STAR Fellows pursue a prestigious "teacher-researcher" career path starting with an original research project for 9 weeks. Weekly education workshops and conferences support Fellows considering how the "doing of science" can be translated into the "teaching of science. Many become STEM leaders and go on to present at state and national teaching and professional society meetings.
This method, to be termed RTB-dynamics does not require the construction of the matrix of second spatial derivatives of the potential energy function, and can be used to compute the classical dynamics of a system moving in an arbitrary anharmonic force field with an efficient way of freezing out the high frequency motions within rigid fragments.
Moreover, an approximation scheme is developed to compute Brownian motion according to the Langevin Equation for a molecular system moving in a harmonic force field and characterized by one or more rigid internal fragments by using the RTB methodology.
To illustrate these methods elementary numerical applications to signal propagation in the small membrane-bound polypeptide gramicidin-A are presented.
Finally, Dynamic Linear Response Theory DLRT is adapted to the problem of computing the time evolution of the atomic coordinates of a protein in response to the unbinding of a ligand molecule from a binding pocket within the protein. DLRT relates the non-equilibrium motion of the protein atoms which ensues after the ligand molecule dissociates to equilibrium dynamics in the force field, or equivalently, on the potential energy surface PES relevant to the unliganded protein.
We numerically illustrate the application of DLRT for a simple harmonic oscillator model of the ferric binding protein, and for an analogous model of T4 lysozyme including the solvent effects on the motion using the Langevin prescription.
Using a physically appropriate value of the viscosity of water to guide the choice of friction parameters, we find relaxation time scales of residue-residue distances on the order of several hundred ps.
Comparison is made to relevant experimental measurements.Sebnem Essiz Gokhan, School of Arts and Sciences’ Department of Chemistry, “Coarse-grained Techniques to Study Dynamics of Longtime Scale Conformational Changes of Proteins,” p.m.
April 6, Room Eberly Hall. COARSE-GRAINED TECHNIQUES TO STUDY DYNAMICS OF LONG-TIME SCALE CONFORMATIONAL CHANGES OF PROTEINS by Sebnem Essiz Gokhan B.S., Koc Universirty, Submitted to the Graduate Faculty of This dissertation was presented by Sebnem Essiz Gokhan It was defended on April 6, UNIVERSITY OF CALIFORNIA AT SAN FRANCISCO Curriculum vitæ Name: Position: Andrej Sali Professor, Step X Department of Bioengineering and Therapeutic Sciences (BTS) Department of Pharmaceutical Chemistry.
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