scholarly journals Efficient and exact sampling of transition path ensembles on Markovian networks

2020 ◽  
Vol 153 (2) ◽  
pp. 024121 ◽  
Author(s):  
Daniel J. Sharpe ◽  
David J. Wales
Keyword(s):  
Transition Path ◽  
Exact Sampling

Rare event simulation

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Rare Event ◽  
Path Sampling ◽  
Rapid Progress ◽  
Computationally Efficient ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Event Simulation ◽  
Reaction Coordinates ◽  
Simulation Techniques ◽  
Transition Interface

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.

scholarly journals Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation

ACS Omega ◽  
2020 ◽  
Vol 5 (34) ◽  
pp. 21374-21384
Author(s):  
Pavel Janoš ◽  
Igor Tvaroška ◽  
Christoph Dellago ◽  
Jaroslav Koča
Keyword(s):  
Catalytic Mechanism ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling

scholarly journals Time-dependent communication between multiple amino acids during protein folding

2021 ◽  
Vol 12 (16) ◽  
pp. 5944-5951
Author(s):  
Song-Ho Chong ◽  
Sihyun Ham
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Transition State ◽  
Time Dependent ◽  
Transition Path ◽  
Contact Formation ◽  
Molecular Origin

Cooperativity in contact formation among multiple amino acids starts to develop upon entering the folding transition path and attains a maximum at the folding transition state, providing the molecular origin of the two-state folding behavior.

The transition path from female workers to neotenic reproductives in the termite Reticulitermes labralis

2017 ◽  
Vol 19 (4-5) ◽  
pp. 218-226 ◽  
Author(s):  
Xiaohong Su ◽  
Xiaojuan Yang ◽  
Jing Li ◽  
Lianxi Xing ◽  
He Liu ◽  
...  
Keyword(s):  
Transition Path ◽  
Female Workers
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