home research lab members teaching publications software Active Research Areas We work at the interface of physics, biology, and computer science; the research is a collective effort of our group members who have background in one or more of these fields. The underlying theme is complexity of the systems: the phenomena we study span multiple scales at both the temporal and spatial levels. The projects range from those based on analytical techniques that require no computation, to ones where computation on highly parallel clusters is essential. The funding comes from the NIH and the NSF. Biomolecular Electrostatics How can one estimate, accurately and efficiently, the long-range electrostatic forces that play crucial role in determining biological properties of macromolecules? How can we use these estimates to gain insights into fundamental properties of biopolymers? Protein Dynamics Biological function of many proteins is intricately related to their dynamical properties. Can we understand these relationships using computational methods? DNA compaction and bending How is the DNA compacted at its most fundamental level inside the cell -- the nucleosome? And exactly how flexible is it? Insights into the RNAi mechanism Can we use bioinformatics to help us understand how small fragments of RNA interact with the messenger RNA? Other things I worked on Protein Folding One of the largest challenges in modern science is working out how proteins curl up into their complex shapes... Theory of Cooperative Ligand Binding Binding of ligands to macromolecules is one of the most important reactions in biology... Proton-pumping mechanism of Bacteriorhodopsin Bacteriorhodopsin is the smallest autonomous light-harvesting system...