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---------------README file for the agent-based modeling setup---------------
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Agent-based modeling of diffusion via 2D random walks is implemented here. 
- Set basal step size limit in the box. Can be uniform ('default') or gradient ('stepwise'/'linear')
- Set if particles can interact with each other via neighbour sensing
- Set viscous regions (in the script, they comprise the variable termed xyHoney)
		- Can be a single rectangular viscous region or a set of circular viscous granules
- Set where, in the simulation zone, are particles initialized (xyStartFigure)
- Control how long do start boundaries, viscous zones last
- Run simulation for the desired number of frames. 

regbox_run.m - main simulation file. Use it to run the diffusion simulations as per desired parameters. Output file - .mat file comprising AllCoords - m x 2 (or 3) x k array of coordinates for mparticles across k frames

Typical workflow:
1. Run regbox_run.m with desired parameters.
2. Call AllCoords_DisplayGifParticles to visualise a timelapse of frames/an individual frame from the run.
3. Call AllCoords_SmoothDensity to obtain the distribution of particles.

Sample workflow run:
1. regbox_run.m
2. AllCoords_DisplayGifParticles(ScriptVar, AllCoords,'tryoutput', [1 50])
3. AllCoords_SmoothDensity(ScriptVar, AllCoords, 'trytry', 1, [1 100 250 500], 500, 100)


Makes use of:

InitialiseParticles.m - for generating the initial set of coordinates
NextSetCoords.m - for generating each succesive frame
	MakeStep.m - Make a step for a particle (interactions between particles considered)
	MakeStep_NoSensing.m - Make a step for a particle (interactions between particles ignored, that is, sensing is not implemented)
		StepLimBasal.m - Determining basal step size based on explicit encoding of viscous zones
			StepLimFunction.m - Determining step size limit based on implicit viscosity gradient (if present)
		StayWithinBounds.m - Ensures that the generated step is within box bounds

Other ancillary functions:
ParticleTypeCalculator.m - Calculate the type belonged to by the particle in question
IsParticleInsideFigure.m - Checks if the particle(s) is/are inside the input bounds

Viscous granules:
GenerateGranules.m - Generate viscous granules as per cubic close packing, shuffle them about incrementally (to be used if the granule generation algorithm in regbox_run.m fails - occurs for packing density >= 0.6)
AreaFraction.m - Computes packing density, void fraction for viscous granules in the simulation region
MinDistToWall.m - Computes minimum distance of the viscous granules to the wall to check if the granules lie within the simulation region

Clustering analysis:
AllCoords_LocalDensity.m - Computes the local density for each particle

For MSD analysis:
AllCoords_ComputeSD.m - Compute squared displacements to be used further in determining mean squared displacements

FRAP analysis:
InSilicoFRAP_sepC - Performs in silico FRAP for the given simulation run (AllCoords, ScriptVar pair)
FRAP_biexpfit.m - Computes t1/2 as per bi-exp fit (for normalization, use a uniform viscosity simulation with the same number of particles as the test run. Uniform viscosity value should be the bulk viscosity in the test run).
AllCoords_DwellTimeSpent.m - Compute dwell time within granules