Computing time scales from reaction coordinates by milestoning.

By Anton Faradjian, R. Elber. Journal of Chemical Physics, 2004

586 citations recorded by the source corpus.

Subfields: Economics and Econometrics, Molecular Biology, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/9b16ce637120d66a76e49eac071eb0b51f5d18df

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Citations in the corpus

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS (2015, methodology): “…reality, researchers are increasingly using large ensembles of simulations, either to simply sample better, or new algorithms such as replica exchange simulation, 24 Markov state models, 22 or milestoning 13 that analyze and exchange data between multiple simulations to improve overall sampling.”
Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (2017, unknown): “, milestoning (27), transition interface sampling (65), and forward flux sampling (5)].”
Forward flux sampling for rare event simulations (2009, methodology): “The ‘Milestoning’ method [26, 27] also uses a series of interfaces between the initial and final states, defined by an order parameter λ.”
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “We note that weighted ensemble methodologies, while falling under the umbrella of adaptive seeding strategies, can be categorized under transition path-finding methods, along with the string method with swarms of trajectories [331], milestoning [332], transition interface sampling [333], forward flu”
Diffusion maps, spectral clustering and reaction coordinates of dynamical systems (2005, unknown): “N A ]”
Experimental accuracy in protein structure refinement via molecular dynamics simulations (2018, background): “While many types of conformational transitions have been studied via many different methods (45, 46), we chose the iterative sampling protocol based on unbiased simulations to study the refinement transition without having to make any pre-sumptions about the pathway(s) or suitable progress…”
Protein storytelling through physics (2020, background): “Another parallelization strategy is milestoning, which is best when a process has a dispersed diffusional route structure (74).”
Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. (2013, background): “These include even the comparatively sophisticated techniques that have now been developed to improve the sampling of rare events, such as milestoning (65), transition path sampling (66), and metadynamics (67).”