Postdoctoral Fellow

Roummel F. Marcia Dept. of Biochemistry Faculty Supervisor: Julie Mitchell Email: rmarcia@biochem.wisc.edu 262-3040

My research involves predicting the structures of protein-ligand complexes. I have previously developed a global optimization method for minimizing the potential energy for binding two molecules, assuming that both molecules are rigid. While this method is generally able to suggest the correct mode of protein-ligand interaction, in cases where the interactions involve some induced fit, this approach has only achieved moderate success. As a CIBM postdoctoral fellow, I will investigate flexibility in the side-chains whose configurations are determined by electrostatic information and shape complementarity near the surface interface of the molecules that will hopefully lead to more accurate and realistic results.

CV

CV 2004 ( pdf format)

Publications

Dunlavy, D., S. Joo, R. Lin, R. F. Marcia, A. Minut and J. Sun (2000). Numerical steady-state solutions of non-linear DAEs arising in RF communication circuit design. Mathematical Modeling in Industry Report, Institute for Mathematics and Its Applications: Preprint 1752.

Marcia, R. F., Mitchell, J. C. and Rosen, J. B. (submitted). Iterative convex quadratic approximation for global optimization in protein docking. Comput. Optim. Appl.

Marcia, R. F. and J. B. Rosen (in press). Convex quadratic approximation. Comput. Optim. Appl.

Bank, R. E., Gill, P. E., and Marcia, R. F. (to appear). Interior methods for a class of elliptic variational inequalities. Proceedings of the First SANDIA Workshop on Large-scale PDE Constrained Optimization.

Marcia, R. F. (2002). Interior-point methods for large-scale optimization. Ph.D. dissertation, University of California-San Diego.

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