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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 |
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I am a PhD student in the Comupter Science
Department 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.
Proteins perform the majority of biological functions in our bodies, and in order to fully understand their role and to be able to therapeutically regulate their actions, we need to understand the types of internal motions that they exhibit. Because protein motion cannot be observed directly, simulation methods have been proposed and implemented; these existing methods are either computationally complex or are not biologically accurate. I am investigating 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 appropriate representation and analysis methods; this is in stark contrast to prevalent simulation tools, which perform either excruciatingly detailed or crude, approximation simulations on all components of a protein. I am studying how rigidity theory can be used to help simplify the representations of proteins, and if such simplified models of a protein can be used so that simulation schemes on these models are computationally efficient and biologically accurate. |