Frontiers in Plant Science (Oct 2013)
Using Cellzilla for Plant Growth Simulations at the Cellular Level
Abstract
Cellzilla is a two-dimensional tissue simulation platform for plant modeling utilizing Celleratorarrows. Cellerator describes biochemical interactions with a simplified arrow-based notation; allinteractions are input as reactions and are automatically translated to the appropriate differentialequations using a computer algebra system. Cells are represented by a polygonal mesh ofwell-mixed compartments. Cell constituents can interact intercellularly via Cellerator reactionsutilizing diffusion, transport, and action at a distance, as well as amongst themselves withina cell. The mesh data structure consists of vertices, edges (vertex pairs), and cells (andoptional intercellular wall compartments) as ordered collections of edges. Simulations may beeither static, in which cell constituents change with time but cell size and shape remain fixed;or dynamic, where cells can also grow. Growth is controlled by Hookean springs associatedwith each mesh edge and an outward pointing pressure force. Spring rest length grows at arate proportional to the extension beyond equilibrium. Cell division occurs when a specifiedconstituent (or cell mass) passes a (random, normally distributed) threshold. The orientationof new cell walls is determined either by Errera’s rule, or by a potential model that weighscontributions due to equalizing daughter areas, minimizing wall length, alignment perpendicularto cell extension, and alignment perpendicular to actual growth direction.
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