Barrett, The Honors College Thesis/Creative Project Collection

The focus of my honors thesis is to find ways to use deep learning in tandem with tools in statistical mechanics to derive new ways to solve problems in biophysics. More specifically, I’ve been interested in finding transition pathways between two known states of a biomolecule. This is because understanding the mechanisms in which proteins fold and ligands bind is crucial to creating new medicines and understanding biological processes. In this thesis, I work with individuals in the Singharoy lab to develop a formulation to utilize reinforcement learning and sampling-based robotics planning to derive low free energy transition pathways between two known states. Our formulation uses Jarzynski’s equality and the stiff-spring approximation to obtain point estimates of energy, and construct an informed path search with atomistic resolution. At the core of this framework, is our first ever attempt we use a policy driven adaptive steered molecular dynamics (SMD) to control our molecular dynamics simulations. We show that both the reinforcement learning (RL) and robotics planning realization of the RL-guided framework can solve for pathways on toy analytical surfaces and alanine dipeptide.