ITR: Center for Computational Biophysics

University Of California-San Diego, La Jolla CA

Investigators

Abstract

A Center for Computational Biological Physics is established at the University of California, San Diego as part of the Information Technology Research Initiative (ITR). This ITR Center, located in La Jolla, CA and operating as a partnership between UC San Diego, the San Diego Supercomputer Center, the Scripps Research Institute and the Salk Institute for Biological Studies, will pioneer new computational paradigms in support of this overall goal. This is critical as biology evolves into a data-rich predictive science and increasingly turns to complex systems physics for help in in developing the necessary conceptual underpinnings and the concomitant calculational strategies. Specifically, the Center will focus on two major projects, one each at the supra-molecular and sub-cellular scales. The first involves combining molecular dynamics with powerful electrostatic solvers so as to enable the study of large-scale biological machines. The system to be used as a testbed is the ribosome, where the recently determined structure allows for the application of these ideas. The second involves extending the MCell concept, originally developed for synapse simulations, into a broadly useful tool for studying sub-cellular-cellular scale signal transduction processes. Here the target applications concern calcium dynamics in cardiac cells and its control by hormonal action. In addition to these research goals, the Center will be actively involved in training a new class of computational scientist, one who can directly communicate with experimentalists and focus the computation so as to answer meaningful questions for these systems. Finally, the ITR Center is directly coupled to a complementary effort, the Physics Frontiers Center for Theoretical Biological Physics, which is focused on the conceptual advances that will eventually serve as a source of new demand for novel computational strategies. The ITR award is jointly funded by the Physics, Materials Research and Chemistry Divisions of the NSF.