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AMS 548, Optimization Techniques in Biomolecular Simulations

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.

0-3 credits, ABCF grading

Offered in the spring semesters

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