Ilya Balabin's page at Duke University

Current position:

Data Engineer
Blaize, Inc.
Cary, NC 27511

Education:

Ph. D. in Physics, University of California, San Diego

M. S. cum laude in Physics, Moscow State University, Russia

Email: ilya dot balabin at duke dot edu

Research Interests

I employ theory, modeling, and computer simulations to explore properties and function of biological and engineered molecular systems. My research addresses a broad range of topics, including (but not limited to):

Protein dynamics and function, broadly taken
Allosteric regulation in biomolecular complexes
Protein-ligand and protein-protein interactions
Molecular recognition and signal transduction
Computer-aided drug design and screening
Energy transduction in protein machines
Biological charge transfer reactions
Molecular electronics and biomolecular engineering
Bioinformatics, cheminformatics, large-scale data mining and analysis
Development of novel methods and software

Pathway dynamics in wild type azurin
(Balabin et al, J. Comp. Chem. 2012)

Representative Publications

Allosteric interactions GPCR (PNAS 2009)

Balabin et al, PNAS 2009

Protein Dynamics and Function

I. A. Balabin, W. Yang, and D. N. Beratan. Coarse-grained modeling of allosteric regulation in protein receptors. Proc. Natl. Acad. Sci. USA 106, 14253-14258 (2009). [PDF]

A. Aksimentiev, I. A. Balabin, R. H. Fillingame, and K. Schulten. Insights into the molecular mechanism of rotation in the F_o sector of ATP synthase. Biophys. J. 86, 1332-1344 (2004). [PDF]

Green's function correlation
Balabin et al, PRL 2008
(cover figure)

Biological Electron Transfer

I. A. Balabin, S. S. Skourtis, and D. N. Beratan. The persistence of structure over fluctuations in biological electron-transfer reactions. Phys. Rev. Lett. 101, 158102 (2008). [PDF] [Supporting information]

J. Lin, I. A. Balabin, and D. N. Beratan. The nature of aqueous tunneling pathways between electron-transfer proteins. Science 310, 1311-1313 (2005). [PDF]

I. A. Balabin and J. N. Onuchic. Dynamically controlled protein tunneling paths in photosynthetic reaction centers. Science 290, 114-117 (2000). [PDF]

Lee, Balabin, et al,
Chem. Phys. Lett. 2005

Molecular Electronics

J. Lee, I. A. Balabin, D. N. Beratan, J.-G. Lee, and J. T. Yates, Jr. Charge transfer though chemisorbed organic molecules – Neutralization of ionization processes at local sites in the molecule. Chem. Phys. Lett. 412, 171-175 (2005). [PDF]

I. A. Balabin and J. N. Onuchic. Connection between simple models and quantum chemical models for electron-transfer tunneling matrix element calculations: A Dyson's equations-based approach. J. Phys. Chem. B100, 11573-11580 (1996).[PDF]

Molecular Modeling and Simulations Software that I have developed

NEW: Pathways plugin version 1.2 for VMD. Pathways identifies, visualizes, and animates dynamics of dominant electron transfer pathways in biomolecular structures, and analyzes statistics of the electronic coupling fluctuations. See an example animation of pathway dynamics in ruthenated wild type azurin (1BEX) (J. Comp. Chem. 33, 906-210 (2012)). Version 1.2 provides a few bugfixes; most notably, it works around an old VMD issue when results of hydrogen bond measurement might depend on whether the atom selection has been moved and/or rotated.
Updated: Meadionize plugin version 1.2 for VMD. Meadionize employs the MEAD program package for calculating electrostatic potential maps and uses the maps to place ions into potential minima.
Autoionize plugin version 1.2 for VMD (included in VMD). Autoionize randomly places counter-ions in solvent around biomolecular structures.
Membrane plugin version 1.1 for VMD (included in VMD). Membrane generates lipid bilayer structures too be used in membrane protein simulations.
Namdplot, a tool for monitoring and analyzing NAMD2 output in real time (enhanced and re-implemented in Perl Namdplot utility from NAMD2).

(C) Ilya A. Balabin

ilya dot balabin at duke dot edu

Modified on 2015-06-26