Reaction-diffusion kinetics on lattice at the microscopic scale

Chew, Wei-Xiang and Kaizu, Kazunari and Watabe, Masaki and Muniandy, Sithi Vinayakam and Takahashi, Koichi and Arjunan, Satya N.V. (2018) Reaction-diffusion kinetics on lattice at the microscopic scale. Physical Review E, 98 (3). 032418. ISSN 2470-0045, DOI

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Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion processes. Some of these schemes that are based on the reaction-diffusion master equation (RDME) can simulate for extended spatial and temporal scales but cannot directly account for the microscopic effects in the cell such as volume exclusion and diffusion-influenced reactions. Nonetheless, schemes based on the high-resolution microscopic lattice method (MLM) can directly simulate these effects by representing each finite-sized molecule explicitly as a random walker on fine lattice voxels. The theory and consistency of MLM in simulating diffusion-influenced reactions have not been clarified in detail. Here, we examine MLM in solving diffusion-influenced reactions in three-dimensional space by employing the spatiocyte simulation scheme. Applying the random walk theory, we construct the general theoretical framework underlying the method and obtain analytical expressions for the total rebinding probability and the effective reaction rate. By matching Collins-Kimball and lattice-based rate constants, we obtained the exact expressions to determine the reaction acceptance probability and voxel size. We found that the size of voxel should be about 2% larger than the molecule. The theoretical framework of MLM is validated by numerical simulations, showing good agreement with the off-lattice particle-based method, enhanced Green's function reaction dynamics (egfrd). MLM run time is more than an order of magnitude faster than egfrd when diffusing macromolecules with typical concentrations observed in the cell. MLM also showed good agreements with egfrd and mean-field models in case studies of two basic motifs of intracellular signaling, the protein production-degradation process and the dual phosphorylation-dephosphorylation cycle. In addition, when a reaction compartment is populated with volume-excluding obstacles, MLM captures the nonclassical reaction kinetics caused by anomalous diffusion of reacting molecules.

Item Type: Article
Funders: JSPS KAKENHI Challenging Research (Pioneering) Grant No. 17H06226
Uncontrolled Keywords: Analytical expressions; Diffusion-influenced reactions; Green's function reaction dynamics; Intracellular signaling; Particle-based methods; Reaction-diffusion kinetics; Spatial and temporal scale; Three dimensional space
Subjects: Q Science > Q Science (General)
Q Science > QC Physics
Divisions: Faculty of Science > Department of Physics
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 04 Sep 2019 07:25
Last Modified: 04 Sep 2019 07:25

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