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Title: Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

Journal Article · · Journal of Chemical Physics
DOI:https://doi.org/10.1063/1.4998926· OSTI ID:1512927

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

Research Organization:
Univ. of Delaware, Newark, DE (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
Grant/Contract Number:
SC0010549
OSTI ID:
1512927
Alternate ID(s):
OSTI ID: 1402107
Journal Information:
Journal of Chemical Physics, Vol. 147, Issue 16; ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 23 works
Citation information provided by
Web of Science

References (67)

Electronic Metal–Support Interactions and the Production of Hydrogen Through the Water-Gas Shift Reaction and Ethanol Steam Reforming: Fundamental Studies with Well-Defined Model Catalysts journal August 2013
Sensitivity analysis for stochastic chemical reaction networks with multiple time-scales journal January 2014
Accurate coverage-dependence incorporated into first-principles kinetic models: Catalytic NO oxidation on Pt (111) journal February 2012
Likelihood Ratio Sensitivity Analysis for Markovian Models of Highly Dependable Systems journal February 1994
A graph-theoretical kinetic Monte Carlo framework for on-lattice chemical kinetics journal June 2011
Distinctions between Supported Au and Pt Catalysts for CO Oxidation: Insights from DFT Study journal October 2013
SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations journal October 2017
Avoiding negative populations in explicit Poisson tau-leaping journal August 2005
Adsorption Energy Correlations at the Metal–Support Boundary journal June 2017
Thermodynamic Consistency in Microkinetic Development of Surface Reaction Mechanisms journal November 2003
Density Functional Kinetic Monte Carlo Simulation of Water–Gas Shift Reaction on Cu/ZnO journal February 2013
Stochastic averaging and sensitivity analysis for two scale reaction networks journal February 2016
Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting journal March 2012
Efficient stochastic sensitivity analysis of discrete event systems journal February 2007
Steam and dry reforming of methane on Rh: Microkinetic analysis and hierarchy of kinetic models journal October 2008
Steady state likelihood ratio sensitivity analysis for stiff kinetic Monte Carlo simulations journal January 2015
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method journal December 2003
Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions journal December 2013
Solving the chemical master equation for monomolecular reaction systems analytically journal September 2006
A local superbasin kinetic Monte Carlo method journal April 2013
On the importance of metal–oxide interface sites for the water–gas shift reaction over Pt/CeO2 catalysts journal January 2014
Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems journal May 2005
Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling journal February 2016
Likelihood ratio gradient estimation for stochastic systems journal October 1990
Degree of rate control approach to computational catalyst screening journal October 2015
An overview of spatial microscopic and accelerated kinetic Monte Carlo methods journal February 2007
Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales journal January 2007
Efficient gradient estimation using finite differencing and likelihood ratios for kinetic Monte Carlo simulations journal August 2012
Generalized Temporal Acceleration Scheme for Kinetic Monte Carlo Simulations of Surface Catalytic Processes by Scaling the Rates of Fast Reactions journal March 2017
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm journal March 2003
Control of Metal Nanocrystal Size Reveals Metal-Support Interface Role for Ceria Catalysts journal July 2013
Unraveling the Complexity of Catalytic Reactions via Kinetic Monte Carlo Simulation: Current Status and Frontiers journal November 2012
Finding the Rate-Determining Step in a Mechanism journal December 2001
CO Oxidation on Pd(111): A First-Principles-Based Kinetic Monte Carlo Study journal May 2014
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics journal October 2002
The chemical Langevin equation journal July 2000
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems journal July 2005
Binomial distribution based τ-leap accelerated stochastic simulation journal January 2005
The water-gas shift reaction on Pt/γ-Al2O3 catalyst: Operando SSITKA-DRIFTS-mass spectroscopy studies journal November 2008
Is the water–gas shift reaction on Pt simple? journal July 2005
Comparison of finite difference based methods to obtain sensitivities of stochastic chemical kinetic models journal February 2013
First-Principles-Based Kinetic Monte Carlo Simulation of the Structure Sensitivity of the Water–Gas Shift Reaction on Platinum Surfaces journal November 2011
Multiscale Modeling Reveals Poisoning Mechanisms of MgO-Supported Au Clusters in CO Oxidation journal June 2012
Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm journal October 2005
Design Principles of Heteroepitaxial Bimetallic Catalysts journal September 2013
Net-event kinetic Monte Carlo for overcoming stiffness in spatially homogeneous and distributed systems journal March 2005
Efficient step size selection for the tau-leaping simulation method journal January 2006
Does phenomenological kinetics provide an adequate description of heterogeneous catalytic reactions? journal May 2007
An Efficient Finite Difference Method for Parameter Sensitivities of Continuous Time Markov Chains journal January 2012
Influence of Step Defects on Methanol Decomposition: Periodic Density Functional Studies on Pd(211) and Kinetic Monte Carlo Simulations journal December 2012
A review of multiscale modeling of metal-catalyzed reactions: Mechanism development for complexity and emergent behavior journal October 2011
Patched bimetallic surfaces are active catalysts for ammonia decomposition journal October 2015
Examination of the concept of degree of rate control by first-principles kinetic Monte Carlo simulations journal June 2009
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions journal February 2005
Optimisation of simulations of stochastic processes by removal of opposing reactions journal February 2016
A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis journal January 2017
Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics journal March 2016
Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants journal May 2010
Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates journal June 2009
Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates journal September 2009
Sensitivity analysis for stochastic chemical reaction networks with multiple time-scales text January 2014
An Efficient Finite Difference Method for Parameter Sensitivities of Continuous Time Markov Chains preprint January 2011
Sensitivity analysis for stochastic chemical reaction networks with multiple time-scales preprint January 2013
Stochastic Averaging and Sensitivity Analysis for Two Scale Reaction Networks text January 2015
Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics text January 2015
Optimisation of Simulations of Stochastic Processes by Removal of Opposing Reactions text January 2016
A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis text January 2016

Cited By (4)

A DFT and KMC based study on the mechanism of the water gas shift reaction on the Pd(100) surface journal January 2020
A Practical Guide to Surface Kinetic Monte Carlo Simulations journal April 2019
Dynamic vs static behaviour of a supported nanoparticle with reaction-induced catalytic sites in a lattice model journal February 2020
A Practical Guide to Surface Kinetic Monte Carlo Simulations text January 2019

Figures / Tables (12)