Chemistry Reference
In-Depth Information
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Figure 9
Configuration for the four fastest paths of an isomerization process for a
two-dimensional Lennard-Jones system obtained using the discrete path sampling
method. (Adapted from Wales.
87
)
each stationary point of the potential energy surface. Overall phenomenologi-
cal rate constants can be extracted using master equations, kinetic Monte
Carlo or graph transformations, and transition-state theory. The algorithm
has been applied to a small pentapeptide
83
and to the GB1 hairpin.
84
Reliance
on statistical rate theory is one of the drawbacks of this methodology. A satis-
factory sampling on stationary points of the potential energy for more com-
plex systems can be difficult as well.
In the string method,
90-94
which is based on the transition path theory
(TPT),
95,96
a ''transition tube'' in configuration space is constructed by sam-
pling the equilibrium distribution of the system in a collection of hyperplanes.
