scholarly journals Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics

2021 ◽  
Vol 155 (12) ◽  
pp. 124109
Author(s):  
Mauricio J. del Razo ◽  
Manuel Dibak ◽  
Christof Schütte ◽  
Frank Noé
Keyword(s):  
Reaction Diffusion ◽  
Markov State ◽  
Markov State Models ◽  
Diffusion Dynamics ◽  
State Models

scholarly journals MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

2018 ◽  
Vol 148 (21) ◽  
pp. 214107 ◽  
Author(s):  
Manuel Dibak ◽  
Mauricio J. del Razo ◽  
David De Sancho ◽  
Christof Schütte ◽  
Frank Noé
Keyword(s):  
Reaction Diffusion ◽  
Markov State ◽  
Markov State Models ◽  
State Models

scholarly journals Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

2021 ◽  
Author(s):  
Arghadwip Paul ◽  
Suman Samantray ◽  
Marco Anteghini ◽  
Mohammed Khaled ◽  
Birgit Strodel
Keyword(s):  
Amyloid Β ◽  
Md Simulations ◽  
Amyloid Β Peptide ◽  
Intrinsically Disordered ◽  
Thermodynamics And Kinetics ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

scholarly journals Markov state models based on milestoning

2011 ◽  
Vol 134 (20) ◽  
pp. 204105 ◽  
Author(s):  
Christof Schütte ◽  
Frank Noé ◽  
Jianfeng Lu ◽  
Marco Sarich ◽  
Eric Vanden-Eijnden
Keyword(s):  
Markov State ◽  
Markov State Models ◽  
State Models
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