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Rate constants for diffusive processes by partial path sampling.
We introduce a path sampling method for the computation of rate constants for complex systems with a highly diffusive character. Based on the recently developed transition interface sampling (TIS)Expand
Investigation of the mechanism of colloidal silicalite-1 crystallization by using DLS, SAXS, and 29Si NMR spectroscopy.
Colloidal silicalite-1 zeolite was crystallized from a concentrated clear sol prepared from tetraethylorthosilicate (TEOS) and aqueous tetrapropylammonium hydroxide (TPAOH) solution at 95 degrees C.Expand
Reaction rate calculation by parallel path swapping.
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we devise a new algorithmic procedure based on the transition interfaceExpand
Efficiency analysis of reaction rate calculation methods using analytical models I: The two-dimensional sharp barrier.
We analyze the efficiency of different methods for the calculation of reaction rates in the case of a simple two-dimensional analytical benchmark system. Two classes of methods are considered: theExpand
Can one predict DNA transcription start sites by studying bubbles?
It has been speculated that bubble formation of several base pairs due to thermal fluctuations is indicatory for biologically active sites. Recent evidence, based on experiments and molecularExpand
Simultaneous computation of free energies and kinetics of rare events.
We introduce a method to evaluate simultaneously the reaction rate constant and the free energy profile of a process in a complex environment. The method employs the partial path transition interfaceExpand
Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables.
Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interfaceExpand
Bubbles and denaturation in DNA
Abstract.The local opening of DNA is an intriguing phenomenon from a statistical-physics point of view, but is also essential for its biological function. For instance, the transcription andExpand
Foundations and latest advances in replica exchange transition interface sampling.
TLDR
This is the aim of this article, which focuses on the most efficient exact path sampling approach, RETIS, as well as its recent applications, extensions, and variations. Expand
Proton-assisted ethylene hydration in aqueous solution.
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