William B. Gleason, Fellow

Applications of Advanced Computation and Digital Simulation to Problems of Biomedical Relevance

Parallel processing strategies of potential widespread utility in mass spectrometry include rapid “on-the-fly” analyses that allow for immediate identification of peptide analytes or, in the case of a failure to identify, immediate interactive modification of instrumental parameters for further experimentation. Such an application is particularly appropriate for small Linux clusters comprised of moderately- priced hardware, e.g. Pentium or AMDbased systems. Off-line analyses still remain of great importance, particularly those that involve large databases such as the everexpanding genomic databases for humans as well as other species. Here, parallel processing using high performance computers with large memory and disk capabilities is attractive. The most recent version (1.0.8) of the free-available program cidentify (a derivative of Pearson’s fasta program) has been compiled and run using the message passing interface (MPI) so that it can be executed on multiple-processor hardware under the Linux operating system on the Supercomputing Institute’s IBM Netfinity cluster. Parallel versions, also MPI-based, have also been developed to run on other multiprocessor computers, currently the Silicon Graphics Origin series and the IBM SP series.

This group is also studying the interaction of proteins with sulfated carbohydrate polymers related to the anticoagulant glycosamiloglycan, heparin. Ab initio calculations, using the gaussian package, are being used to develop suitable parameters for sulfated carbohydrates. Molecular dynamics (using Schulten’s namd/vmd package) simulations of sulfated model carbohydrates, including explicit solvent, are being used to test the parameterization. Schulten’s package is particularly useful because it scales very well when being used in parallel mode on multiple processors. In preparation for studying the interaction of sulfated materials with proteins, we have learned how to interactively control ligand interactions with macromolecules while a simulation is in progress. Ultimately, this capability will allow us to perform simulations more efficiently.

Research Group

Mira S. Chaurushiya, Supercomputing Institute Undergraduate Intern
Eric Eccleston, Faculty Collaborator
Eric R. Johnson, Supercomputing Institute Undergraduate Intern
William Ojala, Research Associate