The central theme of my research is to use theoretical models to understand the physical properties of biomaterials, such as proteins, nucleic acids, and lipid membranes, and to apply this understanding to design novel synthetic systems, including small molecule therapeutics. In particular, I am interested in the self-assembly properties of biomolecules: for example, how do protein and RNA molecules fold and how do lipid vesicles form and fuse? How do proteins misfold and aggregate and how can we use our understanding of this process to tackle misfolding related diseases, such as Alzheimer's or Huntington's Disease?

As these phenomena are complex, spanning from the molecular to mesoscopic length scales and the nanosecond to millisecond timescales, my research employs a variety of statistical mechanical analytic models as well as Monte Carlo, Langevin dynamics, and molecular dynamics computer simulations on workstations and massively parallel supercomputers, superclusters, and large-scale worldwide distributed computing (see http://folding.stanford.edu).

For example, we are currently investigating the nature of protein folding kinetics, i.e. what determines the mechanism and rate of how a given protein folds and how can one redesign or improve these properties. We are also investigating the analogous interplay between self-assembly mechanisms and molecular structure and design in RNA folding and lipid vesicle formation and fusion.

Since such problems are extremely computationally demanding, we have developed distributed computing projects for protein folding dynamics ("Folding@Home": http://folding.stanford.edu) which has attracted over 2,000,000 PCs since the project's beginning in October 1, 2000 and today is more powerful than the equivalent power of a 100,000 CPU cluster. Such enormous computational resources have allowed us to simulate unprecedented folding timescales (microseconds to milliseconds) and statistical precision and accuracy (such as very accurate and precise free energy calculations). For more details, please see
http://pande.stanford.edu.

1) "How well can simulation predict protein folding kinetics and thermodynamics?" C. D. Snow, E. J. Sorin, Y. M. Rhee, and V. S. Pande. Annual Reviews of Biophysics,34, 43-69 (2005)

2) "Sub-millisecond kinetics and intermediates of membrane fusion from molecular dynamics," P. Kasson, N. Kelley, N. Singhal, M. Vrjlic, A. Brunger, and V. S. Pande. Proceedings of the National Academy of Sciences , USA , 103, 11916-21 (2006)

3) "Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory," I. Suydam, C. D. Snow, V. S. Pande and S. G. Boxer. Science, 313, 200-4 (2006)

4) "Simulations of the Role of Water in the Protein Folding Mechanism," Y.M. Rhee, E.J. Sorin, G. Jayachandran, E. Lindahl, V.S. Pande, Proceedings of the National Academy of Science, USA, 101, 6456-6461 (2004).

5) "How Can Proteins be Unfolded and Yet Have Native-like Properties: Structural Correspondence between the Alpha Helix and the Random-Flight Chain," B. Zagrovic and V.S. Pande, Nature Structual Biology, 10, 955-961 (2003).

6) "Folding of a bba Protein: Simulation and Theory," C. Snow, H. Nguyen, M. Gruebele, and V.S. Pande, Nature, 420, 102-106 (2002)

7) "Screen Savers of the World, Unite!" M.R. Shirts and V.S. Pande, Science, 290, 1903-1904 (2000).