Dr. Robert Kalescky

I’m currently the HPC Applications Scientist at Southern Methodist University (SMU) working with the Center for Scientific Computation to help enable research using SMU’s HPC resources. Resume, Curriculum Vitae

I’m an avid distance runner who enjoys training for and running marathons.

Research

My chemical research career has spanned a wide breadth of length and time scales ranging from the most accurate quantum calculations published for several small molecules to classical molecular dynamics simulations of proteins reaching hundreds of nanoseconds.

Expertise

  • Programming in Fortran 77/95, C, C++, Objective-C, Python, Visual Basic

  • Parallel programing using MPI, OpenMP, Pthreads, CUDA, OpenCL

  • Scripting in Bash, CSH, AWK, Perl, sed, Tcl, Visual Basic for Applications

  • Installation and application of quantum chemical and molecular dynamics programs on High Performance Computing (HPC) clusters and workstations:
    • Quantum chemical programs: Gaussian, Q-Chem, GAMESS, CFOUR, Molpro, NWChem, DIRAC, ORCA
    • Molecular dynamics programs: CHARMM, NAMD, LAMMPS, Amber, MPDyn, GROMACS, OpenMM
    • Molecular visualization programs: VMD, Chimera, Avogadro, IQmol, POV-Ray
    • Molecular desktop programs: Spartan, SYBYL
    • Calculation of: optimized geometries, transition states, reaction paths, potential energy surfaces, spectroscopic information, binding free energies
    • Quantum mechanical methods used: Hartree-Fock, Density Functional Theory, Möller-Plesset, Coupled Cluster
    • HPC clusters used: ManeFrame, SMUHPC, CATCO (SMU); Stampede (UT); Big Bird (UTD)
  • 15 years administration experience in UNIX using Linux (Red Hat and Debian derivatives), Mac OS X, FreeBSD, and Solaris including installation and configuration

  • 10 years high performance and scientific programming experience

  • Structured writing and documentation in LaTeX, BibTeX, reStructuredText, Sphinx, MediaWiki, HTML

  • Source code revision control using Git, Mercurial, Subversion

Peer-Reviewed Publications

  1. Kalescky, R.; Liu, J.; Tao, P. Identifying Key Residues for Protein Allostery through Rigid Residue Scan. J. Phys. Chem. A 2015, 119, 1689-1700. PDF
  1. Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D. Quantitative Assessment of the Multiplicity of Carbon-Halogen Bonds: Carbenium and Halonium Ions with F, Cl, Br, and I. J. Phys. Chem. A 2014, 118, 1948–1963. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. Accurate Determination of the Binding Energy of the Formic Acid Dimer: The Importance of Geometry Relaxation. J. Chem. Phys. 2014, 140, 084315. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. Are Carbon-Halogen Double and Triple Bonds Possible? Int. J. Quantum Chem. 2014, 114, 1060–1072. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. Description of Aromaticity with the Help of Vibrational Spectroscopy: Anthracene and Phenanthrene. J. Phys. Chem. A 2014, 118, 223–237. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. New Approach to Tolman’s Electronic Parameter Based on Local Vibrational Modes. Inorg. Chem. 2014, 53, 478–495. PDF
  1. Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D. Vibrational Properties of the Isotopomers of the Water Dimer Derived From Experiment and Computations. Aust. J. Chem. 2014, 67, 426–434. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. Identification of the Strongest Bonds in Chemistry. J. Phys. Chem. A 2013, 117, 8981–8995. PDF
  1. Kalescky, R.; Kraka, E.; Cremer, D. Local Vibrational Modes of the Formic Acid Dimer – The Strength of the Double Hydrogen Bond. Mol. Phys. 2013, 111, 1497–1510. PDF
  1. Zou, W.; Kalescky, R.; Kraka, E.; Cremer, D. Relating Normal Vibrational Modes to Local Vibrational Modes: Benzene and Naphthalene. J. Mol. Model. 2012, 19, 2865–2877. PDF
  1. Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D. Local Vibrational Modes of the Water Dimer – Comparison of Theory and Experiment. Chem. Phys. Lett. 2012, 554, 243–247. PDF
  1. Zou, W.; Kalescky, R.; Kraka, E.; Cremer, D. Relating Normal Vibrational Modes to Local Vibrational Modes with the Help of an Adiabatic Connection Scheme. J. Chem. Phys. 2012, 137, 084114. PDF
  1. Ranatunga, U.; Kalescky, R.; Chiu, C.; Nielsen, S. Molecular Dynamics Simulations of Surfactant Functionalized Nanoparticles in the Vicinity of an Oil/Water Interface. J. Phys. Chem. C 2010, 114, 12151–12157. PDF
  1. Kalescky, R.; Shinoda, W.; Moore, P.; Nielsen, S. Area Per Ligand as a Function of Nanoparticle Radius: A Theoretical and Computer Simulation Approach. Langmuir 2009, 25, 1352–1359. PDF

Publications

  1. Kalescky, R. Description of the Strength of Chemical Bonds Utilizing Local Vibrational Modes. Ph.D. Dissertation, Southern Methodist University, Dallas, TX, 2014.
  1. Kalescky, R. Area Per Ligand as a Function of Nanoparticle Radius: A Theoretical and Computer Simulation Approach. M.S. Thesis, University of Texas at Dallas, Dallas, TX, 2009. PDF