Computational Modeling and Simulations
Nikolay Simakov 

Nikolay Simakov

Address:                                   701 Ellicott St., Buffalo, NY 14203, USA 
E-mail:                                      ns@compmodel.org
Professional web-site:             http://www.compmodel.org

Objective

Develop and apply computational methods in the fields of biophysics, chemistry and other computationally intensive areas. Optimize and parallelize scientific programs for conventional clusters, supercomputers and GPU accelerated computers. Solve challenging problems in computational biophysics/chemistry field through varied skills and interdisciplinary science knowledge.

Education

Ph.D. in Chemistry, 2010
Carnegie Mellon University, Pittsburgh, PA, USA
Chemistry Department
        Advisor: Prof. Maria Kurnikova
        Thesis:   “Theoretical Modeling of Current-Voltage Characteristics of Biological Ion Channels”

M.S. in Applied Physics and Mathematics,  2004
Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Moscow, Russia
        Advisor: Dr. Roman Efremov
        Thesis:   “Theoretical Study of Interactions between Fusion Peptide E5 and DPPC Bilayer”

B.S. in Applied Physics and Mathematics,  2002
Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, Moscow, Russia
        Advisor: Prof. Sergey Andreev
        Thesis:   “Development of Computational Methods for Modeling of Chromosomal Interactions”

 

Experience

Computational Scientist, 09/2012-Present 
Center for Computational Research (CCR)
University at Buffalo, SUNY, Buffalo, NY 

  • I am currently participating in the development of XSEDE Metrics on Demand (XDMoD) project. XDMoD is powerful tool for monitoring of HPC resources utilization. It also provides mechanisms for performance benchmarking as well as detection of hardware/software malfunctions.

Postdoctoral Research Associate, 06/2010-07/2012 
Research Group of Dr. Troy Wymore 
National Resource for Biomedical Supercomputing 
Pittsburgh Supercomputing Center, Pittsburgh, PA, USA 

  • Optimized and parallelized pDynamo, hybrid quantum chemical (QC) molecular mechanics (MM) simulation program. Cross-grained parallelization was implemented for umbrella sampling using distributed memory approach (MPI). The fine-grained was implemented for molecular dynamics simulations using shared memory approach (OpenMP).
  • Modeled enzymatic reaction with hybrid quantum mechanical molecular mechanical potential molecular dynamics simulations (MD)
  • Developed computational toolset aiding the molecular mechanical (MM) force field (FF) developments within the CHARMM/CGenFF Protocol. The toolkit was specifically designed to assist the parameterization of small, drug-like, molecules.
  • Provided a user support for Anton, an MD specialized supercomputer. The user support included teaching of machine operation during the workshops and providing a help to researches on the system and simulation set-up and results analysis.
  • Participated in the screening of participants for NAMD/VMD workshop

Research Assistant, 08/2004-09/2010
Research Group of Dr. Maria Kurnikova    
Carnegie Mellon University, Pittsburgh, PA, USA

  • Developed a numerical solver to predict the current-voltage properties of biological channels using Poisson-Nernst-Planck (PNP) theory
  • Successfully enhanced accuracy of predicting channel selectivity by introducing soft repulsion potential between ions and protein to original PNP theory and parameterization of the introduced potential using all atom MD simulation
  • Implemented parallel version of the solver on conventional clusters and on GPU (Possion equation solver)

Teaching Assistant, 08/2004-05/2010
Chemistry Department
Carnegie Mellon University, Pittsburgh, PA, USA

  • Supervised of undergraduate students in general chemical laboratory. Received a teaching award at 2010.
  • Homework and exam grading for courses including mathematics for chemistry major, physical chemistry and introduction to modern chemistry

Research Assistant, 01/2003-06/2004
Molecular Simulation Group of Dr. Roman Efremov
Institute of Bioorganic Chemistry,Russian Academy of Sciences, Moscow, Russia

  • Performed molecular dynamics simulation to study interactions between fusion peptide E5 and DPPC bilayer
  • Developed utilities for analyzing MD trajectories

Research Assistant, 10/2001-12/2002
Mathematical Biophysics Laboratory of Dr. Sergey Andreev
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia

  • Modeled chromatins packing on multi-domain level using Monte-Carlo simulation

Exchange Student, 07/2002-08/2002
Laboratory of Organic Chemistry
University of Rostock, Rostock, Germany

  • Synthesis of glucose derivative compounds

 

Skills

Programming and Computer Skills

  • Adept at programming and script languages, including C/C++, Python, tcl/tk, and interfacing C/C++ and Python
  • Proficient in parallel programming, using OpenMP, pthreads, MPI and CUDA (GPU accelerated applications)

Programming Experience with Large Scientific Programs

  • pDynamo: parallelization and automation
  • HARLEM: developed computational module to calculate I-V properties of ion-channels
  • GROMACS: customized utilities for MD trajectory analysis
  • AMBER: modified PMEMD to incorporate semi-isotropic barostat
  • VMD: implemented a plug-in to read custom volumetric data

Operation Systems

  • Linux (Advanced user and administrator)
  • Design and maintenance of small clusters (Linux based)
  • Windows XP/7 (Advanced user)

Computational Chemistry and General Computational Tools

  • Proficient in VMD, CHARMM, GROMACS, AMBER,  ANTON, Desmond, HARLEM, Gaussian, SciPy, and NumPy
  • Familiar with AMPAC and Maple

Familiar with Fortran, PHP, MySQL and Joomla

 

Workshops

  • Computer Simulation of Biomolecular Dynamics and Reactions (Instructor)
    Pittsburgh Supercomputing Center, Pittsburgh, PA, 06/2012
  • Anton Training Workshop (Microseconds Long MD Simulations) (Instructor)
    Pittsburgh Supercomputing Center, Pittsburgh, PA, 09/2010, 02/2011, 11/2011
  • NVIDIA CUDA Workshop
    Pittsburgh Supercomputing Center, Pittsburgh, PA, March 15-16, 2011
  • Productivity Study of X10, MPI, and UPC
    Pittsburgh Supercomputing Center, Pittsburgh, PA, May 23-26, 2005
  • Advanced CompuTational Software (ACTS) Collection Workshop
    Lawrence Berkeley National Laboratory, Berkeley, CA, August 23-26, 2005

 

Publications

  • Simakov, N.A. and Wymore, T. “ParamIT: a Toolset for Molecular Mechanical Force Field Parameterization within the CHARMM/CGenFF Protocol”. (in preparation for submission to J. Comp. Chem.)
  • Simakov, N.A. and Kurnikova, M.G. “GPU accelerated numerical solver of Poisson equation”. (in preparation, link to draft)
  • Simakov, N.A. and Kurnikova, M.G. “Position of the Protein Ion Channel in the Membrane Influences its Conductivity Properties”. (submitted to Biophysical Journal)
  • Simakov, N.A. and Kurnikova, M.G. “Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin”. J. Phys. Chem. B, 2010, 114 (46), pp 15180–15190. [link]
  • Volynsky, P.E.; Polyansky, A.A.; Simakov, N.A.; Arseniev, A.S.; Efremov, R.G. “Effect of lipid composition on the membrane response induced by a fusion peptide”. Biochemistry. 2005 Nov 8; 44(44):14626-37.[link]

 

Presentations

  • Simakov, N.A. and Wymore, T. “ParamIT: a Toolset for Molecular Mechanical Force Field Parameterization within the CHARMM/CGenFF Protocol”. Biophysical Society 56th Annual Meeting, to be held February 25-29 in San Diego, CA, 2012.
  • Simakov, N.A. “Theoretical Modeling of Current-Voltage Characteristics of Biological Ion Channels”. Invited Talk at Rush University Medical Center. Chicago, IL. 2011.
  • Simakov, N.A. and Wymore, T. “Computational Study of Glutamate-γ-Semialdehyde Oxidation Catalyzed by Thermus Thermophilus Gamma Glutamyl Semialdehyde Dehydrogenase”. 22nd Enzyme Mechanisms Conference. St. Pete Beach, FL. 2011
  • Simakov, N.A. and Kurnikova, M.G. “Extension of Poisson-Nernst-Planck theory of ion conductivity with soft-repulsion potential between ions and protein. Sensitivity of I-V properties of alpha-hemolysin channel on its penetration depth into membrane”. Biophysical Society Meeting. San-Francisco, CA. 2010.
  • Simakov, N.A. and Kurnikova, M.G. “Calculation of current-voltage properties of biological ion channel, using Poisson-Nernst-Planck (PNP) theory with soft channel walls”. Biophysical Society Meeting. Baltimore, MA. 2009.
  • Simakov, N.A. and Kurnikova, M.G. “Parallel numerical solver of potential of mean force Poisson-Nernst-Planck (PMFPNP) theory equations, application for calculation of current-voltage properties of biochannels”. PA-OH-WV Simulators Meeting. Pittsburgh, PA. 2008.
  • Simakov, N.A. and Kurnikova, M.G. “Calculation of current-voltage characteristics of biochannel, using potential of mean force Poisson-Nernst-Planck (PMFPNP) method”. Biophysical Society Meeting. Baltimore, MD. 2007.
  • Simakov, N.A. and Kurnikova, M.G. “Calculation of current-voltage characteristics of channel formed by anthrax protective antigen (pa63), using potential of mean force Poisson-Nernst-Planck (PMFPNP) theory”. Physical and Chemical Aspects of Molecular Biology. Puebla, Mexico. 2007.
  • Simakov, N.A.Application of non-local response function theory to proteins’ pKas prediction”. Original Proposal. Carnegie Mellon University. Pittsburgh, PA. 2007.
  • Simakov, N.A. Hybrid quantum mechanical and molecular mechanical methods for computational modeling of enzymatic chemical reactions”. Graduate Seminar. CMU. Pittsburgh, PA. 2005.