Ben Robinson
Graduate Student
Chemistry and Biophysics
University of California at Irvine
Natural Sciences I, Room 3216
Irvine, CA 92697-4560
Voice: 949-824-9921
FAX: 949-824-8571
E-Mail:
Research Interests
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Certain proteins embedded in the lipid bilayer of cells allow the passive
transport of protons across the cell membrane. We are interested in
calculating the conductance of protons through such proteins as a function
of the trans-membrane voltage. We are using a combination of Molecular
Mechanics (MM), Self-Consistent Charge-Density Functional Tight Binding
(SCC-DFTB), Generalized Solvent Boundary Potential (GSBP) and Molecular
Mechanics (MM) to sample the Potential of Mean Force (PMF) of a proton as it
moves across the membrane through the protein.
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Normal Mode Analysis (NMA) using a coarse-grained elastic network model is
used to study functionally relevant collective motions of proteins and other
macromolecules. Proteins that are in an inhomogenous environment such as
trans-membrane proteins are less well described by the current methodology
than soluble proteins. We are exploring the importance and effectiveness of
including dissipation which depends on the local viscosity. In addition, we
are exploring new methods of coarse graining which may preserve the benefits
of including all heavy atoms, but at a greatly reduced computational cost.
