Professor Ron Elber

  Cornell University

Department of Computer Science

4130 Upson Hall, Ithaca,  NY 14853




Phone: (607) 255-7416


 FAX: (607) 255-4428

General Field of Investigation:

Structure and dynamics of biological molecules: Theory, algorithm developments and computer simulations. Software for molecular dynamics simulation -- MOIL and for protein recognition -- LOOPP

Figure: The gramicidin ion channel (sticks and green ribbon) and a "permion"  transported through it. A permion is a collective "quasi-particle" that consists of about 8 water molecules (red balls with white spots attached) and a sodium ion (the small pink ball in the middle) that moves coherently   (like in a queue) through the channel. A reaction path algorithm was   implemented into the Molecular Dynamics package MOIL [9] and was used to study the properties of the permion. The picture was made with the program MOIL-View written by Carlos Simmerling [10].






Topics of Research:

Ron Elber’s research focuses on algorithm development and computer simulations of the structure and dynamics of biomolecules.

Currently active research directions include

Recent Representative Publications:

  1. C. Keasar, D. Tobi, R. Elber and J. Skolnick, "Coupling the folding of homologous proteins", Proc. Natl. Acad. Sci. USA, 95,5880-5883(1998)
  2. O. Schueler-Furman, Ron Elber and Hanah Margalit, "Knowledge-based structure prediction of MHC class I bound peptides: A study of twenty-three complexes", Folding and Design, 3,549-564(1998).
  3. J. Meller and R. Elber, Computer simulations of carbon monoxide photo-dissociation in myoglobin: structural interpretation of the B states. Biophys. J. 74,789-802 (1998)
  4. D. Mohanty, R. Elber and Devarajan Thirumalai, Dimitrii Beglov and Benoit Roux, Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variations in water., J. Mol. Biol., 272, 423-442 (1997).
  5. C. Keasar, R. Elber and J. Skolnick, Simultaneous and coupled energy optimization of homologous proteins: A new tool for structure prediction, folding and design, 2,247-259 (1997)
  6. R. Olender and R. Elber, Calculation of classical trajectories with a very large time step: formalism and numerical examples, J. Chem. Phys., 105,9299-9315 (1996)
  7. A. Roitberg, R.B. Gerber, R. Elber and M.A. Ratner, Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI. Science, 268,1319-1322 (1995).
  8. R. Elber, D. Chen, D. Rojewska and R.S. Eisenberg, "Sodium in gramicidin: An example of a permion", Biophys. J., 68,906-924(1995)
  9. R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker, C. Keasar, J. Zhang and A. Ulitsky "MOIL: A program for simulations of macromolecules", Computer Physics Communications, 91,159-189(1995)
  10. C. Simmerling, R. Elber and J. Zhang, "Moil-View - a program for visualization of structure and dynamics of biomolecules and STO - a program for computing stochastic paths", in "The proceeding of the Jerusalem symposium on theoretical biochemistry", Modeling of Biomolecular Structures and Mechanisms, 1995, Ed. A. Pullman et al, 241-265, 1995 (Kluwer Academic Publishers, Netherlands)

Group Members:

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