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Filip Jagodzinski University of Massachusetts Amherst Computer Science Building 140 Governors Drive Amherst, MA 01003-9264 Email: filip [at] cs.umass.edu Telephone: (413) 545-3039

I am a PhD student in the Department of Computer Science at the University of Massachusetts at Amherst. My advisor is Ileana Streinu and I am affiliated with the Linkage Laboratory. I have also worked at length with Oliver Brock, along with Frank Klassner and Lillian (Boots) Cassel at Villanova. My current research is interdisciplinary at the intersection of computer science, biology, and chemistry. I use established graph algorithms to analyze and predict the rigid regions of molecules, to infer important structural properties of disease causing mutant proteins. I co-develop (with Naomi Fox) the KINARI software, which uses an efficient pebble game algorithm to predict the flexible and rigid regions of biomolecules. I am extending KINARI so that it can be used to infer which residues are critical in stabilizing a protein. Knowing which residues are structurally important suggests regions of a protein where a mutation would be deleterious. That information can guide drug design efforts that aim to therapeutically regulate disease-causing biomolecules. I am also interested in how different facets of internal protein motion -- ranging from the reorientation of side chains to the movement of entire protein domains -- can be simulated using kinematic-only representations of molecular structures. In work with Oliver Brock, I proposed and demonstrated a method that leverages insights from kinematics and operational space control from robotics, to simulate the large scale motions of proteins.