My research interests focus on connecting ab initio electronic structure methods with thermodynamic and kinetic properties of matter. I use state-of-the-art electronic structure methods in combination with a wide variety of techniques from quantum mechanics to molecular dynamics, to solve relevant problems in chemistry, biophysics, and materials science.- Olexandr
More specifically there are four focus areas of my work: (1) structure and dynamics of biopolymers, (2) explicit/implicit solvent effects, dynamics of water molecules, (3) first principles calculations, chemical accuracy and (4) high performance computing and visualization. I have been fortunate to be part of several interdisciplinary projects and gained valuable research experience working with colleagues from materials science, physics, chemistry, statistics, and biology.
ACCURACY & FIRST-PRINCIPLES SIMULATIONS
Our research efforts have manifested into two “black box” composite com-putational thermochemistry protocols. First provides the procedure for calculations of interaction Gibbs free energies for intermolecular complexes of biological interests. The second one offers very robust vey to predict redox potential for organic aromatic compounds. Aside from applications of extremely demanding correlated methods composite protocols usually include less CPU-intensive methods (like DFT) that provide reasonable trade-off between desired accuracy and time to solution.
- a) Toward Robust Computational Electro-chemical Predicting the Environmental Fate of Organic Pollutants J. Comp. Chem., 2011, 32, 2195. [doi]
b) Theoretical Calculations: Can Gibbs Free Energy for Inter-molecular Complexes Be Predicted Efficiently and Accurately? J. Comp. Chem. 2007, 28, 1598. [doi]
c) One-electron standard reduction potentials of nitroaromatic and cyclic nitramine explosives. Environ. Pollut., 2010, 158, 3048-53. [doi]
SOLVATION, DYNAMICS OF WATER
Of particular interest to me are hydration properties of DNA and nucleobases. Comprehensive study on interactions between nucleic acid bases and bulk water environment has been performed with use of classical and first principles Car–Parrinello molecular dynamics. Detailed analysis of average number, lifetimes and mobility of water molecules, orientation and 3D organization of hydrogen bond network in the first hydration shell of adenine, guanine, cytosine and thymine has been carried out.
Because MD simulations explicitly include of temperature, such simulations are uniquely suited to study the effects of temperature on chemical properties. I have been using first principles MD simulations to examine the temperature and dynamic effects of environment on DNA bases tautomerization. Obtained rate constants challenge the accepted results obtained using static methods and implicit solvation models. Although successful in many cases, the general applicability of many empirical implicit models with many system-dependent, adjustable parameters is often questionable, when compared to more accurate but computationally expensive explicit molecular dynamics (MD) simulations.
- a) Hydraion of Nucleic Acid Bases: a Car-Parrinello Molecular Dynamics Approach. Phys. Chem. Chem. Phys., 2010, 12, 3363-3375. [doi]
b) Novel View on the Mechanism of Water-Assisted Proton Transfer in the DNA Bases: Bulk Water Hydration. Phys. Chem. Chem. Phys., 2011, 13, 4311. [doi]
c) The Effect of Solvation on Vertical Ionization Energy of Thymine: From Microhydration to Bulk. J. Phys. Chem. A, 2011, 115, 6028. [doi]
HIGH-PERFORMANCE COMPUTING (HPC)
My collaborative efforts with the leading national supercomputing centers address performance and scalability issues in large distributed systems, scalable communication, runtime data analysis. Working together with the Maui High Performance Computing Center (MHPCC) and the Engineer Research and De-velopment Center (ERDC, both DoD DSRC centers) few scientific application were ported and especially optimized for several TOP500 system, including 100Tflop Dell PowerEdge M610 cluster, and 75Tflop Cray XT4.
As a part of collaboration with the Army High Performance Computing Research Center (AHPCRC) my efforts were devoted to benchmarking and per-formance/functionality enhancements computational chemistry codes (e.g. CPMD) on the new Cray X1E supercomputer and Opteron cluster systems.
As part of collaboration with the Mississippi Center for Supercomputing Research (MCSR) I have been involved into testing, benchmarking and tuning many scientific applications for the SGI Altix global shared-memory system.
