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 calculationsInteractions 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.
- Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane.
I.S. Tolokh, V. Vivcharuk, B. Tomberli, C.G. Gray, Phys. Rev. E 80, 031911 (2009). Full text (pdf, 403kB)
- Charge hydration asymmetry: the basic principle and how to use it to test and improve water models.
A. Mukhopadhyay, A.T. Fenley, I.S. Tolokh, and A.V. Onufriev, J. Phys. Chem. B, 116, No.32, p.9776-9783 (2012). Full text (pdf, 1,118kB)
- Introducing charge hydration asymmetry into the generalized Born model.
A. Mukhopadhyay, B.H. Aguilar, I.S. Tolokh, and A.V. Onufriev, J. Chem. Theory Comput., 10, No.4, p.1788-1794 (2014). Full text (pdf, 1.481kB)
- Accurate evaluation of charge asymmetry in aqueous solvation.
A. Mukhopadhyay, I.S. Tolokh, and A.V. Onufriev, J. Phys. Chem. B, 119, No.20, p.6092-6100 (2015). Full text (pdf, 1,617kB)
Computational molecular Biophysics — Monte Carlo and Molecular Dynamics SimulationsModelling 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.
- Nature of the stacking of nucleic acid bases in water: a Monte Carlo study.
V.I. Danilov and I.S. Tolokh, J. Mol. Struct. (Theochem) 123, 109-119 (1985). Full text (pdf, 722kB)
- Hydration of uracil and thymine methylderivatives: a Monte Carlo simulation.
V.I. Danilov and I.S. Tolokh, J. Biomol. Struct. Dyn. 7, No.5, 1167-1183 (1990). - (0kB)
- Nonequilibrium molecular dynamics calculation of the conductance of the KcsA potassium ion channel.
H.W. de Haan, I.S. Tolokh, S. Goldman, and C.G. Gray Phys. Rev. E 74, 030905 (2006). Full text (pdf, 645kB)
- Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on POPC membrane.
V. Vivcharuk, B. Tomberli, I.S. Tolokh, C.G. Gray, Phys. Rev. E 77, 031913 (2008). Full text (pdf, 362kB)
- Why double-stranded RNA resists condensation.
I.S. Tolokh, S.A. Pabit, A.M. Katz, Y. Chen, A. Drozdetski, L. Pollack, N. Baker, and A.V. Onufriev, Nucleic Acid Research, 42, No.16, p.10823-10831 (2014). Full text (pdf, 2,567kB)
- Multi-shell model of ion-induced nucleic acid condensation.
I.S. Tolokh, A.V. Drozdetski, L. Pollack, N.A. Baker, and A.V. Onufriev, J. Chem. Phys., 144, 155101 (2016). Full text (pdf, 3,245kB)
- Opposing effects of multivalent ions on flexibility of DNA and RNA.
A.V. Drozdetski, I.S. Tolokh, L. Pollack, N.A. Baker, and A.V. Onufriev, Phys. Rev. Lett., 117, No.2, 028101 (2016).
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E-mail: itolokh (at) vt.edu