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Vijay Pande
Profile: http://med.stanford.edu/profiles/Vijay_Pande/
Contact: Academic Appointments
Appointment
Organization
Assistant Professor
Chemistry
Assistant Professor (By courtesy)
Member
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Curriculum Vitae PDF
Honors & Awards
Title
Organization
Date(s)
Irving Sigal Young Investigator Award
Protein Society
2006
Teacher-Scholar Award
Dreyfus Foundation
2003
Terman Fellow
Stanford University
2002
TR100
MIT Technology Review
2002
Global Indus Technovators Award
IBC@MIT
2004
Professional Education
Degree
Awarding Institution
Field of Study
Year of Graduation
BA
Princeton University
Physics
1992
PhD
MIT
Physics
1995
Postdoctoral Advisees
Kim Branson,
John Chodera,
Peter Kasson,
Edgar Luttmann,
Michael Schnieders,
Vincent Voelz
Web Site Links
Research/Lab website:
Folding@Home
Research Interests
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. In particular, I am interested in the self-assembly properties of biomolecules, i.e. how do protein and RNA molecules fold and how do lipid vesicles form and fuse? 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, two exciting directions in protein folding theory are the emerging evidence for general physical properties of protein folding and the means to design proteins to fold to a desired conformation. The theory of protein design has gone hand in hand with the theory of protein folding, as design is both a test of our understanding and an application of folding theory. Indeed, analytic models and computer simulations have lead to theories for the equilibrium protein phase behavior as well as methods to design protein sequences to fold to desired conformations. 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. Finally, 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) and sequence design informatics (“Genome@Home”: http://genomeathome.stanford.edu) which combined have attracted over 1,000,000 PCs since the project’s beginning in October 1, 2000. Such enormous computational resources have allowed us to simulate unprecedented folding timescales (microseconds to tens of microseconds) and sequence sampling
(hundreds of thousands of designed sequences). For more details, please see
http://pande.stanford.edu.
For example, two exciting directions in protein folding theory are the emerging evidence for general physical properties of protein folding and the means to design proteins to fold to a desired conformation. The theory of protein design has gone hand in hand with the theory of protein folding, as design is both a test of our understanding and an application of folding theory. Indeed, analytic models and computer simulations have lead to theories for the equilibrium protein phase behavior as well as methods to design protein sequences to fold to desired conformations. 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. Finally, 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) and sequence design informatics (“Genome@Home”: http://genomeathome.stanford.edu) which combined have attracted over 1,000,000 PCs since the project’s beginning in October 1, 2000. Such enormous computational resources have allowed us to simulate unprecedented folding timescales (microseconds to tens of microseconds) and sequence sampling
(hundreds of thousands of designed sequences). For more details, please see
http://pande.stanford.edu.
Publications
- Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS "Simulations of the role of water in the protein-folding mechanism." Proc Natl Acad Sci U S A 2004; 101: 17: 6456-61 More »
- Zagrovic B, Pande VS "Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties." Nat Struct Biol 2003; 10: 11: 955-61 More »
- Snow CD, Nguyen H, Pande VS, Gruebele M "Absolute comparison of simulated and experimental protein-folding dynamics." Nature 2002; 420: 6911: 102-6 More »
- England JL, Park S, Pande VS "Theory for an order-driven disruption of the liquid state in water." J Chem Phys 2008; 128: 4: 044503 More »
- Rhee YM, Pande VS "Solvent Viscosity Dependence of the Protein Folding Dynamics." J Phys Chem B 2008; More »
73 publications: view full list
