Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks

Journal Article · 24 June 2019 · Journal of Chemical Physics

DOI: https://doi.org/10.1063/1.5096774 · OSTI ID:1544696

Lin, Yen Ting  ^[1]; Feng, Song  ^[1]; Hlavacek, William Scott  ^[1]

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1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Various kinetic Monte Carlo algorithms become inefficient when some of the population sizes in a system are large, which gives rise to a large number of reaction events per unit time. In this work, we present a new acceleration algorithm based on adaptive and heterogeneous scaling of reaction rates and stoichiometric coefficients. The algorithm is conceptually related to the commonly used idea of accelerating a stochastic simulation by considering a subvolume λΩ (0 < λ < 1) within a system of interest, which reduces the number of reaction events per unit time occurring in a simulation by a factor 1/λ at the cost of greater error in unbiased estimates of first moments and biased overestimates of second moments. Our new approach offers two unique benefits. First, scaling is adaptive and heterogeneous, which eliminates the pitfall of overaggressive scaling. Second, there is no need for an a priori classification of populations as discrete or continuous (as in a hybrid method), which is problematic when discreteness of a chemical species changes during a simulation. The method requires specification of only a single algorithmic parameter, N_c, a global critical population size above which populations are effectively scaled down to increase simulation efficiency. The method, which we term partial scaling, is implemented in the open-source BioNetGen software package. We demonstrate that partial scaling can significantly accelerate simulations without significant loss of accuracy for several published models of biological systems. Finally, these models characterize activation of the mitogen-activated protein kinase ERK, prion protein aggregation, and T-cell receptor signaling.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE National Nuclear Security Administration (NNSA); Laboratory Directed Research and Development (LDRD)
• Grant/Contract Number: 89233218CNA000001
• OSTI ID: 1544696
• Report Number(s): LA-UR--19-22745
• Journal Information: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 24 Vol. 150; ISSN 0021-9606
• Publisher: American Institute of Physics (AIP)Copyright Statement
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY