Computational Biology Distinguished Speaker: David Case

Professor of of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers University, New Brunswick, New Jersey

Simulating Biomolecules with Implicit Solvent Models

Friday, March 5, 11:00 AM
6014 Biomedical Science Tower 3

 

ABSTRACT: It is often useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. I will discuss one approach, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids, illustrating both static energetic analysis and molecular dynamics simulations using the new methods. The focus will be on mechanical and electrostatic properties of linear and circular DNA and, on divalent ion binding to nucleic acids. New implicit solvent models that go beyond continuum dielectric descriptions will also be discussed.

BIOGRAPHY: Before accepting his current position as Professor in Chemistry and Chemical Biology, as well as BioMaPS Institute for Quantitative Biology, at Rutgers University, Dr. Case was a Professor in the Molecular Biology and The Scrips Research Institute at La Jolla, California. Yet prior he worked as an Assistant Professor in Chemistry and the University of California, Davis.

Research interests include: theoretical chemistry of biomolecules, molecular dynamics simulations of proteins and nucleic acids, electronic structure calculations of transition-metal complexes that model active sites in metalloenzymes, development and application of methods for NMR structure determination.