Long Time Dynamics of Complex Systems

 

RON ELBER
Department of Physical Chemistry and Department of Biolgical Chemistry
The Fritz Haber Research Center and The Wolfson Center of Applied Structural Biology
Hebrew University
Jerusalem 91904, Israel
ron@fh.huji.ac.il

[ slides ]

Abstract:

Molecular dynamics trajectories of large biological molecules are restricted to nanoseconds. We describe a computational method, based on optimization of a functional, to extend the time of molecular simulations by orders of magnitude. Variants of our technique already produced microsecond and millisecond trajectories. The large steps enable feasible computations of atomically detailed approximate trajectories. Numerical examples are provided:

(i)

helix formation of an alanine-rich peptide [1];

(ii)

folding of protein A, and (iii) folding of cytochrome C.

References

1. RON ELBER, AVIJIT GHOSH, AND ALFREDO CARDENAS, Long time dynamics of complex systems, Account of Chemical Research, 35, 396-403(2002)
2. AVIJIT GHOSH, RON ELBER, AND HAROLD SCHERAGA, An atomically detailed study of the folding pathways of Protein A with the Stochastic Difference Equation", Proc. Natl. Acad. Sci., 99, 10394-10398 (2002).
3. ALFREDO CARDENAS AND RON ELBER, Kinetics of Cytochrome C Folding: Atomically Detailed Simulations, [Submitted]

[ abstract ]