Mesoscopic models of plant development

发育生物学的一个中心问题是生物体如何获得它们的形式。计算模型在解决这一问题上发挥着重要作用。它们的相关性在一定程度上是由于许多发展过程的自组织特性，如果不使用模型，很难分析和理解这些过程。 迄今为止构建的植物发育模型大致可分为两类。微观模型旨在解释控制生长的形态发生活性物质的时空模式。这些模型在单个细胞中发生的分子过程的规模上运行。宏观模型将局部生长与整个植物的全球形态联系起来，并在大型植物组件的水平上运行。例子包括分枝系统的元素(顶端和节间)和器官，如叶、花和果实。原则上，微观和宏观模型是互补的，但它们的对应关系一直很薄弱，造成了对发展的理解上的差距。为了解决这一差距，我建议设计一个概念和数学框架、建模方法和软件，用于在中间、中观水平上模拟植物发育。这一水平的特征是空间尺度大于单个细胞但小于整个植物，高度不均匀的生长导致大小和形状的根本变化，图案和生长之间的反馈，以及通过自组织图案出现新的结构元素，包括维管系统的分化。 我建议使用双管齐下的方法来驾驭介观发展的复杂性，其中分子和细胞水平过程的基本图案化属性被提炼成几何本构规则，而大规模模式、形式和结构的发展则根据这些规则来表征。理论概念和计算方法将借鉴计算机科学、数学和物理的思想，并将应用于植根于实验数据的生物学问题。案例研究将包括复叶、花和花序的发育。这些结果有望为发育植物生物学提供一个统一的视角，并推动计算机图形学中植物的逼真建模方法。

A central question of developmental biology is how organisms acquire their form. Computational models play an important role in addressing this question. Their relevance is due, in part, to the self-organizing character of many developmental processes, which is difficult to analyze and understand without the use of models. Models of plant development constructed to date can be broadly divided into two classes. Microscopic models aim at explaining the spatio-temporal patterns of morphogenetically active substances that control growth. These models operate at the scale of molecular processes taking place in individual cells. Macroscopic models relate local growth to the global form of entire plants and operate at the level of large plant components. Examples include the elements of the branching system (apices and internodes) and organs such as leaves, flowers, and fruits. In principle, microscopic and macroscopic models are complementary, but their correspondence has been tenuous, creating a gap in the understanding of development. Addressing this gap, I propose to devise a conceptual and mathematical framework, modeling methods, and software for modeling plant development at the intermediate, mesoscopic level. This level is characterized by spatial scales larger than individual cells but smaller than whole plants, highly non-uniform growth resulting in radical changes in size and shape, feedback between patterning and growth, and the emergence of new structural elements, including differentiation of vasculature, through self-organizing patterning. I propose to harness the complexity of mesoscopic development using a two-prong approach, where the essential patterning properties of molecular and cell-level processes are distilled into geometric constitutive rules, and the development of large-scale patterns, forms and structures is characterized in terms of these rules. Theoretical notions and computational methods will draw on ideas from computer science, mathematics and physics, and will be applied to biological problems rooted in experimental data. Case studies will include the development of compound leaves, flowers and inflorescences. The results are expected to contribute a unifying perspective to developmental plant biology, and advance methods for realistic modelling of plants in computer graphics.