Discrete simulation methods in combustion kinetics
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A stochastic description of pH within nanoscopic water pools
2023, Cell Reports Physical ScienceHigh energy radiation – Induced cooperative reductive/oxidative mechanism of perfluorooctanoate anion (PFOA) decomposition in aqueous solution
2022, ChemosphereCitation Excerpt :Time between irradiations and analysis of samples was no longer than 48 h. The competitive kinetics simulations were performed with the Kinetiscope™ a stochastic kinetics simulations software (Bunker et al., 1974; Gillespie, 1976; Hinsberg and Houle, 2017) freely available on authors web page: http://www.hinsberg.net/kinetiscope/. The rate constants of reactions describing radiolysis of aqueous solutions, required for the competitive kinetics simulation were taken from the compilation of the rate constants (Buxton et al., 1988) and shown in Table S1 in the Supplementary Materials.
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization
2021, Biophysical JournalConformational Dynamics of Damage Processing by Human DNA Glycosylase NEIL1
2019, Journal of Molecular BiologyCitation Excerpt :It should be emphasized that due to the difference in Trp location in NEIL1, Fpg and Nei (Supplementary Figs. 1 and 2), similar structural changes in these proteins may have different impact on the Trp fluorescence curves. For easier comparison of fluorescently discernible steps with different kinds of DNA, we have modeled the flow of enzyme–DNA species through the reaction using the Monte Carlo approach [65,66] with the experimentally determined rate constants. As shown in Fig. 7, the first Trp complex peaked at approximately the same time for all kinds of DNA.
A novel efficient hybrid algorithm for Monte Carlo simulation of controlled radical polymerization: The method integrating reactive and deactivated species
2019, Chemical Engineering JournalCitation Excerpt :Their algorithms can be especially profitable when chain reactivity depends on its DP. Such simplification, replacing the standard time interval between stochastic events, in fact being the exponentially-distributed random variable (4) with the expected value expressed by equation (5), was first used by Bunker et al. [17]. This approach was judged by Gillespie as “a very reasonable approximation” [9].
Predictive simulation of non-steady-state transport of gases through rubbery polymer membranes
2018, PolymerCitation Excerpt :Experimentally, calculated by molecular dynamics simulations, or derived from established theory. The simulation reaction-diffusion code used in this study incorporates stochastic methods, a type of kinetic Monte Carlo that produces an accurate timebase [9,10]. It provides a rigorously accurate solution to the master equation for Markov systems, and is a useful alternative to coupled differential equation integrators for complex materials systems.