Assistant Mechanical

Computational Modeling and Simulations

Nikolay Simakov

Projects:

ParamIT

pDynamo

Anton

GAPS

PNPS

Contacts

Nikolay Simakov

Address: *** *. ***** ******, **********, PA 15213, USA

E-mail: ********@******.***.***

Professional web-site: http://www.compmodel.org

Objective

Develop and apply computational methods in the fields of biophysics and chemistry.

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

Postdoctoral Research Associate, 06/2010-present

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, 08/2004-05/2010Chemistry DepartmentCarnegie 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, 10/2001-12/2002Mathematical 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 ChemistryUniversity 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, 06/2012Anton 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

Contact this candidate