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Figure 1 | BMC Systems Biology

Figure 1

From: Spatially-resolved metabolic cooperativity within dense bacterial colonies

Figure 1

s3DdFBA methodology at a glance. (A) Cells, agar, and air are discretized to a 3D cubic lattice. (B) Substrate diffusion is accounted for using a seven-point stencil finite difference scheme. (C) Substrates can be passively or actively taken up by the cells. Those that cannot passively penetrate cell membranes experience hindered diffusion around cells in the extracellular space (D) Flux balance analysis predicts substrate usage and cell growth. (E) Cell volume grows exponentially until it surpasses a maximum volume fraction, ρ max, at which time intercellular forces create pressure that pushes cell volume outward into neighboring lattice sites of lesser volume fraction. (F) Cells of different species or in different regulatory states can be simultaneously simulated. Those in different states can transform back and forth at rates that can depend on up to two local substrate concentrations, (ϕ m and ϕ n , or ϕ o and ϕ p ).

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