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PeriodicBC.zip 2014-10-06 33.8 kB 0
Open_Boundaries.zip 2014-10-06 36.3 kB 0
README.txt 2014-10-06 2.7 kB 0
Corrected_concentration_field.pdf 2014-10-06 317.5 kB 0
Totals: 4 Items   390.3 kB
==================================================================================== ***** UPDATED ***** Matlab implementation of simulation code used for the paper "Migration of cells in a social context" Proceedings of the National Academy of Sciences of the USA vol. 110, 129-134 (2013) ==================================================================================== Please see pdf document for details of corrections made to the originally published code, and performance of the simulations. ==================================================================================== The code is provided with periodic boundary conditions, and with open boundaries. In either case, the model is executed via the script model_runscript.m which is opened and executed (F5 from the Matlab editor). The promt indicates simulation progress. MODEL PARAMETERS All user-defined parameters are given at the top of the script. These include - NumCells: the number of cells to be simulated - dt: simulation time step. We have used dt = 0.25 min for all results presented - TEnd: Total simulation time [min] - CompDomainLength: size of simulation domain is CompDomainLength*CompDomainLength. This is where cells are placed initially, and for periodic boundary conditions, these are placed at x = {0, CompDomainLength} and y = {0, CompDomainLength}. - IntervalLength: Sampling interval for evaluating performance of model. We have used 4-6 min similar to the experiments CONTROLS The code currently allows for random initial placement of cells or using initial positions from an experiment. Initial conditions (activation and life time of initial pseudopods) are random. - UseExpInitially: 1 = use experimental conditions initially / 0 = use random initial position within domain of size CompDomainLength*CompDomainLength - SaveData: 1 = saves / 0 = does not save simulation results - FileName: Filename used if saving data - FilePath: Filepath where simulation results will be saved under the name specified in FileName (i.e. data is saved to FilePath\FileName if SaveData=1) - PlotAtAll: 1 = plots / 0 = does not plot upon completion of simulation A NOTE ON CELL SPACING The code will attempt to place the number of cells specified by NumCells in the square domain specified by CompDomainLength (size: CompDomainLength*CompDomainLength). If it is not possible to do this wihtout having overlapping cells in 2X10^5 attempts, the code will tell the user in the prompt, but will otherwise proceed with the simulation. Results from such simulations are not trustworthy. A figure illustrating all initial positions is generated when the simulation is done.
Source: README.txt, updated 2014-10-06

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