Council on Academic Computing

January 16, 2008

Meeting Summary

Lillian Chong, Department of Chemistry

Lillian Chong, Assistant Professor in the Department of Chemistry, discussed her research on protein folding.  Professor Chong uses theory and simulation to study how proteins fold, bind their partners, and catalyze reactions, with an emphasis on how malfunctions at the molecular level can be linked to clinical data for various diseases.  Recently, many proteins that perform essential roles in cellular signaling and regulatory pathways have been found to be unstructured, thus challenging the assumption that proteins must fold into well-defined, globular structures in order to carry out their functions. These proteins fold, or become ordered, only upon binding their partner proteins, suggesting a new paradigm of protein-protein recognition. 

Experiments often do not provide the structural details necessary to study these processes.  A natural alternative is to use atomistic molecular dynamics simulations, which provide the time resolution and detail necessary for monitoring the step-by-step progression of conformational changes.  Due to the large computational cost required for simulating these conformational changes, Professor Chong applies methods that take advantage of distributed computing by making effective use of a large ensemble of short, independent simulations.  A distributed computing network that is available to researchers like Professor Chong, who study protein folding, is Stanford University’s Folding@home.

David Earl, Department of Chemistry

David Earl, Assistant Professor in the Department of Chemistry, uses the tools of computer simulation and statistical mechanics to study chemical, biological, and material processes.  He focuses upon several areas, including immune system dynamics and vaccine design, coarse-grained models of complex molecular species, and biological evolution.  Examples of his research include:

  • The immune system response to pathogens that are troublesome due to their high evolutionary rates, such as influenza (including H5N1), HIV, and cancers, as well as autoimmune diseases.  He uses models of protein structure and function, Monte Carlo simulations, and genetic algorithms to mimic selection in the immune system and pathogen evolution.
  • Fundamental theories of biological evolution and the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space.  He focuses on explaining how modularity, canalization, and robustness can evolve in biological systems and determining how these properties influence the evolution and evolvability of populations.
  • The properties of mesomorphic materials composed of complex molecular species with novel architectures.  In these systems, microphase separation, induced by chemical interactions between different parts of molecules, can be used as a tool to build new materials that contain structures that are ordered on the nanoscale.  He is developing coarse-graining procedures and new computer simulation techniques that can bridge both time and length scales.

Report from Computing Services and Systems Development

Jinx Walton, Director of Computing Services and Systems Development, discussed several aspects of CSSD operations:

  • Optimization of wireless access ports
  • Wireless access at regional campuses
  • iTunes and the University
  • Printing quotas in campus computing labs
  • Love Your Computer Week

Miscellaneous

Members of the Council discussed several other issues:

  • The Center for Energy soon will be launched.
  • Simulation and Modeling Center will be launched later in the year.
  • Computing groups and departments continue to work on Pittgrid.