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Molecular biophysics
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. Specific 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.
Active Research Areas                           
Biomolecular Electrostatics
How can one estimate, accurately and efficiently, long-range electrostatic interactions that play crucial role in determining biological properties of macromolecules? How can we use these estimates to gain insights into fundamental properties of biopolymers?
Algorithms to speed-up molecular simulations
Realistic molecular dynamics simulations of even small structures require the computational power of today's fastest supercomputers. Can we combine novel computational methods with "better hardware" (for example, general purpose graphical processing units (GPGPU) ) to deliver computational power exceeding the fastest supercomputers, to your desktop?
DNA compaction and deformation
DNA compaction plays vital role in key cellular processes such as cell differentiation, DNA replication, repair, and transcription. Which fundamental physical principles control the DNA compaction? And exactly how flexible is the DNA polymer?
Nucleic acid condensation induced by ions
Our goal is to develop a quantitative, atomic-level understanding of how multivalent ions, including biologically relevant polyamines, mediate attractive forces between nucleic acid molecules (DNA, RNA) that lead to various nucleic acid condensation phenomena observed in experiments.
3D organization of the genome: the basic principles.
Our goal is to elucidate, through a combination of of computation and experiment, the mechanisms of nonrandom genome organization.

Other things I worked on in the past
Protein Folding
One of the largest challenges in modern science is working out how proteins curl up into their complex shapes...
Functional dynamics of biomolecules
Biological function of many biomolecules, such as proteins or DNA, is intricately related to their dynamical properties. Can we understand these relationships using computational methods?
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...
Insights into the RNAi mechanism
Can we use bioinformatics to help us understand how small fragments of RNA interact with the messenger RNA?