Project page: http://www.math.wm.edu/~buckaroo/research/squid
Topic description: One way to determine protein structure is to minimize the energy in the molecule due to the stretching of bonds, distortion of bond angles, van der Waal's forces, &c. Unfortunately, standard energy force field models lead to optimization problems with huge numbers of local minimizers that are not of physical interest, but which can trap optimization algorithms. This project focuses on a new approach to force field models based on distance geometry that leads to more tractable optimization problems.
Research opportunities: Development of the large-scale constrained optimization algorithm; numerical experimentation on real proteins; improved modeling of force field components; investigation of alternative methods of treating constraints; analysis, implementation, and experimentation with alternative problem formulations based on nonconvex duality.
Suggested prerequisites: Math 413, Math 414, experience with Matlab, C
Contact: R. M. Lewis
Last updated at Wednesday, 09-Apr-2008 16:03:56 EDT.