PARALLEL COMPUTER FOR MEMBRANE AND PROTEIN SIMULATIONS

This proposal requests funds to purchase a parallel-processing computer
system that will provide a highly cost effective solution to the problem
of carrying out large-scale computations of direct relevance to many of
the N.I.H.-funded research projects in Chemistry Dept. at the University
of Pennsylvania. The group of researchers in question is currently
studying structural and dynamical behavior in problems, ranging from
macromolecules, micelles, and membranes, to proteins and genes, using a
variety of experimental and theoretical techniques. Computer simulation molecular dynamics calculations have now emerged as
a powerful complement to real experiments such as X-ray and neutron
scattering, NMR laser-light scattering and synthesis, which are currently
underway at Penn. to probe biophysical systems. The request parallel-processing computer system will mainly be used to
carry out simulations and modelling designed to aid the interpretation
of experiments relating to: a) model membranes and membrane-protein interactions b) structure-assisted protein design c) molecular motions in ligands bound to proteins d) lipid monolayers and bilayers, plus coupled protein-membrane systems e) protein structure refinement, constrained via NMR data f) Conformational studies of macromolecules