Research Interests:
My main focus is the development of mathematical tools and numerical
methods for the analysis of dynamical systems which are both
stochastic and multiscale. The particular areas of applications I am
interested in include molecular dynamics, chemical and biological
networks, materials science, atmosphere-ocean science, and fluids
dynamics. My main objectives are to understand the pathways and rate
of occurrence of rare events in complex systems; to develop and
analyze multiscale algorithms for the simulation of random dynamical
systems; and, more generally, to quantify the effects of random
perturbations on the systems dynamics.
For more details and publications, see:
- Sampling techniques for rare events
- Random perturbations of dynamical systems
- Multiscale analysis: modeling and computations
- Stochastic PDEs and other models in turbulence theory and beyond
- The string method page
News:
Together with international collaborators we used novel
computational methods in combination with molecular
dynamics simulations to identify the pathways of
diffusion of a carbon monoxide
molecule inside myoglobin,
a protein involved in oxygen transport and
storage in various animal species including humans.
These results shed light on the important mechanism of
ligand-protein binding and indicate how dynamical aspects
of protein function are related to its structure.
The full article was published in the Journal of the American
Chemical Society and can be found
here.
In collaboration with Cameron Abrams (Drexel University) we used a
new molecular dynamics simulation method to investigate the conformational
variability of large proteins, a problem of interest e.g. in drug design.
The
method was applied to two complex proteins, a subunit of GroEL, a protein that
catalyzes folding of substrate proteins, and the HIV-1 envelope gp120, a
protein responsible for the fusion of the virus with a target cell. In this second
example, the method generates plausible all-atom models of the unliganded conformation of HIV-1 gp120, which was
uncharacterized so far and may prove
useful in the development of inhibitors and immunogens. The full article was published in the Proceeding of the National Academy of Science and can be
found
here.