Article,
Precision shooting: Sampling long transition pathways
JOURNAL OF CHEMICAL PHYSICS, (November 2008)
DOI: {10.1063/1.2978000}
Abstract
The kinetics of collective rearrangements in solution, such as protein
folding and nanocrystal phase transitions, often involve free energy
barriers that are both long and rough. Applying methods of transition
path sampling to harvest simulated trajectories that exemplify such
processes is typically made difficult by a very low acceptance rate for
newly generated trajectories. We address this problem by introducing a
new generation algorithm based on the linear short time behavior of
small disturbances in phase space. Using this ``precision shooting''
technique, arbitrarily small disturbances can be propagated in time,
and any desired acceptance ratio of shooting moves can be obtained. We
demonstrate the method for a simple but computationally problematic
isomerization process in a dense liquid of soft spheres. We also
discuss its applicability to barrier-crossing events involving
metastable intermediate states.
