CompuCell3d manual and Tutorial Version 2
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- III. GGH Simulation Overview
II. GGH ApplicationsBecause it uses a regular cell lattice and regular field lattices, GGH simulations are often faster than equivalent Finite Element (FE) simulations operating at the same spatial granularity and level of modeling detail, permitting simulation of tens to hundreds of thousands of cells on lattices of up to 10243 pixels on a single processor. This speed, combined with the ability to add biological mechanisms via terms in the effective energy, permit GGH modeling of a wide variety of situations, including: tumor growth (5-9), gastrulation (10-12), skin pigmentation (13-16), neurospheres (17), angiogenesis (18-23), the immune system (24, 25), yeast colony growth (26, 27), myxobacteria (28-31), stem-cell differentiation (32, 33), Dictyostelium discoideum (34-37), simulated evolution (38-43), general developmental patterning (14, 44), convergent extension (45, 46), epidermal formation (47), hydra regeneration (48, 49), plant growth, retinal patterning (50, 51), wound healing (47, 52, 53), biofilms (54-57), and limb-bud development (58, 59). III. GGH Simulation OverviewAll GGH simulations include a list of objects, a description of their interactions and dynamics and appropriate initial conditions. Objects in a GGH simulation are either generalized cells or fields in two dimensions (2D) or three dimensions (3D). Generalized cells are spatially-extended objects (Figure 1), which reside on a single cell lattice and may correspond to biological cells, sub-compartments of biological cells, or to portions of non-cellular materials, e.g. ECM, fluids, solids, etc. (8, 48, 60-72). We denote a lattice site or pixel by a vector of integers,  , the cell index of the generalized cell occupying pixel by  and the type of the generalized cell by  . Each generalized cell has a unique cell index and contains many pixels. Many generalized cells may share the same cell type. Generalized cells permit coarsening or refinement of simulations, by increasing or decreasing the number of lattice sites per cell, grouping multiple cells into clusters or subdividing cells into variable numbers of subcells (subcellular compartments). Compartmental simulation permits detailed representation of phenomena like cell shape and polarity, force transduction, intracellular membranes and organelles and cell-shape changes. For details on the use of subcells, which we do not discuss in this chapter see (Directory: BinDoc -> cc3d binaries -> Manuals Manuals -> 111Equation Chapter 1 Section 1 CompuCell3d reference Manual Version 4 Download 6.67 Mb. Share with your friends:
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