Transition path sampling and forward flux sampling. Applications to biological systems
نویسندگان
چکیده
منابع مشابه
Transition path sampling and forward flux sampling. Applications to biological systems.
The last decade has seen a rapid growth in the number of simulation methods and applications dealing with the sampling of transition pathways of rare nanoscale events. Such studies are crucial, for example, for understanding the mechanism and kinetics of conformational transitions and enzymatic events associated with the function of biomolecules. In this review, a broad account of transition pa...
متن کاملNon-stationary forward flux sampling.
We present a method, Non-Stationary Forward Flux Sampling, that allows efficient simulation of rare events in both stationary and non-stationary stochastic systems. The method uses stochastic branching and pruning to achieve uniform sampling of trajectories in phase space and time, leading to accurate estimates for time-dependent switching propensities and time-dependent phase space probability...
متن کاملTransition Path Sampling
Often, the dynamics of complex condensed materials is characterized by the presence of a wide range of different time scales, complicating the study of such processes with computer simulations. Consider, for instance, dynamical processes occurring in liquid water. Here, the fastest molecular processes are intramolecular vibrations with periods in the 10-20 fs range. The translational and rotati...
متن کاملSteered transition path sampling.
We introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying the dynamics based on that probability, and then reweighting to calculate averages. Because the progress constraint can be formulated in terms of occurrences o...
متن کاملTransition Path Sampling Methods
Transition path sampling, based on a statistical mechanics in trajectory space, is a set of computational methods for the simulation of rare events in complex systems. In these lecture notes we give an overview of these techniques and describe their statistical mechanical basis as well as their application.
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Physics: Condensed Matter
سال: 2009
ISSN: 0953-8984,1361-648X
DOI: 10.1088/0953-8984/21/33/333101