This is the repository for the Matlab codes for generating the results in: Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa, Nan Luo, Shangying Wang, Jia Lu, Xiaoyi Ouyang, Lingchong You. Molecular Systems Biology, 2021
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Optimization models: The codes for the optimization models of colony growth.
- OptimalModel1D.m: The model with 1D branch extension. Generates results in Figure 2 and Figure 3.
- OptimalModel2D.m: The model with 2D branch extension. Generates results in Figure S3 and Figure S4.
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Pattern prediction: The codes for simulating colony patterns using the optimization principle.
- OptimalPattern_uniform.m: Predicting colony patterns under uniform conditions. Generates results in Figure 4 and Figure S5.
- OptimalPattern_hetero.m: Predicting colony patterns under heterogeneous conditions. Generates results in Figure 5.
- OptimalPattern_multiseeding.m: Predicting colony patterns with various seeding configurations. Generates results in Figure 6 and Figure S8.