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Vijay Pande

Assistant Professor, Chemistry and (by courtesy) of SSRL, Chemistry, Stanford University

IRG 2

Telephone: (650) 723-3660
Fax: (650) 725-0259
Email: pande@stanford.edu | Web site

Stanford University, Stanford, CA (b. 1970).
B.A.with Honors, Physics, 1992, Princeton University;
Ph.D., Physics, 1995, Massachusetts Institute of Technology.   

Pande’s background has centered around molecular biophysics, including his PhD at MIT, where he was an NSF fellow in biophysics, and during his tenure as a Miller Fellow at UC Berkeley.

Pande is interested in understanding the theory of the self-assembly phenomena of biopolymers and applying this understanding to non-biological systems. For example, he works on understanding how proteins and RNA fold and then use the lessons learned to design and characterize synthetic ” foldamers,” such as poly-phenyl acetylene. In order to study these systems, he also develops new computer simulation techniques for studying the kinetics and thermodynamics of proteins, including new algorithms for massively parallel supercomputers and new techniques to greatly speed molecular dynamics calculations, allowing him to reach the microsecond timescale with atomic-resolution models.

Selected Publications:

  1. Kasson, P., Pande, V. S.;  "Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide".  PSB, 2006
  2. Kasson, P., Kelley, N., Singhal, N., Vrjlic, M., Brunger, A.,  Pande, V. S.;  "Sub-Millisecond Kinetics and Intermediates of Membrane Fusion from Molecular Dynamics".  Proceedings of the National Academy of Sciences, USA, 103 11916-21, 2006.
  3.  

    Glazer, M.I., Fidanza, J.A., McGall, G.H., Trulson, M.O., Forman, J.E., Frank, C.W.; “Kinetics of Oligonucleotide Hybridization to DNA Probe Arrays on High-Capacity Porous Silica Substrates,” Biophysical Journal, 93, 1661-1676, 2007.

     

    Stalgren, J.J.R., Botschkova, K., Ericsson, J.-C., Frank, C.W., Knoll, W., Satija, S., Toney, M.F.; “Enrichment of Deuterium Oxide at Hydrophilic Interfaces in Aqueous Solutions,” Langmuir, 23, 11943-11946, 2007.

     

    Shen, Y., Powell, R. L., Longo, M. L.; “Interfacial and Stability Study of Microbubbles Coated with a Monostearin/Monopalmitin-Rich Food Emulsifier and PEG40 Stearate”, Journal of Colloid and Interface Science, 321, 186–194, 2008.

     

    Lee, J.S., Dylla-Spears, R., Teclemariam, N.P., Muller, S.J.; “Microfluidic Four-Roll Mill for all Flow Types”. Applied Physics Letters, 90, 074103, 2007.

    Kasson, P., Pande, V. S.; “Ensemble Molecular Dynamics Simulation Predicts Membrane Fusion Mechanism Controlled by Lipid Composition”. PloS Computational Biology, 3, 220, 2007

     

    Kasson. P., Zomorodian, A., Park, S., Singhal, N., Guibas, L., Pande, V. S.; “Persistent Voids: a New Structural Metric for Membrane Fusion”. Bioinformatics, 23, 1753-9, 2007.

     

    Lee, J.S., Shaqfeh, E.S.G., Muller, S.J.; “Dynamics of DNA Tumbling in Shear to Rotational Mixed Flows: Pathways and Periods”. Phys. Rev. E., 75, 040802(R), 2007.

     

    Teixeira, R., Dambal, A.K., Richter, D.H., Shaqfeh, E.S.G., Chu, S.; “The Individualistic Dynamics of Entangled DNA in Solution”. Macromolecules, 40, 7, 2461-2476, 2007.

     

  4. Sly, J.; Bonifacio, C. S.; Chang, L.; Glab, K. L.; Lee, V. Y.; McNeil, M.; Jefferson, C. M.; Frommer, J. E.; Risk, W. P.; Miller, R. D.; “Reaching for the Stars:Layered Polyvalent Self-Assembly of Hyperbranched Pigment Arrays”. PMSE Preprints, 97, 200-201, 2007.

    Sills, S., Unal, K., Bozano, L., Frommer, J., Scott, J. C.; "Local characterization of vapor-deposited electrode edges in thin film organic electronic devices". J. Vac. Sci. Technol., B 25, 421-425, 2007.

    Riposan, A.; Li, Y.; Tan, Y.H.; Galli, G.; Liu, G.-Y. “Structural Characterization of Aldehyde–Terminated Self-Assembled Monolayers”. J. Phys. Chem. B., 111; 12727-12739, 2007.

    Gowrishankar, V., Scully, S R., Chan, A.T., McGehee, M.D., Wang, Q., Branz, H.M.; “Exciton Harvesting, Charge Transfer, and Charge-Carrier Transport in Amorphous-Silicon Nanopillar/Polymer Hybrid Solar Cells”. Journal of Applied Physics, 103, 064511, 1-8, 2008.

     

    Gowrishankar, V., Scully, S.R., Chan, A.T., McGehee, M. D., Wang, Q., Branz, H.M.; “Exciton Harvesting, Charge Transfer, and Charge-Carrier Transport in Amorphous-Silicon Nanopillar/Polymer Hybrid Solar Cells”. Journal of Applied Physics, 103, 064511, 1-8, 2008.

    Sly, J.; Samuel, J. D. J.; Bonifacio, C. S.; Chang, L.; Lee, V. Y.; McNeil, M.; Risk, W. P.; Jefferson, C. M.; Miller, R. D.; “Versatile Layer-by-Layer Surface Modification using Functionalized Star-Polymers and Epitaxial Polyvalent Self-Assembly”. PMSE Preprints, 96, 319-320, 2007.

    Kasson, P., Pande, V.S.; “Ensemble Molecular Dynamics Simulation Predicts Membrane Fusion Mechanism Controlled by Lipid Composition”. PloS Computational Biology, 3, e220, 2007.

    Li, Y., Lu, D., Swanson, S. A., Scott, J. C., Galli, G.; "Microscopic Characterization of the Interface between Aromatic Isocyanides and Au(111): a First-Principles Investigation", Phys. Chem. C 112, 6413 2008.

  5. Tanaka, M., Hermann, J., Haase, I., Fischer, M., Boxer, S.; "Frictional Drag and Electrical Manipulation of Recombinant Proteins in Polymer Supported Membranes". Langmuir, 23, 5638-5644, 2007.

     

    Chan, Y.-H., Lenz, P., Boxer, S.; "Kinetics of DNA-Mediated Docking Reactions between Vesicles Tethered to Supported Lipid Bilayers". Proceedings of the National Academy of Sciences, 104, 18913-18918, 2007.

     

    ChanY.-H., Boxer,S. "Model Membrane Systems and their Applications". Current Opinion in Chemical Biology, 11, 581-587, 2007.

     

    Lin, W-C., Blanchette, C. D., Longo, M.L.; “Fluid-Phase Chain Unsaturation Controlling Domain Microstructure and Phase in Ternary Lipid Bilayers Containing GalCer and Cholesterol”. Biophysical Journal, 92, 2831-2841, 2007.

     

    Blanchette, C. D., Lin, W-C., Orme, C. A., Ratto, T. V., Longo, M. L., “Using Nucleation Rates to Determine Interfacial Line Tension of Symmetric and Asymmetric Lipid Bilayer Domains”. Langmuir, 23, 5875-5877, 2007.

     

    Blanchette, C. D., Orme, C. A., Ratto, T. V., Longo, M. L.; “Quantifying Growth of Symmetric and Asymmetric Lipid Bilayer Domains”. Molecular and Surface Forces, Langmuir Special Issue, 24, 1219-1224, 2008.

     

    Blanchette, C. D., Lin, W-C., Orme, C. A., Ratto, T. V, Longo, M. L., “Domain Nucleation Rates and Interfacial Line Tensions in Supported Bilayers of Ternary Mixtures Containing Galactosylceramide”. Biophysical Journal, 94, 2691–2697, 2008.

     

    Kasson, P., Pande, V. S.; “Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide.” Pacific Symposium on Biocomputing, 12, 40-50, 2007.

     

    Teclemariam, N.P., Beck, V.A., Shaqfeh, E.S.G., Muller, S.J.; “Dynamics of DNA Polymers in Post Arrays: Comparison of Single Molecule Experiments and Simulations”. Macromolecules, 40, 3848-3859, 2007.

    Lueth, C.A., Shaqfeh, E.S.G., “Tethered DNA Shear Dynamics in the Flow Gradient Plane: Application to Double Tethering”. Korea-Australia J. Rheol., 19, 3, 141-146, 2007.

     

    Beck, V.A., Shaqfeh, E.S.G., “Ergodicity-Breaking and the Unravelling Dynamics of a Polymer in Linear and Non-Linear Extensional Flows”. J. Rheol., 51, 3, 561-574, May/June, 2007.

     

    Hoffman, B., Shaqfeh, E.S.G., “The Dynamics of the Coil-Stretch Transition for Long, Flexible Polymers in Planar Mixed Flows''. J. Rheol., 51, 5, 947-969, 2007 (see also Virtual Journal of Biological Physics Research September 1, 2007.)

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