MATLAB code for the figure plots from Multiphysics modelling of photon, mass and heat transfer in coral microenvironments

Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O₂ gradients in the coral tissue and skeleton, under environmental conditions simulating e.g. tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure–function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.

珊瑚礁由钙化珊瑚虫构建而成，这类珊瑚虫与其组织内寄生的甲藻微藻（dinoflagellate microalgae）形成共生关系。该共生过程处于光照、温度及化学物种的剧烈动态梯度环境中，而这些梯度会受到珊瑚的结构与光学特性，以及其与入射辐照度、水流的相互作用的影响。现有微环境分析已实现对这类梯度的量化，以及对珊瑚整体组织和骨骼光学特性的测定，但珊瑚的多层结构及其对光学、热学和化学微环境的影响，仍有待更深入的研究。本研究提出一种多物理场建模方法：以具有多层组织的简单珊瑚平板形态的光场三维蒙特卡洛（Monte Carlo）模拟结果作为输入，用于模拟由光子吸收驱动的热耗散与光合产氧过程。通过耦合光子、热量与质量传递过程，该模型可预测珊瑚组织与骨骼内的光照、温度及O₂梯度，模拟条件涵盖组织收缩/扩张、因珊瑚白化导致的共生体丢失，或不同分布模式的珊瑚宿主色素等场景。该模型揭示了调控珊瑚共生体微环境与生态生理过程的基础结构-功能机制，以响应环境变化。