Resume

Looking for: Post-doc or Researcher position in Theoretical Biophysics or related area.

Education:        • 11-year School-lyceum #157, Kiev. Physical-mathematical specialized class. Finished in 1997 with honor.
• The University of Kiev-Mohyla Academy, Kiev, Ukraine.
Undergraduate:
        Major – Physics. Finished with honor.
        Minor – Biology.
Graduate:
        Masters in Biophysics. Finished with honor.
• PhD studies: Kiev Institute of Physics. PhD in Biophysics obtained in 2005.
        Title of the thesis: “Stochastic collective effects in the functioning of the ion channels and the process of protein folding”.

Honors: • 1995–1997: 3 gold medals of annual regional, city and state biology Olympiads, gold and silver medals on physics Olympiads.

• Gold medals of the annual Soros biological Olympiads, 1996-1997.
• Silver medal in theoretical part and bronze medal in practical part of second international biology competition “First step to Nobel prize in bioilogy”, 5-7 February 1996, Istanbul, Turkey.
• Silver medal of 7^th international biology Olympiad, 30.06-07.07 1996, Crimea, Ukraine.
• Gold medal of 8^th international biology Olympiad, 13-20 July 1997, Ashgabat, Turkmenistan.
• Gold medal of the young scientists competition, 1996. Work title: “Simulation of the molecular mechanisms that maintain Ca⁺ concentration in smooth muscles.”.
• Gold medal of the young scientists competition, 1997. Work title: “Simulation of simple two-enzyme systems: the search of oscillatory behavior”.
• First prize of the competition “Best student of Kiev – 1999”.

Grants: • 2004: INTAS Young Scientist grant 03-55-1502. Title: “Interactions of fluorescence probes with phospholipid bilayers studied by

molecular dynamics simulations (MDS) and nonbond calculations”.
• 2005: STCU grant on theoretical study of the cell-penetrating peptides.

Research interests:
General:
Theoretical and molecular biophysics, computer modelling and simulations.
Specific subjects:
• Ion channels. Mechanism of permeation in the multi-ion channels. Possible self-organization phenomena in the ion channels gating and inactivation, numerical simulations.
• Protein folding. Simplified models, role of collective dynamics in folding, numerical simulations.
• Investigation of slow motions in proteins and supra-molecular complexes. Theoretical approaches for bridging the gap between fast dynamics and “physiological” time scales.
• Data processing using Maximum Entropy Method.
• Combination of Molecular Dynamics and related techniques with analytical approaches.

• 1996: Kiev Institute of Biochemistry, Department of Muscle Biochemistry. Simulation of molecular mechanisms that maintain Ca⁺ concentration in cytosole of smooth muscles.

• 1996-1997: Theoretical investigations and numerical simulations of two-enzyme systems behavior. Oscillations of intermediate substrates concentrations are investigated.

• 1997-2001: Collaborative program of Kiev Botany Institute and University of Kiev-Mohyla academy. Development of numerical techniques for paleoclimatic reconstructions based on the data of spore-polen analysis. Development of the software package, statistical analysis and data interpretation.

• Since 1998: Laboratory of Biophysics, Institute of Physics, Kiev, under the guidance of Prof. V. N. Kharkyanen:

(1) 1999-2004: Development of the theoretical models of voltage-dependent and inward-rectifying potassium ion channels. Main task of the work is to create comprehensive model of the ion channel operation based on the concept of ion-conformational interactions (ICI). ICI considers the channel and the ion flux through it as a self-organized system, which can become bistable. These states are interpreted as open and closed states of the channel.
2003-2005: Novel description of the multi-ion channels is developed. The motion of the ions is considered as a motion of a single quasi-particle, which move in the effective potential created by the pore walls and the ion-ion interactions. It is shown that this method simplifies the problem greatly reducing it to the single-particle problem without considerable loss of quality. The method is viewed as a supplement to MD and BD simulations, which allows to bridge the gap between the nanosecond and “physiological” time scales.

(2) 2000-2005: Developing techniques and corresponding software for the Maximum Entropy deconvolution of the multi-exponential decay curves. The program MEMfit is developed and maintained (http://www.oocities.org/memfit_group/). The progranm is used to investigate the spectra of bacterial photoreaction centers, fluorescent response of the yellow fluorescent protein and other objects.

(3) 2004-2005: Development of the HCCP (Hierarchical clustering of the correlation patterns) method of domain identification in proteins. The method utilizes residue-residue correlation matrices f any origin (GNM, MD etc.) and allows to find the dynamic domains reliably even for different conformations of the same protein. The method is especially attractive because it does not contain any adjustable parameters and thus is not biased. The work is in progress.

(4) 2005: Theoretical investigation of membrane translocation of the cell-penetrating peptides (HIV TAT, penetratin etc.). The work is in the staring stage.

(5) 2004-2005: Molecular dynamics studies of lipid bilayers with the fluorescent dyes embedded.

• Since 1998: Department of Enzyme Chemistry and Biochemistry, Institute of Biochemistry, Kiev, under the guidance of Prof. A. P. Demchenko.

(1) 1998-2000: Numerical simulation of the large-scale protein dynamics influence on the enzymatic catalysis. The goal is to explain non-Arrhenius temperature dependencies of enzymatic reaction rates postulating existence of different dynamical modes of protein motion for different temperatures. Investigations are based on numerical simulations of elementary catalytic events in enzyme active site which are under control of slow conformational motions. The project was suspended.

(2) 1999-2005: Numerical simulations of the protein folding based on the model of sequential hierarchical relaxation. The novel algorithm of folding of the lattice proteins – CMC is developed. The method is designed to take into account collective motions on the lattice in the physically consistent way. It was shown that existing methods underestimate the importance of collective motions. CMC corrects the artifacts in designability and folding rates.

(3) 2004-2005: Studies of noveltwo-color fluorescent dyes using quantum chemistry and MD. The main goal is to predict the properties of new dyes and guide the synthesis.

• Methods of theoretical physics. Mainly worked with statistical mechanics and stochastic differential equations.
• Methods of computational physics. Various numerical algorithms (Monte-Carlo, Brownian Dynamics, Solving complex stochastic equations etc.)
• Biomolecular modeling, simulations and visualization. Familiar with RasMol, VMD (including complex scripting), Gromacs, NAMD. Some experience with CHARMm.
• Quantum chemistry: OPAC, HyperChem, nwchem/ECCE.
• General computer skills: MS Windows and UNIX/LINUX systems.
• Programming: Overall experience – 10 years. Languages: Basic, Pascal, Delphi, Fortran 90/95, Javascript, Perl, TCL/TK.

Fast-learning, independently thinking, creative, responsible, honest, can adapt to new tasks quickly, but somewhat impractical in everyday life.

1. Yesylevskyy S.O., Kharkyanen V.N. Hierarchy of motions and quasi-particles in a simplified model of potassium channel selectivity filter // J. Biol. Phys. – 2004 – V. 30. - №2. – P. 187-201.

2. Yesylevskyy S.O., Kharkyanen V.N. Quasi-particles in the selectivity filter can explain permeation in a channel with multiple occupancy // Phys. Chem. Chem. Phys. – 2004 – №. 6. – P. 3111-3122.

3. Alagem N., Yesylevskyy S., Reuveny E. Control of Open State Stability by the Pore Helix in Inwardly rectifying K+ Channels // Biophys. J. – 2003. – Vol. 85. – P. 300-312.

4. Yesylevskyy S.O., Demchenko A.P. Modeling the hierarchical protein folding using clustering Monte-Carlo algorithm // Protein and Peptide Letters. – 2001. – Vol 6. – P. 437-442.

5. Yesylevskyy S.O., Demchenko A.P. Towards Realistic Description of Collective Motions in the Lattice Protein Folding Models //J. Biophys. Chem. – 2004. – Vol. 109. – P. 17-40.

6. Yesylevskyy S.O., Demchenko A.P. Designability of lattice small-size protein models: is it sufficient to use the compact ground states? // Chem. Phys. Lett. – 2004. – Vol. 388, № 4-6. – P. 348-352.

7. S.O. Yesylevskyy, V.N. Kharkyanen. Barrier-less knock-on conduction in ion channels: peculiarity or general mechanism? // Chem. Phys. 2004., 6, 3111-3122.

8. S.O. Yesylevskyy, A.S. Klymchenko and A.P. Demchenko. Semi-empirical study of two-color fluorescent dyes based on 3-hydroxychromone. Submitted to J. Mol. Struct.

9. S. O. Yesylevskyy, V.N. Kharkyanen, A. P. Demchenko. Hierarchical clustering of the correlation patterns: new method of domain identification in proteins. // Accepted by J. Biophys. Chem., 2005.