scholarly journals Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation

2021 ◽  
Vol 125 (16) ◽  
pp. 3473-3488
Author(s):  
Darya Shchepanovska ◽  
Robin J. Shannon ◽  
Basile F. E. Curchod ◽  
David R. Glowacki
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Intermediate Coupling

Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations†

2005 ◽  
Vol 109 (14) ◽  
pp. 6479-6484 ◽  
Author(s):  
Saravanapriyan Sriraman ◽  
Ioannis G. Kevrekidis ◽  
Gerhard Hummer
Keyword(s):  
Molecular Dynamics ◽  
Bayesian Analysis ◽  
Master Equation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics

2019 ◽  
Author(s):  
David De Sancho ◽  
Anne Aguirre
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Md Simulations ◽  
Distinctive Features ◽  
Markov State Models ◽  
Software Packages ◽  
Long Time ◽  
State Models ◽  
Definition Of ◽  
Kinetics Of

<div>Markov state models (MSMs) have become one of the most important techniques for understanding biomolecular transitions from classical molecular dynamics (MD) simulations. MSMs provide a systematized way of accessing the long time kinetics of the system of interest from the short-timescale microscopic transitions observed in simulation trajectories. At the same time, they provide a consistent description of the equilibrium and dynamical properties of the system of interest, and they are ideally suited for comparisons against experiment. A few software packages exist for building MSMs, which have been widely adopted. Here we introduce MasterMSM, a new Python package that uses the master equation formulation of MSMs and provides a number of new algorithms for building and analyzing these models. We demonstrate some of the most distinctive features of the package, including the estimation of rates, definition of core-sets for transition based assignment of states, the estimation of committors and fluxes, and the sensitivity analysis of the emerging networks. The package is available at https://github.com/daviddesancho/MasterMSM.</div>

MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics

2019 ◽  
Author(s):  
David De Sancho ◽  
Anne Aguirre
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Md Simulations ◽  
Distinctive Features ◽  
Markov State Models ◽  
Software Packages ◽  
Long Time ◽  
State Models ◽  
Definition Of ◽  
Kinetics Of

<div>Markov state models (MSMs) have become one of the most important techniques for understanding biomolecular transitions from classical molecular dynamics (MD) simulations. MSMs provide a systematized way of accessing the long time kinetics of the system of interest from the short-timescale microscopic transitions observed in simulation trajectories. At the same time, they provide a consistent description of the equilibrium and dynamical properties of the system of interest, and they are ideally suited for comparisons against experiment. A few software packages exist for building MSMs, which have been widely adopted. Here we introduce MasterMSM, a new Python package that uses the master equation formulation of MSMs and provides a number of new algorithms for building and analyzing these models. We demonstrate some of the most distinctive features of the package, including the estimation of rates, definition of core-sets for transition based assignment of states, the estimation of committors and fluxes, and the sensitivity analysis of the emerging networks. The package is available at https://github.com/daviddesancho/MasterMSM.</div>

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

2011 ◽  
Vol 7 (5) ◽  
pp. 1244-1252 ◽  
Author(s):  
David R. Glowacki ◽  
Emanuele Paci ◽  
Dmitrii V. Shalashilin
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Time Scales

scholarly journals A Master equation for the probability distribution functions of forces in soft particle packings

Soft Matter ◽  
2015 ◽  
Vol 11 (7) ◽  
pp. 1253-1258 ◽  
Author(s):  
Kuniyasu Saitoh ◽  
Vanessa Magnanimo ◽  
Stefan Luding
Keyword(s):  
Molecular Dynamics ◽  
Probability Distribution ◽  
Master Equation ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Soft Particle ◽  
Probability Distribution Functions ◽  
Soft Particles ◽  
Dynamics Simulations ◽  
Particle Packings

We study the microscopic response of force-chain networks in jammed soft particles to quasi-static isotropic (de)compressions by molecular dynamics simulations.

scholarly journals Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

2017 ◽  
Vol 375 (2092) ◽  
pp. 20160206 ◽  
Author(s):  
David R. Glowacki ◽  
W. J. Rodgers ◽  
Robin Shannon ◽  
Struan H. Robertson ◽  
Jeremy N. Harvey
Keyword(s):  
Molecular Dynamics ◽  
Energy Transfer ◽  
Master Equation ◽  
Gas Phase ◽  
Reasonable Agreement ◽  
Chemical Vapour ◽  
Md Simulations ◽  
State Theory ◽  
Structure Theory ◽  
Non Equilibrium

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH 3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

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