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

• Membrane generation plugin for VMD [Membrane plugin page at the VMD site]


• Autoionize ion placement plugin for VMD  [Autoionize plugin page at the VMD site]

• 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.

• Renerr. Estimates of sampling error are vital for any analysis of biomolecular simulations. The renerr.pl utility provides sampling error estimates using an approach based on renormalization group theory. For command syntax, run "renerr.pl -help". For a description of the method, see H. Flyvbjerg and H. G. Petersen, J. Chem. Phys. 91, 461 (1989). New!
  

• Namdplot. Namdplot is an enhanced and rewritten in Perl version of the old namdplot utility for monitoring NAMD2 runs.