Abstract. The stochastic description of chemical reaction networks with the kinetic chemical master equation (CME) is important for studying biological cells, but it suffers from the curse of dimensionality: The amount of data to be stored grows exponentially with the number of chemical species and thus exceeds the capacity of common computational devices for realistic problems. Therefore, time-dependent model order reduction techniques such as the dynamical low-rank approximation are desirable. In this paper, we propose a dynamical low-rank algorithm for the kinetic CME using binary tree tensor networks. The dimensionality of the problem is reduced in this approach by hierarchically dividing the reaction network into partitions. Only reactions that cross partitions are subject to an approximation error. We demonstrate by two numerical examples (a 5-dimensional lambda phage model and a 20-dimensional reaction cascade) that the proposed method drastically reduces memory consumption and shows improved computational performance and better accuracy compared to a Monte Carlo method. Reproducibility of computational results. This paper has been awarded the “SIAM Reproducibility Badge: Code and data available” as recognition that the authors have followed reproducibility principles valued by SISC and the scientific computing community. Code and data that allow readers to reproduce the results in this paper are available at https: //github. com/jmangott/atropos/tree/ttn and in the supplementary materials (M168571SM1. pdf 313KB) (M168571SM2. zip 111KB). Formula: see text
Einkemmer et al. (Mon,) studied this question.