Curriculum Vitae

 Victor Anisimov

Education:

Ph.D., Physical Chemistry, Oct. 7, 1997

  Institute of Chemical Physics in Chernogolovka, Russian Academy of Sciences

M.Sc., Organic Chemistry, Jun. 30, 1989

  Chuvash State University, Cheboksary, Russia

Employment history:

2011 - Present: Senior Research Programmer 

  National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

2008 - 2011: Postdoctoral Research Associate 

  University of Texas Health Science Center at Houston

2003 - 2008: Postdoctoral Research Associate

  University of Maryland at Baltimore, Dept. Pharm. Sciences

1999 - 2003: Senior Software Researcher

  FQS Poland (Fujitsu), Krakow, Poland

1994 - 1998: Research Scientist

  Institute of Chemical Physics in Chernogolovka Russian Academy of Sciences

Experience:

• High Performance Computing. Performance optimization for petascale platforms. Cray Programming Environment. Allinea DDT (Forge). Cray Performance Analysis Tools. I/O optimization for Lustre filesystem.
• Parallel programming with OpenMP, MPI, CUDA, and Global Arrays.
• Fortran 90, C / C++, SQL, Perl, Python, Awk, UNIX shell, relational database schema design.
• Industrial experience in molecular modeling software development and customer support.
• Optimization of CCSD code in NWChem. Implementation of FITCHARGE module in CHARMM. Development of molecular dynamics in LocalSCF.
• NDDO methods. Fast multipole method. Viriational Finite LMO approximation. Linear scaling LocalSCF method. Semiempirical parameter development. Charge transfer.
• DNA structure and function. The role of sugar-phosphate backbone in Watson-Crick DNA conformation.
• Development of CHARMM polarizable force field based on Drude model.
• Structure based drug design. Protein-ligand docking. Protein-ligand binding free energy computation.
• AMBER, CHARMM, NAMD, LAMMPS, GROMACS, NWChem, GAMESS US, ACESIII, Quantum Espresso, Gaussian, Q-Chem, VASP packages.
• Additional fields of experience: Organic chemistry and X-ray crystal structure resolution.

Reviewer for:

• Nucleic Acids Research
• Journal of Chemical Theory and Computation
• Journal of Computational Chemistry
• Journal of Chemical Information and Modeling
• Journal of Molecular Modeling
• Journal of Biomolecular Structure and Dynamics
• Journal of Molecular Graphics and Modeling
• Environmental Science and Technology
• Challenges and Advances in Computational Chemistry and Physics
• Open Chemistry

Research interests:

Soft matter physics; methods and techniques for accuracy and performance improvement of computer simulation of materials and macromolecular systems. Development of approximate computational methods for simulation of condensed-phase, parameter optimization, semiempirical NDDO methods, fast multipole method, linear scaling methods, molecular dynamics techniques, charge transfer, protein-ligand interaction, DNA structure, excited state simulation. 

Work address:

National Center for Supercomputing Applications 
University of Illinois at Urbana-Champaign 
1205 W. Clark St, MC-257 
Urbana, IL 61801 
E-mail: anisimov@illinois.edu

ACS talks:

• 248^th ACS National Meeting, San Francisco, CA, 2014; Petascale optimization of the coupled cluster method in NWChem on NCSA Blue Waters
• 246^th ACS National Meeting, Indianapolis, IN, 2013; Computationally efficient treatment of long-range polarization effects in large molecular systems
• 238^th ACS National Meeting, Washington, DC, 2009; Quantum-mechanical simulation of biological macromolecules and its application in structure-based drug design
• 234^th ACS National Meeting, Boston, MA, 2007; Classical CHARMM Drude oscillator polarizable force field for nucleic acid bases
• 234^th ACS National Meeting, Boston, MA, 2007; All-atom semiempirical LocalSCF quantum-mechanical protein-ligand docking
• 231^st ACS National Meeting, Atlanta, GA, 2006; Validation of quantum-mechanical docking and scoring procedures
• 230^th ACS National Meeting, Washington, DC, 2005; CHARMM Drude polarizable force field parameter development for model compounds representative of biological systems
• 227^th ACS National Meeting, Anaheim, CA, 2004; Novel techniques for QM modeling of ultra-large bio-molecular systems: Evolution of quantum-mechanical and force field methods
• 225^th ACS National Meeting, New Orleans, LS, 2003; Accurate prediction of protein-ligand binding energy in the QCPFF approach
• 224^th ACS National Meeting, Boston, MA, 2002; New semiempirical method for fast and accurate protein modeling

Invited Book chapters:

V. M. Anisimov, C. N. Cavasotto, “Quantum-Mechanical Molecular Dynamics of Charge Transfer“, in Challenges and Advances in Computational Chemistry and Physics, Springer, 2010, Volume 12, Chapter 9, pp. 247-266, Kinetics and Dynamics: From Nano- to Bio-scale, Eds. P. Paneth, and A. Dybala-Defratyka author manuscript

A. Panczakiewicz, V. M. Anisimov, “The Linear Scaling Semiempirical LocalSCF Method and the Variational Finite LMO Approximation”, in Challenges and Advances in Computational Chemistry and Physics, Springer, 2011, Volume 13, Chapter 15, pp. 409-437, Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications, Eds. R. Zalesny, M. G. Papadopoulos, P. G. Mezey, and J. Leszczynski author manuscript

Publication list:

QM Methods

V. M. Anisimov, G. H. Bauer, K. Chadalavada, R. M. Olson, J. W. Glenski, W. T. C. Kramer, E. Aprà, K. Kowalski, Journal of Chemical Theory and Computation, 2014, Volume 10, Issue 10, Pages 4307-4316; Optimization of the coupled cluster implementation in NWChem on petascale parallel architectures

A. Schleife, E. W. Draeger, V. M. Anisimov, A. A. Correa, Y. Kanai, Computing in Science and Engineering, 2014, Volume 16, Issue 5, Pages 54-60; Quantum dynamics simulation of electrons in materials on high-performance computers

V. M. Anisimov, A. A. Bliznyuk, Journal of Physical Chemistry B, 2012, Volume 116, Issue 22, Pages 6261-6268; Charge Transfer Effects in the GroEL-GroES Chaperonin Tetramer in Solution

V. M. Anisimov, A. Ziemys, S. Kizhake, Z. Yuan, A. Natarajan, C. N. Cavasotto, Journal of Computer-Aided Molecular Design, 2011, Volume 25, Issue 11, Pages 1071-1084; Computational and Experimental Studies of the Interaction Between Phospho-Peptides and the C-terminal Domain of BRCA1

V. M. Anisimov, C. N. Cavasotto, Journal of Physical Chemistry B, 2011, Volume 115, Issue 24, Pages 7896-7905; Hydration Free Energies Using Semiempirical Quantum Mechanical Hamiltonians and a Continuum Solvent Model with Multiple Atomic-Type Parameters

V. M. Anisimov, C. N. Cavasotto, Journal of Computational Chemistry, 2011, Volume 32, Issue 10, Pages 2254-2263; Quantum Mechanical Binding Free Energy Calculation for Phosphopeptide Inhibitors of the Lck SH2 Domain

V. M. Anisimov, V. L. Bugaenko, C. N. Cavasotto; ChemPhysChem, 2009, Volume 10, Issue 18, Pages 3194-3196; Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution

V. M. Anisimov, V. L. Bugaenko; Journal of Computational Chemistry, 2009, Volume 30, Issue 5, Pages 784-798; QM/QM Docking Method Based on the Variational Finite Localized Molecular Orbital Approximation 

V. M.  Anisimov, V. L. Bugaenko, V. V. Bobrikov, Journal of Chemical Theory and Computation, 2006, Volume 2, Issue 6, Pages 1685-1692; Validation of linear scaling semiempirical LocalSCF method 

N. A. Anikin, V. M. Anisimov, V. L. Bugaenko, V. V. Bobrikov, A. M. Andreyev; Journal of Chemical Physics, 2004, Volume 121, Issue 3, Pages 1266-1270; LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules 

V. M. Anisimov, N. Anikin, V. Bugaenko, V. Bobrikov, A. Andreyev; Theoretical Chemistry Accounts, 2003, Volume 109, Issue 4, Pages 213-219; Accuracy assessment of semiempirical molecular electrostatic potential of proteins 

Polarizable Force Fields

C. M. Baker, V. M. Anisimov, A. D. MacKerell, Journal of Physical Chemistry B, 2011, Volume 115, Issue 3, Pages 580-596; Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

H. Yu, T. W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V. M. Anisimov, A. D. MacKerell Jr., B. Roux; Journal of Chemical Theory and Computation, 2010, Volume 6, Issue 3, Pages 774-786; Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

A. D. MacKerell Jr., J. H. Shim, V. M. Anisimov; Journal of Chemical Theory and Computation, 2008, Volume 4, Issue 8, Pages 1307-1312; Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide

E. Harder, V. M. Anisimov, T. W. Whitfield, A. D. MacKerell Jr., B. Roux; Journal of Physical Chemistry B, 2008, Volume 112, Issue 11, Pages 3509-3521; Understanding the dielectric properties of liquid amides from a polarizable force field 

I. V. Vorobyov, V. M. Anisimov, S. Greene S, R. M. Venable, A. Moser, R. W. Pastor, A. D. MacKerell Jr.; Journal of Chemical Theory and Computation, 2007, Volume 3, Issue 3, Pages 1120-1133; Additive and classical drude polarizable force fields for linear and cyclic ethers 

V. M. Anisimov, I. V. Vorobyov, B. Roux, A. D. MacKerell Jr.; Journal of Chemical Theory and Computation, 2007, Volume 3, Issue 6, Pages 1927-1946; Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model 

E. Harder E, V. M. Anisimov, I. V. Vorobyov, P. E. M. Lopes, S. Y. Noskov, A. D. MacKerell Jr., B. Roux; Journal of Chemical Theory and Computation, 2006, Volume 2, Issue 6, Pages 1587-1597; Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator 

I. V. Vorobyov, V. M. Anisimov, A. D. MacKerell Jr.; Journal of Physical Chemistry B, 2005, Volume 109, Issue 40, Pages 18988-18999; Polarizable empirical force field for alkanes based on the classical Drude oscillator model 

V. M. Anisimov, G. Lamoureux, I. V. Vorobyov, N. Huang, B. Roux, A. D. MacKerell Jr.; Journal of Chemical Theory and Computation, 2005, Volume 1, Issue 1, Pages 153-168; Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator 

V. M. Anisimov, I. V. Vorobyov, G. Lamoureux, S. Y. Noskov, B. Roux, A. D. MacKerell Jr.; Biophysical Journal, 2004, Volume 86, Issue 1, Pages 415A-415A; CHARMM all-atom polarizable force field parameter development for nucleic acids

DNA Structure

V. Poltev, V. M. Anisimov, V. Dominguez, E. Gonzalez, A. Deriabina, D. Garcia, F. Rivas, N. A. Polteva; Journal of Molecular Modeling, 2018, Volume 24, Issue 2, Pages 46; Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments

V. I. Poltev, V. M. Anisimov, C. Sanchez, A. Deriabina, E. Gonzalez, D. Garcia, F. Rivas, N. A. Polteva; Biofizika, 2016, Volume 61, Issue 2, Pages 259-269; Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods

V. Poltev, V. M. Anisimov, V. I. Danilov, D. Garcia, C. Sanchez, A. Deriabina, E. Gonzalez, F. Rivas, N. Polteva; Biopolymers, 2014, Volume 101, Issue 6, Pages 640-650; The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures

V. I. Poltev, V. M. Anisimov, V. I. Danilov, D. Garcia, A. Deriabina, E. Gonzalez, R. Salazar, F. Rivas, N. Polteva; Computational and Theoretical Chemistry, 2011, Volume 975, Issue 1-3, Pages 69-75; DFT Study of DNA Sequence Dependence at the Level of Dinucleoside Monophosphates

V. I. Poltev, V. M. Anisimov, V. I. Danilov, T. van Mourik, A. Deriabina, E. Gonzalez, M. Padua, D. Garcia, F. Rivas, N. Polteva; International Journal of Quantum Chemistry, 2010, Volume 110, Issue 13, Pages 2548-2559; DFT Study of Polymorphism of the DNA Double Helix at the Level of Dinucleoside Monophosphates

V. I. Poltev, V. M. Anisimov, V. I. Danilov, A. Deriabina, E. Gonzalez, D. Garcia, F. Rivas F, A. Jurkiewicz, A. Les, N. Polteva; Journal of Molecular Structure – THEOCHEM, 2009, Volume 912, Issue 1-3, Pages 53-59; DFT study of minimal fragments of nucleic acid single chain for explication of sequence dependence of DNA duplex conformation 

V. I. Poltev, V. M. Anisimov, V. I. Danilov, A. Deriabina, E. Gonzalez, A. Jurkiewiez, A. Les, N. Polteva; Journal of Biomolecular Structure & Dynamics, 2008, Volume 25, Issue 5, Pages 563-571; DFT study of B-like conformations of deoxydinucleoside monophosphates containing Gua and/or Cyt and their complexes with Na+ cation

B. Habtemariam, V. M. Anisimov, A. D. MacKerell Jr.; Nucleic Acids Research, 2005, Volume 33, Issues 13, Pages 4212-4222; Cooperative binding of DNA and CBF beta to the Runt domain of the CBF alpha studied via MD simulations 

V. I. Danilov, V. M. Anisimov; Journal of Biomolecular Structure & Dynamics, 2005, Volume 22, Issue 4, Pages 471-482; Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: Molecular structure and the nature of stability 

N. Kurita, V. I. Danilov, V. M. Anisimov; Chemical Physics Letters, 2005, Volume 404, Issue 1-3, Pages 164-170; The structure of Watson-Crick DNA base pairs obtained by MP2 optimization 

V. I. Danilov, V. M. Anisimov, N. Kurita, D. Hovorun; Chemical Physics Letters, 2005, Volume 412, Issue 4-6, Pages 285-293; MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases 

Isotope Effect

V. M. Anisimov, P. Paneth; Journal of Mathematical Chemistry, 1999, Volume 26, Issue 1, Pages 75-86; ISOEFF98. A program for studies of isotope effects using Hessian modifications 

Computational Chemistry

V. M. Anisimov, M. J. Hallock, T. V. Pogorelov; Proceedings of the XSEDE 2015 Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. Association for Computing Machinery, Jul 26 2015, Vol. 2015-July, a43; CDD: Computational discovery desktop

V. M. Anisimov, E. Bartnicka, A. Dybala-Defratyka, P. Paneth; Polish Journal of Chemistry, 2002, Volume 76, Issue 5, Pages 737-744; A theoretical study on (eta(5)-C5H5)Fe(CO)(PPh3)(C(O)CHMe) anion structure and stereoselectivity

T. S. Zyubina, V. F. Razumov, S. B. Brichkin, V. M. Anisimov; Russian Chemical Bulletin, 2002, Volume 51, Issue 12, Pages 2145-2156; Quantum-chemical study of supramolecular complexes (DPEt)(n)(AgNO3)(m) 

E. T. Denisov, V. M. Anisimov, Journal of Molecular Structure – THEOCHEM, 2001, Volume 545, Pages 49-60; Quantum-chemical study of sulfoxide decomposition

I. V. Vystorop, A. B. Zolotoi, V. M. Anisimov, V. G. Kartsev, R. G. Kostyanovskii; Bulletin of the Russian Academy of Sciences-Division of Chemical Science, 1992, Volume 41, Issue 7, Pages 1235-1243; Autoassembly of cage structures .4. Stereochemistry of 2,5-di-tert-butyl-gamma-butyrolactone-4-carboxy-S-(alpha)-phenylethylamide

A. Rauk, C. Jaime, I. V. Vystorop, V. M. Anisimov, R. G. Kostyanovsky; Journal of Molecular Structure – THEOCHEM, 1995, Volume 342, Pages 93-101; 2,5-Dioxybicyclo[2.2.2]octane-3,6-diones - A conformational study by ab-initio molecular-orbital methods and molecular mechanics calculations 

N. N. Sveshnikov, A. M. Sipyagin, V. M. Anisimov; Russian Chemical Bulletin, 1995, Volume 44, Issue 12, Pages 2319-2322; N-oxides of polychloropyridines. C-13 NMR study 

S. V. Chapyshev, V. M. Anisimov; Khimiya Geterotsiklicheskikh Soedinenii, 1997, Issue 5, Pages 676-686; Quantum-chemical investigation of character of regioselectivity in reaction of 2,4,6-triazidopyridines with tert-butylphosphaacetylene

I. M. Rakov, V. M. Anisimov, S. A. Lermontov; Journal of Molecular Structure – THEOCHEM, 1997, Volume 419, Pages 201-204; The role of electronic and steric factors in the fluorination of P(III) compounds by Ph3BiF2  

S. V. Chapyshev, V. M. Anisimov; Khimiya Geterotsiklicheskikh Soedinenii, 1997, Issue 11, Pages 1521-1532; Stereo- and regioselective cycloaddition of norbornene to 2,4,6-triazidopyridines  

I. V. Vystorop, A. N. Utienyshev, V. M. Anisimov, R. G. Kostyanovsky; Mendeleev Communications, 1999, Issue 6, Pages 229-230; 1,4-dimethyl-2,5-dioxabicyclo[2.2.1]heptane-3,6-dione: optical resolution, absolute configuration and circular dichroism

T. S. Zyubina, V. F. Razumov, S. B. Brichkin, V. M. Anisimov, S. H. Lin, A. M. Mebel; Russian Journal of Inorganic Chemistry, 2006, Volume 51, Issue 6, Pages 925-940; Quantum-chemical study of crystal formation of supramolecular silver compounds with trans-1,2-bis(4-pyridyl)ethylene and their electronic absorption spectra 

V. Y. Popkova, V. M. Anisimov, G. N. Dolenko, M. N. Semenenko, V. M. Fedoseev; Journal of the Chemical Society-Perkin Transactions 2, 1995, Issue 7, Pages 1375-1379; Reversible intramolecular 1,3-chlorine migration in the triad carbon-carbon-sulfur 

V. M. Anisimov, S. M. Aldoshin; Journal of Molecular Structure – THEOCHEM, 1997, Volume 419, Pages 77-84; Quantum-chemical study of electronic properties of model spirooxazines

V. M. Anisimov, A. B. Zolotoi, M. Y. Antipin, P. M. Lukin, O. E. Nasakin, Y. T. Struchkov; Mendeleev Communications, 1992, Issue 1, Pages: 24-25;  Hexacyanocyclopropane – synthesis and structure