Computational Chemistry and Neutron Scattering of Biological and Materials Systems
Joseph E. Curtis
Mentor: Dan A. Neumann
Neutron Condensed Matter Science Group
Materials Science and Engineering Laboratory
Room E19, Building 235, Mail Stop 8562
Phone: (301) 829-9023, Fax: (301) 921-9847
I am not a Sigma Xi member
We are applying the tools of computational chemistry to a diverse set of neutron scattering experiments of biophysical and material systems. We use modern classical and ab-initio computational chemistry methods to advance our understanding of the structure and dynamics of complex systems and synergistically we are using experimental measurements to guide the development of our simulation efforts.
One area of active research is the investigation of methyl dynamics as a probe of dynamical activity in biological systems. We have found that there are hydration dependent and hydration independent activation mechanisms of methyl protons in proteins in native and glassy powders. The activation of such dynamical motions has direct implications in the elucidation of both the maintenance and preservation of biological function. Additionally, we are developing methods to investigate methyl dynamics in more controlled environments. For example, we are studying methyl bearing organic molecules in clathrate hydrate cages to refine our computational methods.
A second area of research we will present is the use of classical molecular dynamics to investigate the structural and dynamical changes of polyaromatic hydrocarbons as a function of pressure. We have developed force-field based methods that reproduce both neutron scattering spectra and ab-initio calculations of crystalline tetracene at a variety of pressures. These computational methods may be useful to determine the factors that govern conductivity in these important materials.
The last area of research is the application of constrained molecular dynamics simulations, bioinformatics, and stochastic optimization methods to determine structures of biological molecules in solution that are consistent with observed small-angle neutron scattering (SANS) spectra. By applying a uniform restraining force proportional to the observed radius of gyration of macromolecules we have determined structures consistent with SANS data for a variety of systems. Using this approach to determine otherwise unknown structures, we have calculated the dynamics of both folded and unfolded forms of a catalytic RNA in solution. And finally, we have developed the first complete models of the full-length HIV gag protein monomer using combined molecular dynamics, bioinformatics, and Monte Carlo techniques.