Ocean microbes in the petascale age: towards the billion-particle model

“世界海洋约占全球初级生产力的50%，因此在全球碳平衡和生物地球化学循环中发挥着关键作用。海洋也是全世界人口的主要食物来源。微生物构成了这两种生态系统功能的基础，预测海洋微生物之间复杂的相互作用以及这些相互作用的结果仍然是气候和环境研究的重大挑战之一[1，2]。由于海洋处于不断运动中，微生物生命和海洋生态系统涉及许多固有的拉格朗日过程，可以使用基于个体的模型（IBM）进行建模。这些模型，在生态建模中使用的传统的基于人口的方法相比，可以解决精细尺度的过程和复杂的非线性基础拉格朗日运动驱动的微生物之间的接触使用大量的虚拟粒子。该项目针对的关键生物挑战将是将种群内和生命周期变异性、快速驯化/适应和微生物-微生物竞争/入侵动态纳入拉格朗日运动IBM模型，以预测气候温度和洋流的气候强迫变化如何改变生态系统动态。一个有希望的额外途径将是模拟海洋微生物物种与处于较高营养水平的物种（例如，该项目定量/计算创新的主要目标是解决目前拉格朗日模型受到所需大量粒子产生的高计算需求的严重限制的问题，这反过来又限制了预测能力。学生将通过建立在OceanPARCELS（Parcel）软件设计的伦敦帝国理工学院结合微生物生理学的真实的数据从BioTraits数据库也在ICL开发的这个问题。OceanPARCELS框架允许通过简单的高级语言以编程方式定义单个代理的行为来快速创建复杂的运动驱动的生态系统模型，同时通过现代计算技术（如即时（JIT）编译）利用高性能计算（HPC）资源的功能。其结果将是开发一个具有现实的海洋微生物IBM所需的大量颗粒的模型--数十亿颗粒，与模拟开放海洋中真实的微生物-微生物相互作用有关。将通过BioTraits数据实现模型微生物的实际生态行为和变化的参数化，该数据涵盖数百个物种和数千个微生物生理学和与微生物-微生物生活史和相互作用结果相关的其他特征的实验测量。参考文献：[1]艾伦等人，《地球系统应用的海洋生态系统模型：MarQUEST经验》。海洋系统杂志，2009年[2]多尼。海洋生物地球化学建模面临的主要挑战。《1999年全球生物地球化学循环》

"The world's oceans are responsible for about 50% of the global primary productivity and therefore play a key role in the global carbon balance and bio-geochemical cycles. The oceans are also a major source of food for human populations worldwide. Microbes form the basis for both these ecosystem functions, and predicting the complex interactions between marine microbes as well as the outcomes of these interactions remains one of the grand challenges in climate and environmental research [1, 2]. Because the ocean is in constant motion, microbial life and the marine ecosystem involve many inherently Lagrangian processes that can be modelled using individual-based models (IBMs). These models, in contrast to traditional population-based methods used in ecological modelling, can resolve fine-scale processes and complex nonlinearities underlying Lagrangian movement-driven contact between microbes using large numbers of virtual particles. The key biological challenge targeted by this project will be to incorporate intra-population and life-cycle variability, rapid acclimation/adaptation and microbe-microbe competition/invasion dynamics, into the Lagrangian movement IBM model to predict how climate-forced changes in climatic temperature and oceanic currents may alter ecosystem dynamics. One promising additional avenue would be to model interactions of marine microbial species with species at higher trophic levels (e.g., zooplankton, fish) to predict effects of incomplete mixing conditions and strong spatial variability/patchiness on population dynamics in food chains.The key target for quantitative/computational innovation in this project will be to tackle the problem that current Lagrangian models are severely limited by the high computational demand arising from the large numbers of particles required, which in turn limits predictive capabilities. The student will tackle this problem by building upon the OceanPARCELS (Parcels) software designed at Imperial College London combined with real data on microbial physiology from the BioTraits database also developed at ICL. The OceanPARCELS framework allows rapid creation of complex movement-driven ecosystem models by programmatically defining the behaviour of individual agents in a simple high-level language, while utilising the power of high performance computing (HPC) resources through modern computational techniques, such as the Just-in-Time (JIT) compilation. The result will be development of a model with the vast numbers of particles required for a realistic oceanic microbial IBM --- billions of particles, relevant to modelling real microbe-microbe interactions in the open ocean. The parameterisation of realistic ecological behaviour and variation of the model microbes will be achieved through the BioTraits data, which covers hundreds of species and thousands of experimental measurements of microbial physiology and other traits relevant to microbe-microbe life history and interaction outcomes. References: [1] Allen et al. Marine ecosystem models for earth systems applications:The MarQUEST experience. Journal of Marine Systems, 2009[2] Doney. Major challenges confronting marine biogeochemical modeling. Global Biogeochemical Cycles, 1999"