Data-Driven Methods for Building Reduced Kinetic Monte Carlo Models of Complex Chemistry from Molecular Dynamics Simulations

2019 ◽  
pp. 209-227
Author(s):  
Qian Yang ◽  
Carlos A. Sing-Long ◽  
Enze Chen ◽  
Evan J. Reed
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Molecular Dynamics Simulations ◽  
Kinetic Monte Carlo ◽  
Data Driven ◽  
Dynamics Simulations ◽  
Complex Chemistry

scholarly journals Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

2017 ◽  
Vol 8 (8) ◽  
pp. 5781-5796 ◽  
Author(s):  
Qian Yang ◽  
Carlos A. Sing-Long ◽  
Evan J. Reed
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Molecular Dynamics Simulations ◽  
Statistical Learning ◽  
Large Scale ◽  
Kinetic Monte Carlo ◽  
Reaction Networks ◽  
Learning Framework ◽  
Dynamics Simulations ◽  
Complex Chemistry

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD).

Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins

2019 ◽  
Vol 16 (1) ◽  
pp. 553-563 ◽  
Author(s):  
Benedikt Rennekamp ◽  
Fabian Kutzki ◽  
Agnieszka Obarska-Kosinska ◽  
Christopher Zapp ◽  
Frauke Gräter
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Molecular Dynamics Simulations ◽  
Kinetic Monte Carlo ◽  
Dynamics Simulations

scholarly journals Transferable Kinetic Monte Carlo Models with Thousands of Reactions Learned from Molecular Dynamics Simulations

2019 ◽  
Vol 123 (9) ◽  
pp. 1874-1881 ◽  
Author(s):  
Enze Chen ◽  
Qian Yang ◽  
Vincent Dufour-Décieux ◽  
Carlos A. Sing-Long ◽  
Rodrigo Freitas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Molecular Dynamics Simulations ◽  
Kinetic Monte Carlo ◽  
Dynamics Simulations

scholarly journals Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins

2020 ◽  
Vol 118 (3) ◽  
pp. 140a
Author(s):  
Benedikt Rennekamp ◽  
Fabian Kutzki ◽  
Agnieszka Obarska-Kosinska ◽  
Christopher Zapp ◽  
Frauke Gräter
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Molecular Dynamics Simulations ◽  
Kinetic Monte Carlo ◽  
Dynamics Simulations
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