About
Articles by Vijay
Activity
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This summer, insitro hosted an exceptional group of students taking a pause from their BS, MS or Ph.D. studies. They hailed from near – University…
This summer, insitro hosted an exceptional group of students taking a pause from their BS, MS or Ph.D. studies. They hailed from near – University…
Liked by Vijay Pande, PhD
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Check out "Reengineering Life: The Next Frontiers in Science" - the latest Fareed Zakaria GPS special report on CNN profiling Nobel Laureate and…
Check out "Reengineering Life: The Next Frontiers in Science" - the latest Fareed Zakaria GPS special report on CNN profiling Nobel Laureate and…
Liked by Vijay Pande, PhD
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It's time to build new healthcare approaches to tackle chronic diseases. Casey Means, MD joins me on our podcast and lays out a compelling argument…
It's time to build new healthcare approaches to tackle chronic diseases. Casey Means, MD joins me on our podcast and lays out a compelling argument…
Shared by Vijay Pande, PhD
Experience & Education
Patents
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Method for rapidly approximating similarities
Issued US US 8706427 B2
Methods and algorithms are presented that implement linear algebraic techniques for rapidly estimating chemical similarities for several popular measures. The methods of the present invention reflect source similarity measures for both Tanimoto calculation and rank ordering. After a precalculation step on a database, the methods of the present invention afford several orders of magnitude of speedup in database screening. The present invention also provides an asymptotic speedup for large…
Methods and algorithms are presented that implement linear algebraic techniques for rapidly estimating chemical similarities for several popular measures. The methods of the present invention reflect source similarity measures for both Tanimoto calculation and rank ordering. After a precalculation step on a database, the methods of the present invention afford several orders of magnitude of speedup in database screening. The present invention also provides an asymptotic speedup for large similarity matrix construction problems, reducing the number of conventional slow similarity evaluations required from quadratic to linear scaling.
Other inventorsSee patent -
Accelerated molecular dynamics of proteins and other biomolecules
Issued US WO 2009151696 A3
Embodiments herein relate to the field of computational biochemistry, in particular to accelerated molecular dynamics of proteins and other biomolecules. Various embodiments disclosed herein include methods, systems, and apparatus for determining the state, for example the kinetics or thermodynamics, of a biomolecule system. In some embodiments, the methods include partitioning the system's degrees of freedom into a subspace and a subspace complement according to frequency using Normal Mode…
Embodiments herein relate to the field of computational biochemistry, in particular to accelerated molecular dynamics of proteins and other biomolecules. Various embodiments disclosed herein include methods, systems, and apparatus for determining the state, for example the kinetics or thermodynamics, of a biomolecule system. In some embodiments, the methods include partitioning the system's degrees of freedom into a subspace and a subspace complement according to frequency using Normal Mode Analysis (NMA), determining a harmonic approximation to the system around an initial equilibrium structure using a Mass Reweighted Hessian (MRH) of a biomolecular force field, using the partitioning to construct a damping matrix for the Langevin equation that overdamps and propagates high frequency modes using Brownian dynamics, propagating the low frequency modes using full Langevin dynamics, and accelerating the Brownian dynamics on the high frequency modes using an energy minimization. A coarse-grained normal mode analysis (CNMA) is also presented that enables application of this approach to very large proteins and long timescales.
Other inventorsSee patent
Honors & Awards
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Delano Award for Computational Biosciences
American Society for Biochemistry and Molecular Biology
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Mentoring Award, Stanford University Postdoctoral Association
Stanford University Postdoctoral Association
“In recognition of his excellent mentoring of postdocs."
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Michael and Kate Bárány Award for Young Investigators
Biophysical Society
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Thomas Kuhn Paradigm Shift Award
American Chemical Society
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Fellow
American Physical Society
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Netxplorateur of the Year
Netxplorateur
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Guinness World Record, Folding@home First to a Petaflop
Guinness
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Irving Sigal Young Investigator Award
Protein Society
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Technovators Award
Global Indus
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TechReview TR 100
MIT TechReview
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National Science Foundation Graduate Fellowship
National Science Foundation
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Fourth place, Westinghouse Science Talent Search Scholarship
Westinghouse Science
Languages
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English
Native or bilingual proficiency
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French
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I just had the experience of a lifetime. This past weekend, a group of 11 Omadans accomplished their first ultra endurance event 29029 Everesting…
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great opportunity to learn from a master!
great opportunity to learn from a master!
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I can't think of anything scarier than cognitive motor dissociation nor more hopeful than neural implants that allow people to communicate…
I can't think of anything scarier than cognitive motor dissociation nor more hopeful than neural implants that allow people to communicate…
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New blog post, and the first collaborative one with Tommaso Dreossi, on the human side of biotech! This one compares and contrasts the good, bad and…
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