Ilya Balabin's
page at Duke
Research Interests
- Theory and computer simulations of biomolecular structure,
dynamics, and function
- Multiscale modeling of functional motions in proteins and nucleic
acids
- Charge transfer in biological and organic molecules
- Development of novel methods and software for molecular modeling
- Engineering and medical applications of biomolecules
Representative Publications
- J. Lin, I. A. Balabin, D. N. Beratan. The Nature of Aqueous
Tunneling Pathways Between Electron-Transfer Proteins. Science 310, 1311-1313 (2005) [HTML]
[PDF]
- S. S. Skourtis, I. A. Balabin, T. Kawatsu, D. N. Beratan. Protein
Dynamics and Electron Transfer: Electronic Decoherence and Non-Condon
Effects. Proc. Natl. Acad. Sci. USA
102, 3552-3557 (2005) [HTML]
[PDF]
- J. Lee, I. A. Balabin, D. N. Beratan, J.-G. Lee, J. T. Yates, Jr.
Charge Transfer Through Chemisorbed Organic Molecules - Neutralization
of Ionization Processes at Local Sites in the Molecule. Chem. Phys. Lett. 412, 171-175 (2005) [HTML]
[PDF]
- A. Aksimentiev, I. A. Balabin, R. H. Fillingame, K. Schulten.
Insights Into the Molecular Mechanism of Rotation in the F0
Sector of ATP Synthase. Biophys. J.
86, 1332-1344 (2004) [HTML]
[PDF]
- I. A. Balabin, J. N. Onuchic. Dynamically Controlled Protein
Tunneling Paths in Photosynthetic Reaction Centers. Science 290, 114-117 (2000) [HTML]
[PDF]
Software Developed
VMD
plugins:
- Meadionize ion
placement plugin
for VMD. Meadionize
is an improved version
of Autoionize. It places ions to the minima of an electrostatic
potential
map computed using the MEAD
program package (Don
Bashford,
the Scripps Research
Institute) by solving the Poisson-Boltzmann equation. Medionize
supports all MEAD configuration parameters. It generates all necessary
input files for MEAD, runs it, and uses the MEAD output to place ions -
no user intervention required. Updated! Meadionize
version 1.1 can now add
divalent ions.
Standalone
tools:
- Namdplot. Namdplot
is an enhanced
and rewritten in Perl version of the old
namdplot utility for monitoring NAMD2 runs.