Grigory Kolesov Curriculum Vitae

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1 GRIGORY KOLESOV School of Engineering and Applied Sciences Harvard University Cambridge, MA USA Mobile: WWW: gkolesov Education 2013 UNIVERSITY OF WYOMING PhD in Physics, December TECHNICAL UNIVERSITY OF MUNICH PhD in Computational Biology, April NOVOSIBIRSK STATE UNIVERSITY MS in Molecular Genetics, June 1998 Research experience 2013 now Postdoctoral fellow at School of Engineering and Applied Sciences, Harvard University 2012 Summer research internship at the Los Alamos National Laboratory Graduate student at the department of Physics and Astronomy, University of Wyoming Postdoctoral fellow at the University of Wyoming Postdoctoral fellow at Harvard-MIT Division of Health Sciences and Technology Graduate student at MIPS, Institute for Bioinformatics (IBI), German National Center for Health and Environment and Technical University of Munich Research Interests Non-adiabatic dynamics, computational materials science, condensed matter, quantum chemistry, molecular dynamics Biophysics, protein structure and function Electrochemistry Bionformatics, genomics; evolution and phylogenetics, evolution of gene order Research Projects: Current and Planned Polarons in transition metal oxides 1

2 Photocatalysis Excitations in 2D materials Teaching experience 2015 Harvard University. Co-taught course Computational Material Design 2009 Teaching Assistant, University of Wyoming, general physics I 2009 Teaching Assistant, University of Wyoming, general physics II 2002 Technical University of Munich. Co-taught course Evolution and phylogenetics Selected scientific software TDAP-2.0 Non-adiabatic excited state molecular dynamics with real-time time-dependent density functional theory (RT-TDDFT) and mean-field classical ions; based on SIESTA 2TSE Quantum kinetics; Kadanoff-Baym equation solver in two-time Chebyshev polynomials elarraysim Electrochemistry diffusion and chemical step simulator for interdigitated ultramicroelectrode arrays Knot server Online prediction of knots in 3D-structures of proteins. ( SNAPper Jaba Prediction of gene function based on gene order in prokaryotes using Similarity-Neighborhood Approach. Multithreaded distributed UNIX daemon and web interface Genome annotation tool, used in Arabidopsis thaliana and Neurospora crassa genome projects. Computational skills Numerical methods and simulations; finite difference, spectral and Monte Carlo methods C/C++, FORTRAN, Perl, Python, Java, Haskell, Modula-2, Pascal, Matlab, Assembly Parallel programming, multi-threading, distributed computing, MPI, OMP, SCALAPACK, GPU programming (CUDA) Quantum chemistry and solid state packages: SIESTA, ASE, Gaussian, QuantumEspresso, VASP, Abinit, YAMBO, ATAT (Alloy-Theoretic Automated Toolkit) Bioinformatics tools: structural bioinformatics, Bioperl, Bioconductor, alignments and phylogeny/evolution tools Linux/UNIX/POSIX application/system-level programming, administration, clusters, Kerberos/AFS administration and programming HPC, batch systems adminstration - LSF, Sun grid engine databases, SQL web programming, UI programming in Java 2

3 Conference talks Kolesov, G., Grånäs, O., Hoyt, R., Kaxiras, E. Time-dependent density functional theory and non-adiabatic Ehrenfest dynamics with localized basis sets: method and applications. ES2015 Electronic Structure workshop, Kolesov, G., Vinichenko, D., Tritsaris, G. A., Friend, C. M., Kaxiras, E. Polarons in rutile TiO2 surfaces: a non-adiabatic excited-state dynamics study. APS March Meeting, 2015 Kolesov, G., Vinichenko, D., Tritsaris, G. A., Friend, C. M., Kaxiras, E. Non-Adiabatic Excited-State Dynamics Study of Methoxy photo-oxidation on TiO2 Surface, Material Research Society (MRS) Fall Meeting, 2014 Kolesov, G., Vinichenko, D., Tritsaris, G., Friend, C., Kaxiras, E. Methoxy photo-oxidation on rutile TiO2 surface : excited-state non-adiabatic dynamics study, Dynamics Interactions and Electronic Transitions at surfaces (DIET) meeting, 2014 Kolesov, G., Thermodynamic properties and band structure of zinc stannate Zn2SnO4, APS March Metting, 2014 Kolesov, G., and Dahnovsky, Y., Correlated electron transfer and nonlinear optical effects in QD sensitized solar cells, APS April Meeting, 2013, 58, 4. Kolesov, G., and Dahnovsky, Y., Nonequilibrium Green s function calculations in quantum dot sensitized solar cells: uncorrelated quantum dot electrons, ACS National Meeting, 2011 Publications [1] Kolesov, G., Kolesov, B. A., & Kaxiras, E. Polaron-induced phonon localization and stiffening in rutile TiO 2. submitted (2016). [2] Islam, M. M., Kolesov, G., Verstraelen, T., Kaxiras, E. & van Duin, A. ereaxff: A pseudo-classical treatment of explicit electrons within reactive force field simulations. Journal of Chemical Theory and Computation (2016). URL [3] Kolesov, G., Grånäs, O., Hoyt, R., Vinichenko, D. & Kaxiras, E. Real-time TD-DFT with classical ion dynamics: Methodology and applications. Journal of Chemical Theory and Computation 12, (2016). URL [4] Kolesov, G., Vinichenko, D., Tritsaris, G. A., Friend, C. M. & Kaxiras, E. Anatomy of the photochemical reaction: Excited-state dynamics reveals the C H acidity mechanism of methoxy photooxidation on titania. The Journal of Physical Chemistry Letters 6, (2015). [5] Tritsaris, G. A., Vinichenko, D., Kolesov, G., Friend, C. M. & Kaxiras, E. Dynamics of the photogenerated hole at the rutile TiO 2 (110)/water interface: A nonadiabatic simulation study. The Journal of Physical Chemistry C 118, (2014). [6] Liu, F., Kolesov, G. & Parkinson, B. A. Preparation, applications, and digital simulation of carbon interdigitated array electrodes. Analytical chemistry 86, (2014). [7] Liu, F., Kolesov, G. & Parkinson, B. A. Time of flight electrochemistry: diffusion coefficient measurements using interdigitated array (IDA) electrodes. Journal of The Electrochemical Society 161, H3015 H3019 (2014). 3

4 [8] Nepomnyashchii, A. B., Kolesov, G. & Parkinson, B. A. Electrogenerated chemiluminescence of BOD- IPY, Ru (bpy) 32+, and 9, 10-diphenylanthracene using interdigitated array electrodes. ACS applied materials & interfaces 5, (2013). [9] Pimachev, A., Kolesov, G., Chen, J., Wang, W. & Dahnovsky, Y. Internal relaxation in dye sensitized solar cells based on Zn 2 SnO 4 nanostructures. The Journal of chemical physics 137, (2012). [10] Kolesov, G. & Dahnovsky, Y. Correlated electron dynamics in quantum-dot sensitized solar cell: Kadanoff-Baym versus Markovian approach. Physical Review B 85, (2012). [11] Huzurbazar, S. et al. Lineage-specific differences in the amino acid substitution process. Journal of molecular biology 396, (2010). [12] Liberles, D. A., Kolesov, G. & Dittmar, K. Understanding gene duplication through biochemistry and population genetics. Evolution After Gene Duplication. Hoboken (NJ): Wiley-Blackwell (2010). [13] Kolesov, G. & Mirny, L. A. Using evolutionary information to find specificity-determining and coevolving residues. Computational Systems Biology (2009). Book chapter. [14] Tellgren-Roth, Å., Kolesov, G., Sifuentes-Rincón, A. M. & Liberles, D. A. Complex microsatellite dynamics in the myostatin gene within ruminants. Journal of molecular evolution 66, (2008). [15] Kolesov, G., Wunderlich, Z., Laikova, O. N., Gelfand, M. S. & Mirny, L. A. How gene order is influenced by the biophysics of transcription regulation. Proceedings of the National Academy of Sciences 104, (2007). [16] Kolesov, G., Virnau, P., Kardar, M. & Mirny, L. A. Protein knot server: detection of knots in protein structures. Nucleic acids research 35, W425 W428 (2007). [17] Kolker, E. et al. Identification and functional analysis of hypothetical genes expressed in Haemophilus influenzae. Nucleic acids research 32, (2004). [18] Frishman, D. et al. The PEDANT genome database. Nucleic acids research 31, (2003). [19] Wong, P., Kolesov, G., Frishman, D. & Houry, W. A. Phylogenetic web profiler. Bioinformatics 19, (2003). [20] Kota, R. et al. Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Molecular Genetics and Genomics 270, (2003). [21] Schoof, H. et al. MIPS Arabidopsis thaliana database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Research 30, (2002). [22] Kolesov, G., Mewes, H.-W. & Frishman, D. SNAPper: gene order predicts gene function. Bioinformatics 18, (2002). [23] Kolesov, G., Mewes, H.-W. & Frishman, D. Prediction of gene function in bacterial genomes based on context information (Springer-Verlag, Berlin Heidelberg, 2002). [24] Kolesov, G., Mewes, H.-W. & Frishman, D. SNAPping up functionally related genes based on context information: a colinearity-free approach. Journal of molecular biology 311, (2001). [25] Tabata, S. et al. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 408, (2000). [26] Kolpakov, F. A., Ananko, E. A., Kolesov, G. B. & Kolchanov, N. A. GeneNet: a gene network database and its automated visualization. Bioinformatics 14, (1998). 4

5 [27] Kolchanov, N. A. et al. Genexpress: A computer system for description, analysis and recognition of regulatory sequences in eukaryotic genome. ISMB Proc. 6, (1998). [28] Ananko, E., Kolpakov, F., Kolesov, G. & Kolchanov, N. Automatic generation of gene network schemes based on their formalized description in the GeneNet database. Biofizika 44, (1998). (Russian). 5