Ilya Balabin

About Me

Current position:

Research Scholar
Department of Chemistry
Duke University
Durham, NC 27708-0349

Education:

Ph. D. in Physics, University of California, San Diego
M. S. cum laude in Physics, Moscow State University, Russia

Principal Research Interests

I employ theory, modeling, and computer simulations to explore properties and function of biological 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
Signal transduction in cells
Computer-aided drug design and screening
Energy transduction in protein machines
Biological charge transfer reactions
Molecular electronics and biomolecular engineering
Bioinformatics, large-scale data mining and analysis
Development of novel methods and software

Pathway dynamics in wild type azurin
(Balabin et al, submitted)

Selected 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 1.0 for VMD, now with major performance enhancements. Pathways identifies, visualizes, and animates dynamics of dominant electron transfer pathways in biomolecular structures. Pathways features simple and intuitive, yet fully flexible user interface, making even most complex pathway calculations a breeze. See an example animation of pathway dynamics in ruthenated wild type azurin (1BEX) (paper in preparation).
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. Meadionize can handle mono- and divalent ions.
Namdplot, a Perl script for monitoring and analyzing NAMD2 output in real time, an enhanced version of the old Namdplot.
Autoionize plugin version 1.2 for randomly placing ions in biomolecular structures with small total charge (VMD web page).
Membrane plugin version 1.1 for generating lipid bilayer structures used in membrane protein simulations (VMD web page).

Modified on 2011-03-04

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