics: The models for these systems are specially
structured lattices which are evolved in time and their global dynamics observed.
The models are large and consist of thousands of components, each of them following
local rules. Since in complex systems prediction of long term system's behavior based
on the initial configurations is not in general analytically solvable (except for
some simple cases), simulations are necessary and generally requiring many processors.