"Physical determinants of vesicle mobility and supply at a central synapse"
Rothman et al. 2016
Figures 7B
Source Data

Title: Parameters file for one Monte-Carlo AZ simulation of EM series #3


***************************************
#D3D Parameter File v1.6
#Wed, 20 Jul 2016 11:05:18 +0100

Class=Project
name=Monte Carlo AZ EM
initClassAndFunction=InitAZEMJason.initMonteCarloAZ
simTime=100000.0
dt=0.06944444444447896
dx=0.05554854185077642
maxD=5.9999999999970166E-5
batchNum=0
timeUnits=ms
freqUnits=kHz
spaceUnits=um
concUnits=mM
date=Wed, 20 Jul 2016 11:05:18 +0100
EM_iseries=3
EM_azSelect=0

Class=RunMonteCarloAZEM
minVesicleRadius=0.02777427092538821
maxVesicleRadius=0.02777427092538821
minAllowedDistanceBetweenVesicles=0.05554854185077642
minDistanceBetweenVesicles=0.0494382515821882
numVesicles=16394
vesicleDensity=1891.9281033745158
vesicleVolumeFraction=0.16979357024226527
totalVesicleVolume=1.471301042352914
Dcyto=1.2696940661241425E-4
voxelVolume=1.7140283054776953E-4
mobileVesicles=12295
immobileVesicles=4099
mobilePercent=0.7499695010369647
immobilePercent=0.25003049896303525
mobileVolumeFraction=0.1273399991538765
immobileVolumeFraction=0.04245357108838876
minVesicleStep=0.0050
removeVesicleOverlapStep3=5.773502691896258E-4
PBC=false
freeDiffusion=false
removeVesicleOverlap=false
frapOn=false
hydrodynamicsLocalD=true
hydrodynamicsDscale=false
hydroWallZ=true
hydrodynamicsLocalDVoxels=true
overlapTrialLimit=10000
absLimit=1000000
vesicleVolume=8.974631220889482E-5
dockingOn=true
dockedVesiclesMax=2
releaseRate=Infinity
releaseStartTime=0.0
releaseProb=1.0
saveRelease=true
saveNumDocked=false

EMseries=3
EMseriesAZ=0
extendAZ=0.012624668602449188
xStep_T=0.5
removeShrinkage=true
importVesicleXYZ=true
importVesicleXYZ_dr=/Jason/FrapVGlut1/Simulations/Sims24_AZ_SupplyRate_EMs/VesiclePositions/
extraReserve=true
emptyGeometry=false
openGeometry=false
openGeometryForwardX=0
openGeometryForwardY=0
openGeometryForwardZ=0
reserveVesicleDensity=0.17
reserveImmobileFraction=0.25
reserveX1=true
reserveX2=true
reserveY1=true
reserveY2=true
reserveZ1=false
reserveZ2=false
dockRefractoryPeriod=0.0

Class=Save
name=Release
outputFile=Release_0
dataPoints=1
sampleRate=14.399999999992843
sampleInterval=0.06944444444447896
samples2save=1440000
skipSamples=0
save2TextFile=true
save2BinaryFile=false
saveWhileComputing=true
saveWhileComputingAppend=true
save2array=false
xdim=
ydim=ms
autoDimensions=true
skipCounter=0
dataCounter=0

***************************************

Class=Geometry
name=Cuboid
voxelPriority=true
xWidth=3.555106678449691
yWidth=3.88839792955435
zWidth=0.666582502209317
volume=9.214616170248089
x1=-1.7775533392248455
y1=-1.944198964777175
z1=-0.3332912511046585
x2=1.7775533392248455
y2=1.944198964777175
z2=0.3332912511046585
xCenter=0.0
yCenter=0.0
zCenter=0.0
voxelWidth=0.044
xVoxels=64
yVoxels=70
zVoxels=12
voxels=53760
spaceVoxels=50573
spaceVolume=8.668355349292348
xVoxel1=0
yVoxel1=0
zVoxel1=0
xVoxel2=63
yVoxel2=69
zVoxel2=11
xVoxelCenter=31.5
yVoxelCenter=34.5
zVoxelCenter=5.5
xScale=1
yScale=1
zScale=1
simpleCuboid=false
forceEvenVoxels=true
forceOddVoxels=false
cubeWidth=0.0

***************************************

Class=DiffusantVesiclesAZ
C0=0.0
D=5.9999999999970166E-5
h=0.0013503409306129472
reaction=true
saveConc=false
numSubRegions=0
useGeometryCoordinates=true
displaySelect=C0
minRadius=0.02777427092538821
maxRadius=0.02777427092538821
meanRadius=0.027774270925378732
setMeanRadius=0.02777427092538821
meanVolume=8.974631220891266E-5
totalVolume=1.471301042352914
meanFluorescence=1.0
meanStep3=0.002886751345947853
density=1891.9281033745158
volumeFraction=0.16979357024226527
numVesicles=16394
mobileVesicles=12295
immobileVesicles=4099
mobileVolumeFraction=0.1273399991538765
immobileVolumeFraction=0.04245357108838876
mobilePercent=0.7499695010369647
immobilePercent=0.25003049896303525
setImmobilePercent=0.25
saveXYZ=true
saveMSD=false
saveDisplacementAfterCollisions=false

***************************************
