Curriculum Vitae
Roummel F. Marcia, Ph.D.
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706-1544
rmarcia@biochem.wisc.edu
RESEARCH INTERESTS
Scientific Computation, Mathematical Biology, Large-Scale Numerical Optimization,
Interior-Point Methods, Global Optimization, Numerical Analysis, Numerical Partial
Differential Equations
EDUCATION
June, 2002
Ph.D. in Mathematics,
University of California, San Diego
Thesis: Primal-Dual Interior-Point Methods for Large-Scale Optimization
Dr. Philip E. Gill, advisor
1995
B.A. in Mathematics,
Columbia College, Columbia University, New York NY
1993-1994
Clare College, Cambridge University, UK
PROFESSIONAL EXPERIENCE
October 2003 - Present
Post-Doctoral Research. Department of Biochemistry and Mathematics, University of
Wisconsin-Madison, Madison, WI.
Advisor: Dr. Julie Mitchell.
Parallel version of global optimization algorithm using General Quadratic Convex
Approximation (GQCA) software. Benchmarking molecular docking software Docking
Mesh Evaluator (DoME) on 59 test cases.
June 2002 - September 2003
Postdoctoral Research. San Diego Supercomputer Center, UC San Diego, San Diego,
CA.
Advisors: Dr. Julie Mitchell and Dr. J. Ben Rosen.
Global optimization in protein docking. Developed GQCA. Implemented global
optimization algorithm using GQCA in DoME.
2000-2001
Research Assistant. University of California, San Diego.
Advisor: Dr. Philip E. Gill and Dr. Randy Bank.
Multi-scale methods for PDE-based optimization. Interfaced a primal-dual interior-point
algorithm with Piecewise Linear Triangle Multi-Grid (PLTMG) software for solving PDEs
with constraints. Analyzed theoretical properties and implemented Constrained
Optimization ProblemS large-scale problems to test algorithm robustness.
1997-1999
Research Assistant. University of California, San Diego.
Advisor: Dr. Philip E. Gill.
Large-scale unconstrained optimization. Developed an iterative method for solving
linear systems in unconstrained optimization. Tested algorithm performance on
problems from Constrained and Unconstrained Testing Environment (CUTE).
1995 - 2001
Teaching Assistant. University of California, San Diego.
Taught lower and upper division mathematics classes covering calculus, linear algebra,
numerical linear algebra, numerical approximation and interpolation, numerical ordinary
differential equations, linear and nonlinear programming, and numerical partial
differential equations. Led discussion groups, held review sessions and met one-on-one
with students. Prepared homework solutions and graded homework and exams. Taught
students basic UNIX skills and MATLAB programming. Worked closely with students
during a one-quarter course implementing a Finite Element Method in FORTRAN 77.
PRESENTATIONS
•
The Docking Mesh Evaluator, 2004 SIAM Annual Meeting, Portland, OR, July 13,
2004.
•
The Docking Mesh Evaluator, Research in Computational Molecular Biology
(RECOMB), San Diego, CA, March 28, 2004.
•
An LBL' Factorization of Symmetric Indefinite Tridiagonal Matrices, Numerical
Analysis Seminar, University of California, San Diego, April 9, 2003.
•
Convex Quadratic Approximation and Global Optimization in Protein Docking.
2003 SIAM Conference on Computational Science and Engineering, San Diego,
CA, February 10-12, 2003.
•
Convex Quadratic Approximation. Numerical Analysis Seminar, University of
California, San Diego, November 5, 2002.
•
Multiscale Methods for PDE-based Optimization. 2002 SIAM Optimization
Conference, Toronto, Canada, May 20-22, 2002.
•
Primal-Dual Interior-Point Methods for Large-Scale Optimization. Ph.D. Defense.
University of California, San Diego, March 18, 2002.
PUBLICATIONS
•
R. F. MARCIA, J. MITCHELL AND J. B. ROSEN, Iterative convex quadratic
approximation for global optimization in protein docking. Submitted to Comput.
Optim. Appl.
•
R. F. MARCIA, A pivoting strategy for the LBL' factorization of symmetric
tridiagonal matrices. In progress.
•
J. B. ROSEN AND R. F. MARCIA, Convex quadratic approximation. Comput.
Optim. Appl., Accepted for publication.
•
R. F. MARCIA, Interior-point methods for large-scale optimization. Ph.D.
dissertation, 2002.
•
R. E. BANK, P. E. GILL, AND R. F. MARCIA, Interior methods for a class of
elliptic variational inequalities. Proceedings of the First SANDIA Workshop on
Large-scale PDE Constrained Optimization. To appear.
•
D. DUNLAVY, S. JOO, R. LIN, R. F. MARCIA, A. MINUT, AND J. SUN,
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, 2000.
FELLOWSHIPS
•
•
•
•
Computational and Informatics in Biology and Medicine Fellowship, UW-Madison
RECOMB 2004 Travel Fellowship
San Diego Graduate Fellowship, UC San Diego
Columbia College King's Crown Award
REFERENCES
Dr. Randy Bank <rbank@ucsd.edu>
Department of Mathematics, University of California, San Diego
La Jolla, CA 92093-0112.
Dr. Philip Gill <pgill@math.ucsd.edu>
Department of Mathematics, University of California, San Diego
La Jolla, CA 92093-0112.
Dr. Julie Mitchell <mitchell@math.wisc.edu>
Departments of Mathematics and Biochemistry
University of Wisconsin-Madison
Madison WI 53706
Dr. J. Ben Rosen <jbrosen@cs.ucsd.edu>
Department of Computer Science and Engineering, University of California, San Diego
La Jolla, CA 92093-0114.