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An Unstructured Mesh Convergent Reaction-Diffusion Master Equation for Reversible Reactions

机译:一种非结构网格收敛反应扩散主方程   可逆反应

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摘要

The convergent reaction-diffusion master equation (CRDME) was recentlydeveloped to provide a lattice particle-based stochastic reaction-diffusionmodel that is a convergent approximation in the lattice spacing to anunderlying spatially-continuous particle dynamics model. The CRDME was designedto be identical to the popular lattice reaction-diffusion master equation(RDME) model for systems with only linear reactions, while overcoming theRDME's loss of bimolecular reaction effects as the lattice spacing is taken tozero. In our original work we developed the CRDME to handle bimolecularassociation reactions on Cartesian grids. In this work we develop severalextensions to the CRDME to facilitate the modeling of cellular processes withinrealistic biological domains. Foremost, we extend the CRDME to handlereversible bimolecular reactions on unstructured grids. Here we develop ageneralized CRDME through discretization of the spatially continuous volumereactivity model, extending the CRDME to encompass a larger variety ofparticle-particle interactions. Finally, we conclude by examining severalnumerical examples to demonstrate the convergence and accuracy of the CRDME inapproximating the volume reactivity model.
机译:最近开发了收敛反应-扩散主方程(CRDME),以提供基于晶格粒子的随机反应-扩散模型,该模型是晶格间距对基本空间连续粒子动力学模型的收敛近似。对于只有线性反应的系统,CRDME被设计为与流行的晶格反应扩散主方程(RDME)模型相同,同时当晶格间距设为零时,克服了RDME失去的双分子反应效应。在我们的原始工作中,我们开发了CRDME来处理笛卡尔网格上的双分子缔合反应。在这项工作中,我们开发了对CRDME的一些扩展,以促进对真实生物域内细胞过程的建模。首先,我们将CRDME扩展到在非结构化网格上难以处理的双分子反应。在这里,我们通过空间连续体积反应性模型的离散化来开发广义CRDME,将CRDME扩展为涵盖更大范围的粒子间相互作用。最后,我们通过检查几个数值示例得出结论,以证明CRDME逼近体积反应模型的收敛性和准确性。

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