AMS 548 Optimization Techniques in Biomolecular Simulations

AMS 548: OPTIMIZATION TECHNIQUES IN BIOMOLECULAR SIMULATIONS
Instructor: Dima Kozakov (dmytro.kozakov@stonybrook.edu)
Mondays/Wednesdays: 4:00-5:20 PM

This practical course allows students to build computational models of physical process from the ground up. Described mathematical techniques are useful not only for molecular simulations but also in robotics, as well as in various computational physics applications. The course also provides introduction to HPC simulations. No special background is required.

COURSE DESCRIPTION: This practical hands-on course will teach basic techniques for building mathematical models, algorithms, and software for biomolecular simulations of macromolecular interactions. The topics of this course include, but are not limited to: the basics of statistical mechanics and its connection to the sampling algorithms; the origin of and approximations for the computation of molecular forces; geometry of the molecular configuration search space and multidimensional optimization; basics of software development and programming for high performance computing (HPC). During the course, the students will develop a multiscale approach for modeling protein-protein interactions from the ground up. The course  is a recommended elective for Laufer Track students as well as within IACS course catalogue. 

NOTE: Each week consists of a lecture on theory and a practical seminar. During the seminars, the students will develop software based on the theoretical material presented in the lectures. By the end of the course, the students will have put together a very simple but fully functional package for the modeling of macromolecular interactions. All the algorithms and the software will be developed by each student from the ground up using molecular modeling library.