Igor S Tolokh

Senior Research Scientist


Bogolyubov Institute for Theoretical Physic, Kyiv, Ukraine
Ph.D., Theoretical Physics, 1996

Lomonosov Moscow State University, Moscow, Russia
M.S., Physics (Biophysics), 1983


Implicit solvent models for Biomolecular Electrostatics and Free energy calculations

Interactions between biomolecules and structural changes in macromolecules are conviniently characterized by free energy profile along reaction coordinate or potential of mean force (PMF). Calculation of PMF involves averaging over all degrees of freedom but the reaction coordinate. For the interactions in aqueous environment it means averaging over water molecules thermal motion. Replacing explicit water molecules by a dielectric continuum with a proper set of electrostatic and nonpolar properties allows one to reduce a considerable, sometimes prohibitive, computational cost involved in biomolecular system simulations. This approach named the implicit solvent framework has been implemented in major molecular simuation packages (eg. AMBER, CHARMM). One of the directions of futher improvement of computational speed within this approach is a developement of the analytical Generalized Born model.


Computational molecular Biophysics — Monte Carlo and Molecular Dynamics Simulations

Modelling the thermodynamical properties or dynamical behaviour of biomolecular systems at the atomic/molecular level helps to understand the nature of the effects obseved experimentally. With a large number of the degrees of freedom usually involved for the proper description of the relevant interactions in the systems, utilization of the computers is the only practical way to do this modelling. Monte Carlo and Molecular Dynamics methods were initially developed as computational tools in molecular and condensed matter physics. But soon, with the expansion and improvement of the force fields, these methods were applied to biologically relevant systems.


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E-mail: itolokh (at) vt.edu