NIKOLAY V. PLOTNIKOV Stanford University 333 Campus Drive Stanford, CA 94305-4401 Mudd Building 121, MB 88 Work: 650-926-3304 Mobile: 213-769-6159 Email: nplotnikov@gmail.com nplotnik@stanford.edu Education 2008-2013 PhD, Chemistry University of Southern California, Los Angeles, CA Dissertation: Advancing ab initio QM/MM free energy calculations: refining, validating and quantifying the reference potential approach Adviser: Arieh Warshel 2002-2007 Diploma with Honors in Chemistry Saint Petersburg State University, Saint Petersburg, Russia Graduate qualification work: Modeling of acid-base equilibrium in nanostructured diblock copolymer gels Adviser: Alexey Victorov Research Experience 2013-present Postdoctoral Research Fellow, Department of Chemistry, Stanford University and PULSE Institute, Stanford Linear Accelerator Center PI Prof. Todd Martinez Modeling the effect of mechanical stimuli on chemical reactivity Development of sampling strategies and free energy calculation algorithms Accelerating ab initio molecular dynamics 2009-2013 Graduate Research Assistant, Department of Chemistry, Univ. of Southern California PI Prof. Arieh Warshel Developed the Paradynamics approach for accelerated calculations of ab initio QM/MM free energy barriers in condensed phases Implemented methods for calculating the free energy profiles of chemical reactions Improved and implemented algorithms for refining empirical force-fields Modeled enzymatic catalysis and photochemical cycles in fluorescent proteins (in collaboration with Prof. Anna Krylov)
Designed computational protocols for ab initio QM/MM molecular dynamics simulations on high-performance supercomputers 2005-2007 Undergraduate Research Assistant, Department of Chemistry, St Petersburg State University PI Prof. Alexey Victorov Developed a mesoscale molecular thermodynamics model of morphological transitions in phsensitive diblock copolymers Modeled effect of external stimuli (ph and ionic strength) on swelling behavior and mesoscale structure of ionic diblock copolymer gels Research and Technical Skills Method development in statistical thermodynamics: molecular dynamics (classical, parallel in time and ab initio), rare events sampling, free energy calculations, force-field development Multi-scale modeling: mesoscale, atomistic, electronic structures and hybrid QM/MM, MC- QM/MM Modeling environmental effects on chemical processes: solvation and mechanical stress Experienced scientific programing: FORTAN, C (with OpenMP and MPI) Experienced scripting for data processing and analysis: Perl, bash, Maple, python High-performance computing Familiar with GPU-acceleration using CUDA, OpenACC Experienced user: MOLARIS, QCHEM, MOPAC, Gaussian, TeraChem Peer- Reviewed Publications N. V. Plotnikov and T.J. Martinez. Towards the Rational Design of Mechanosensitive Materials: Elucidating the Pressure Dependence of the Isomerization Rate of Anthracene Cyclophane with ab initio Computer Modeling, 2015, in preparation. N. V. Plotnikov. Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model. Journal of Chemical Theory and Computation, 2014, doi: 10.1021/ct500109m. B. R. Prasad, N. V. Plotnikov, J. Lameira and A. Warshel. Quantitative exploration of the Molecular Origin of the Activation of GTPase, Proc. Natl. Acad. Sc., 2013, doi: 10.1073/pnas.1319854110 N. V. Plotnikov, B. R. Prasad, S. Chakrabarty, Z. T. Chu, and A. Warshel. Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant ab initio QM/MM Free Energy Surfaces, J. Phys. Chem. B, 2013, doi:10.1021/jp4020146 2
B. R. Prasad, N. V. Plotnikov and A. Warshel Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping, J. Phys. Chem. B, 2013, 117, 153-163 N. V. Plotnikov and A. Warshel. Exploring, Refining and Validating the Paradynamics QM/MM Sampling. J. Phys. Chem. B, 2012, 116(34), 10342-10356 N. V. Plotnikov, S. C. L. Kamerlin, A. Warshel. ParaDynamics: An Effective and Reliable Model for Ab Initio QM/MM Free Energy Calculations and Related Tasks. J. Phys. Chem. B, 2011, 115(24), 7950 A. I. Victorov, N. V. Plotnikov, P. Hong. Molecular thermodynamic modeling of the morphology transitions in the solution of a diblock copolymer containing a weak polyelectrolyte chain, J. Phys. Chem. B, 2010, 114(27), 8846 Plotnikov N. and Victorov A. Mesoscale morphology and dissociation equilibrium in ph-sensitive block copolymer gels, Fluid Phase Equilibria, 2007, 261, 26 Other Contributions N.V. Plotnikov Using Empirical Valence Bond Constructs as Reference Potentials for High-Level Quantum Mechanical Calculations in From Physical Chemistry to Chemical Biology: Theory and Applications of the Empirical Valence Bond Approach S.C. L. Kamerlin and F. Duarte in preparation B. R. Prasad, S. C. L. Kamerlin, N. V. Plotnikov and A. Warshel. Studying Catalysis by QM/MM Approaches should not be a Black Box Process. J. Thermodynam. Cat., 2012, 3, e111. doi:10.4172/2157-7544.1000e111 Software Development Plotnikov, N. PDM (method library for free energy calculations) https://bitbucket.org/mtzgroup/pdm Warshel, A. et al; MOLARIS-XG, University of Southern California, Los Angeles, CA, 2012 http://stevens.usc.edu/molaris_xg_software.php Donation to wham2.0.8: Grossfield, A, http://membrane.urmc.rochester.edu/content/wham/, version 2.0.8 Donation to MOPAC20012: MOPAC2012, James J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO, USA, HTTP://OpenMOPAC.net Selected Presentations N. Plotnikov, T. Martinez. Theoretical insight on mechanical sensitivity of chemical reactions rates from ab initio molecular dynamics free energy modeling. 248th National Meeting of the American Chemical Society, San Francisco, California, U.S.A., 2014 3
N. Plotnikov. Accurately computing fine-physics free energy barriers at a reduced computational cost using coarse-physics models. San Francisco, California, U.S.A., 2014 N. Plotnikov, T. Martinez. Modeling the Mechanical Sensitivity of Chemical Reaction Rates. American Conference on Theoretical Chemistry, Telluride, CO, U.S.A., 2014 N. Plotnikov, A. Warshel. Validation of linear response approximation of the free energy perturbation while moving from the reference potential to the ab initio QM/MM potential, 244th National Meeting of the American Chemical Society, Philadelphia, U.S.A., 2012 N. Plotnikov, A. Warshel. Catalytic effect of enzymes from ab initio QM/MM free energy calculations: Application of the refined paradynamics approach, 242nd National Meeting of the American Chemical Society, Denver, U.S.A., 2011 N. Plotnikov, S. Kamerlin, A. Warshel. Paradynamics: Accelerated calculation of the reaction free energy barriers by an ab initio QM/MM method with an automatically refined reference EVB, 241st National Meeting of the American Chemical Society, Anaheim, U.S.A., 2011 Plotnikov Nikolay and Victorov Alexey. Swelling and Dissociation Equilibrium in Weakly Acidic Nanostructured Block Copolymer Gels, XVI International Conference on Chemical Thermodynamic, Suzdal, Russia, 2007 Plotnikov N. and Victorov A. Mesoscopic Morphology and Dissociation Equilibrium in ph-sensitive Block Copolymer Gels, XI International Conference on Properties and Phase Equilibria for Product and Process Design, Crete, Greece, 2007 Additional Professional Training 2008-2009 Graduate research assistantship University of Southern California, Los Angeles, CA (Prof. Stephen Bradforth lab) Femtosecond and nonlinear spectroscopy Summer 2006 Research internship Kaiserslautern Technical University, Kaiserslautern, Germany 2006 (Prof. Gerd Maurer lab) Synthesis and study of selling behavior of hydrogels in aqueous salt Awards 2012 Computers in Chemistry Division of American Chemical Society and Chemical Computing Group Excellence Award 2011 USC Graduate Research Award 2010-2013 USC Department of Chemistry scholarship Research grants 4
XSEDE start-up research allocation of computer time on supercomputers (sponsored by the National Science Foundation) https://www.xsede.org/active-xsede-allocations PI: Nikolay Plotnikov Project: Modeling the effect of mechanical stimuli on chemical reactivity by ab initio MD free energy simulations Awarded Resources: SDSC Appro with Intel Sandy Bridge Cluster (Gordon Compute Cluster): 50000 TACC Dell PowerEdge C8220 Cluster with Intel Xeon Phi coprocessors (Stampede): 100000 GaTech HP/NVIDIA, Heterogeneous Computing System (KIDS): 10000 Peer- review for journals International Journal of Quantum Chemistry Structural Chemistry 5