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Simulating Biomolecules with 3D-RISM Implicit Solvent Models

Speaker: David Case, Rutgers University
Series: CBE Departmental Seminars
Location: Elgin Room (E-Quad A224)
Date/Time: Wednesday, December 11, 2013, 4:00 p.m. - 5:00 p.m.

Simulations of biomolecules often use a simplified description of solvation effects, instead of explicitly representing individual solvent molecules.  Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, but they often have problems describing non-polar solvation and in dealing with mixed salts or high electrolyte concentrations.  Other implicit solvent models, such as the dielectrically-consistent 3D-RISM model, go beyond continuum dielectric descriptions and provide estimates of details of the solvent distributions.  I will discuss the performance of such methods for aqueous electrolytes, comparing results to explicit solvent molecular dynamics and to experiment.  More biochemical applications include mechanical and electrostatic properties of linear and circular DNA, binding of monovalent and divalent ions to nucleic acids, and interactions of inhibitors with Factor Xa.