Computational Modeling and Simulations
Nikolay Simakov 

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Nikolay Simakov


Computational Scientist

Center for Computational Research

University at Buffalo, SUNY

701 Ellicott St., Buffalo, New York 14203

E-mail: or



My professional interests are in general computational modeling and simulations. In particular, my passions fall in the following two areas of work: (i) Development, implementation and application of computational methods in the fields of biology, chemistry and physics; and (ii) Optimization and parallelization of scientific programs for conventional clusters, supercomputers and ones utilizing GPU accelerators. Though they might target the same scientific problems, these two areas differ by their emphasis. One is focused on the proof of concept of a scientific program, and the other is oriented by achieving a greater scalability of an existing program.

My love of natural sciences has driven me to obtain my BS and MS in Applied Physics and Mathematics from Moscow Institute of Physics and Technology in 2002 and 2004, respectively, followed by my PhD in Chemistry from Carnegie Mellon University in 2010. I am currently working as a postdoctoral associate at PSC on biophysics scientific programming. Through years of professional training and education in the fields of biology, chemistry, mathematics, and physics, I am able to quickly understand particular scientific problems and figure out the key methods and theories behind. I have been developing or/and optimizing several scientific programs and gained lots of experiences in how to effectively implement scientific programs. In brief, my knowledge and experiences in multidisciplinary fields along with my broad expertise in multiple programming languages make me a fast learner and a problem solver who can identify hot spots for implementation/optimization given a scientific problem or existing program codes.

Below are several computational projects that I have been involved in.


pDynamo is an open-source program for modeling enzymatic reaction using hybrid quantum chemical/ molecular mechanical potentials. I am participating in optimization, parallelization and automation of the codes. The work is done in Dr. Troy Wymore’s group.

ParamIT is a toolkit developed by me to aid the molecular mechanical (MM) force field (FF) development for small drug-like molecule within the CHARMM/CGenFF Protocol. The work is done in Dr. Troy Wymore’s group.

Anton is a specialized supercomputer specifically designed to perform all-atom molecular dynamics simulation. I am a member of Anton user’s support team at Pittsburgh Supercomputing Center.

PNPS is a solver of Poisson and Nernst-Planck equations. These systems of partial derivative equations are used in biophysics to model ion-permeation in ion-channels. I was developing a code and had introduced soft repulsion potentials to PNP theory during my PhD studies in Dr. Maria Kurnikova Group. (More details are coming up)

GAPS –(Graphical Processing Unit Accelerated Poisson Equation Solver.) is GPU and CPU implementation of Poisson equation solver used for biological macromolecules. I developed this program during my PhD study in Dr. Maria Kurnikova’s Group.