Title: Exploring dynamic pathways by action-derived molecular dynamics

Authors: In-Ho Lee, Sukky Jun, Hanchul Kim, Seung-Yeon Kim, Jooyoung Lee

Addresses: Korea Research Institute of Standards and Science, Daejeon 305-600, Korea. ' Department of Mechanical and Materials Engineering, Florida International University, Miami, FL 33174, USA. ' Korea Research Institute of Standards and Science, Daejeon 305-600, Korea. ' School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea. ' School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea

Abstract: Action-derived molecular dynamics for the simulation of rare event and slow mode systems is reviewed. Theoretical background, implementation details, and comparison with other methods are presented. Numerical examples demonstrated include the structural formation and transformation of carbon fullerenes, and molecular reconfiguration of alanine dipeptide and valine dipeptide. It is shown that the action-derived molecular dynamics is efficient to explore the dynamic pathways of various chemical reactions.

Keywords: transition pathway; activation energy; action-derived molecular dynamics; rare event systems; slow mode systems; simulation; carbon fullerenes; molecular reconfiguration; alanine dipeptide; valine dipeptide; dynamic pathways; nanotechnology; Korea.

DOI: 10.1504/IJNT.2006.009587

International Journal of Nanotechnology, 2006 Vol.3 No.2/3, pp.334 - 352

Published online: 01 May 2006 *

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