Multiscale integrators for dynamics of biomolecules

The approach we take is to do stability analysis of linear and nonlinear model problems for proposed MTS integrators (like MOLLY). We implement them into PROTOMOL and test first in a water system. Then stability and accuracy of the method applied to real problems is determined with numerical experiments. This process takes about six months for a new method. Generalizing the method to biomolecules and testing usually takes six additional months. Optimizations to the method come later. This is the criterion for the plan presented here. Eventually, the methods may be implemented in popular MD programs, particularly in NAMD, since we have maintained an active collaboration starting at the PI's day as a graduate student in the Theoretical Biophysics group at the University of Illinois.

A graduate student will be 100% devoted to this project for the whole duration of this grant. Currently, the student is Mr. Marc Ma, a graduate student at the department of computer science and engineering at the University of Notre Dame, who has a M.S. in theoretical mechanics and mechanical engineering.