Supporting data for "ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks"

Spatial organisation plays an important role in the function of many biological systems, from cell fate specification in animal development to multi-step metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the <i>in silico</i> testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling. <br>Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chastes existing capabilities. In particular, ChemChaste enables: (i) simulation of an arbitrary number of spatially diffusing chemicals; (ii) spatially heterogeneous chemical diffusion coefficients; and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chastes core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modelling bulk chemical reactions and their coupling with intracellular reactions.

空间组织在诸多生物系统的功能行使中发挥关键作用，涵盖动物发育过程中的细胞命运特化，乃至微生物群落内的多步骤代谢转化。对这类系统的研究，可通过空间显式计算模型有效开展：此类模型将细胞的离散化描述，与周围体相介质中一种或多种扩散化学物质的连续场描述相结合。此类模型可支持计算机模拟（in silico）环境下的机制假说验证与优化。然而，当前多数此类模型均未兼顾体相与胞内生化反应的同步进行，以及二者间潜在的耦合关系。
本文介绍ChemChaste——一款面向开源C++计算生物学库Chaste的扩展工具。通过拓展Chaste的既有功能，ChemChaste可实现多细胞与体相生物化学过程的空间模拟。具体而言，ChemChaste支持以下功能：(i) 任意数量空间扩散化学物质的模拟；(ii) 空间异质性化学扩散系数的配置；(iii) 体相与胞内生化反应及其耦合关系的整合。此外，ChemChaste还提供了基于文件的交互接口，用户可通过该接口定义上述功能相关的参数，无需直接操作Chaste的核心C++代码。本文详细阐述ChemChaste的设计，并选取若干化学与生化示例演示其功能，重点展示其在体相化学反应建模以及体相反应与胞内反应耦合模拟方面的增强能力。