CV

Curriculum vitae:

Areas of Expertise:

Theoretical chemistry, theoretical molecular spectroscopy, computational chemistry, quantum chemistry, molecular mechanics, molecular dynamics, combined quantum mechanical - molecular mechanical calculations (QM/MM - a computational method which was awarded by the Nobel Prize in Chemistry), massive parallel computing, programming - research and teaching. A referee of scientific journals: Journal of the American Chemical Society and Inorganic Chemistry, and a referee of grant programs: CUNY Collaborative Incentive Research Grant Program and Israel Science Foundation, in a field of combined QM/MM calculations

Education:

M.S. (with honors) in Chemistry, minor in Physics, Jagiellonian University (Poland) 1976-1981
Ph.D. (with honors) in Chemistry, minor in Physics, Jagiellonian University (Poland) 1983-1988

Personal:

Married, US citizen

Professional Experience:

Research Assistant Professor, Southern Methodist University, Dallas TX, 2010-present
Research Scientist, Q-Chem Inc., Pittsburgh PA, 2009-2010
Computational Scientist, University at Buffalo NY, 2004-2009
Adjunct Assistant Professor, University at Buffalo NY, 2003-2010
Research Associate, University at Buffalo NY, 2001-2004
Research Associate, University of Louisville KY, 2000-2001
Assistant Professor, Jagiellonian University (Poland), 1991-2000
Research Associate, Jagiellonian University (Poland), 1981-1991
Postdoctoral Research Associate, University at Buffalo NY, 1995-1997 (on sabbatical leave)
Postdoctoral Researcher, University of Bonn (Germany) 1989-1991 (on sabbatical leave)
Exchange Visitor, Oxford University (England), June 1987

Teaching Experience in the USA:

Fall 2010 - present; Supervision of graduate students, undergraduate students, postdoctoral associates, SMU, Dallas TX
Spring 2018; Hartree-Fock and DFT Computational Lab, SMU, Dallas TX, 6 students
Fall 2017; Computational Chemistry Lab, SMU, Dallas TX, 5 students
Summer 2012; General Chemistry, SMU, Dallas TX, 32 students
Fall 2008; Computer Modeling of Biological Systems; University at Buffalo NY; 1 student
Fall 2007 - Spring 2008; Computer Modeling of Biological Systems; University at Buffalo NY; 4 students
Fall 2006 - Spring 2007; Computer Modeling of Biological Systems; University at Buffalo NY; 12 students

Teaching Experience in Poland:

Fall 1981 - Fall 2000; Quantum Chemistry, Quantum Mechanics, Theoretical Spectroscopy, Group Theory, Thermodynamics, Statistical Mechanics, Algebra with Math Analysis, and Computer Programming; Jagiellonian University, Krakow. (An average teaching load included 1 to 2 courses per semester with an average class group involved about 8 students)

Workshop Organization and Teaching:

CATCO Workshop, SMU, Dallas TX, June 2016
CATCO Workshop, SMU, Dallas TX, December 2015
CATCO Workshop, SMU, Dallas TX, December 2012
Q-Chem Workshop, Texas A&M University, College Station TX, October 2012
Q-Chem Workshop, University of North Texas, Denton TX, August 2011
Q-Chem Workshop, University of Louisville KY, March 2010
Q-Chem Workshop, University of California, Berkeley CA, December 2009
Q-Chem Workshop, University of Illinois at Urbana-Champaign, Il, National Center for Supercomputing Applications, Urbana-Champaign IL, November 2009
Q-Chem Workshop, NIH Bethesda campus, Washington DC, August 2009
Q-Chem Workshop, Penn State University, State College PA, May 2009
Q-Chem Workshop, Pittsburgh Supercomputing Center, Pittsburgh PA, March 2009

Teaching Interest:

Lecture presentations in an electronic version using own sketches, plots, and diagrams
Hands-outs for students including all lecture topics
Individual work with students in scientific research in a form of smaller computer tasks and bigger computational projects
Development of graphic computational programs written in JavaScript for molecules (JSMol) for presentations of lecture topics

Presentation at International Conferences:

27th Austin Symposium on Molecular Structure and Dynamics at Dallas TX, SMU, Dallas TX, USA, 2018, poster presenter
26th Austin Symposium on Molecular Structure and Dynamics at Dallas TX, SMU, Dallas TX, USA, 2016, poster presenter
25th Austin Symposium on Molecular Structure and Dynamics at Dallas TX, SMU, Dallas TX, USA, 2014, poster presenter
24th Austin Symposium on Molecular Structure and Dynamics at Dallas TX, SMU, Dallas TX, USA, 2012, poster presenter
The 239th meeting of the American Chemical Society, San Francisco CA, USA, 2010, poster presenter
The 238th meeting of the American Chemical Society, Washington DC, USA, 2009, poster presenter
The 9th Annual Conference on Structure-Based Drug Design, Cambridge Healthtech Institute, Boston, MA, USA, 2009, poster presenter
The 7th International Conference on Bioinformatics and Bioengineering, Harvard Medical School, Boston, MA, USA, 2007
The 2006 International Accelrys Conference, Baltimore, MD, USA, 2006, invited lecturer
The 2006 International Conference on Bioinformatics and Computational Biology, Las Vegas, NV, USA, 2006, discussion presenter
230th meeting of the American Chemical Society, Washington DC, USA, 2005, invited lecturer
Gordon Research Conference, New Hampshire, USA, 1996, poster presenter
Computational Chemistry Conference, Lyon, France, 1995, invited lecturer

Research Interest:

Modeling chemical reactions in protein active sites using a combined quantum chemical - molecular mechanical (QM/MM) method
Modeling of protein - drug interactions using docking and molecular dynamics simulations in explicit water solution and utilizing the QM/MM method
Development of computational methods and their applications for biological systems, using massive parallel computing and utilizing the QM/MM method

Participation in Grant Proposals:

D. Kofke, V. Chaudhary, A. Schultz, T. Furlani, J. Kong, M. Freindorf, and H. King; University at Buffalo and Q-Chem. Submitted to NSF in 2009
J. Garvey, M. Freindorf, and J. Kong; University at Buffalo and Q-Chem. Submitted to NSF in 2009
V. Cody, M. Freindorf, and J. Kong; University at Buffalo and Q-Chem. Submitted to NIH in 2009
T. Furlani, M. Jones, M. Freindorf, and J. Kong; University at Buffalo and Q-Chem. Submitted to Army Air Forces in 2008
M. Freindorf, and J. Kong; University at Buffalo and Q-Chem. Submitted to NSF in 2008
J. Autschbach, J. Kong, T. Furlani, and M. Freindorf, University at Buffalo and Q-Chem. Submitted to NSF in 2006

Professional Knowledge:

Computational modeling using quantum chemical programs: Q-Chem, GAUSSIAN, ORCA, CFOUR, MOLPRO, GAMESS, TURBOMOLE, JAGUAR, NWChem, COLUMBUS, MOLCAS, ADF, DALTON, MRD-CI, AMPAC/MOPAC, SPARTAN, GAUSSVIEW; and molecular mechanical programs: CHARMM, AMBER, BOSS
Ab initio quantum mechanical calculations: RHF, UHF, CIS, CIS(D), CASSCF, RASSCF, ORMAS, CASPT2, CASPT3, MRCI, CCSD, CCSD(T), CCSD(T)-F12, CCSDT, DLPNO-CCSD(T), OO-CCD, EOM-CCSD, EOM-SF-CCSD, MP2, MP3, SOS-RI-MP2, O2-SOS-MP2, DKH3/CASSCF, DKH2/MR-CISD, SOC/CASSCF
Quantum mechanical calculations based on density functional theory (DFT), time dependent DFT (TD-DFT) and spin flip DFT (SF-DFT) methods
Calculations of molecular properties such as geometry optimization, molecular oscillations, potential energy surfaces (PES), chemical reaction profiles, transition states, PES curvatures, excited electronic states, spectroscopic parameters, electronic transition moments, spin-orbit couplings, relativistic corrections, molecular force field
Effective core potential (ECP) calculations involving heavy elements
Effective fragment potential (EFP) and fragment molecular orbital (FMO) calculations
SFC calculations with the polarizable continuum model (PCM) of solvent effects including the isotropic dielectrics, the anisotropic dielectrics, and the COSMO model
Molecular mechanical calculations: standard molecular mechanical Newton and Langevin dynamics in the gas phase and in water solution with periodic boundary conditions using the Particle Mesh Ewald method, Poisson-Boltzmann dynamics, molecular mechanical Monte Carlo simulations; calculations of solutions, proteins, DNA and inorganic polymers
Combined quantum mechanical - molecular mechanical (QM/MM) calculations: geometry optimization, molecular oscillations, transition states, and reaction profiles of an active site inside inorganic polymers and biopolymers like proteins and DNA in explicit water solution; binding drug molecules to active sites of proteins and DNA in explicit water solution, using molecular mechanical dynamics combined with high-level quantum mechanical calculations on ab initio and DFT levels of theory
Theoretical models of molecular electronic spectroscopy including vibronic transitions, Franck-Condon factors, Renner-Teller effect, Jahn-Teller effect, Herzberg-Teller effect, vibronic interactions in molecular dimers and trimers

Computer Experience:

Parallel and sequential computing using batch schedulers SLURM, Condor and Portable Batch System on HP Linux Cluster, DELL Linux Cluster, IBM SP Cluster, IBM RS/6000 Workstation, SGI Altix, SGI Origin, SGI Linux Cluster, SGI Workstation, Sun Enterprise Cluster, Sun Workstation, Convex, Cyber
Programming in computational languages: FORTRAN (expert level), PASCAL (expert level), Delphi (expert level), Perl (expert level), Python (entry level), HTML (entry level), Java (entry level), WordPress (entry level). Modification and installation of quantum chemical programs such as Q-Chem, Gaussian, and GAMESS
Scientific visualization and website designing using professional graphic software such as Adobe Illustrator, Photoshop, InDesign, Lightroom, Dreamweaver, WordPress, supported by knowledge of photography at an expert level