| Bob Sinkovits
Baker CryoEM Laboratory San Diego Supercomputer Center |
I hold a Ph.D. in physics and previously worked as a research physicist in the Laboratory for Computational Physics at the Naval Research Laboratory (NRL). My work at NRL focused mainly on molecular dynamics, Monte Carlo, and direct simulation Monte Carlo (DSMC) calculations for a number of problems in granular materials, diamond chemical vapor deposition, and statistical physics.
While a member of the Scientific Computing Department (SciComp) at SDSC, my main contributions were in the performance tuning of numerically intensive applications in a number of areas, including:
During this time, I also led the user transitions from the Cray C90 to the Cray T90 and from the Cray T3D to SDSC's first large IBM system. In June '01, I left SciComp to join the Alliance for Cellular Signaling so that I could focus my attention on problems in computational biology.
In the fall of '05, I joined Tim Baker's cryoEM laboratory and have since taken charge of software development for 3D image reconstruction of viruses. Through a combination of scalar optimization, parallelization of existing serial codes, and the development of the AUTO3DEM automated image reconstruction system (in collaboration with Xiaodong Yan), structure determination projects that used to take many months to complete can now be finished, in the best cases, in a matter of hours.
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San Diego Supercomputer Center
University of California, San Diego 9500 Gilman Drive, MC-0505 La Jolla, CA 92093-0505 email: sinkovit at sdsc.edu |