"Physical determinants of vesicle mobility and supply at a central synapse"
Rothman et al. 2016
Figures 3D, 4B, 4D
Source Data

Title: Parameters file for best-match Monte-Carlo FRAP simulation

Dshort = 0.060 um^2/s
Immobile Vesicles = 25%

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#D3D Parameter File v1.6
#Fri, 23 Oct 2015 18:48:58 +0100

Class=Project
name=Monte Carlo FRAP
initClassAndFunction=InitFrapJason.initMonteCarloFrap
simTime=10570.0
dt=0.011111111111115343
dx=0.05
maxD=5.999999999997713E-5
saveRate=20.0
saveDT=0.05
printRate=0.0040
printDT=250.0
batchNum=0
timeUnits=ms
freqUnits=kHz
spaceUnits=um
concUnits=mM
directory=/cluster/project3/silverlab1/d3d/jason/frap/dx002/c20_d060_im25/
folder=c20_d060_im25_0
date=Fri, 23 Oct 2015 18:48:58 +0100

Class=RunMonteCarlo
minVesicleRadius=0.0245
maxVesicleRadius=0.0245
minAllowedDistanceBetweenVesicles=0.049
minDistanceBetweenVesicles=0.049000411748313655
numVesicles=16232
vesicleDensity=2759.6055763345794
vesicleVolumeFraction=0.1699941108451915
totalVesicleVolume=0.9999053599914167
initVesicleRandom=true
mobileVesicles=12174
immobileVesicles=4058
immobileVesicleFraction=0.25
minVesicleStep=0.0020
removeVesicleOverlapStep3=5.773502691896258E-4
PBC=false
freeDiffusion=false
removeVesicleOverlap=true
frapOn=true
saveFluorescence=true
mitoCoordinatesOn=false
mitoRadius=0.1404494382022472
mitoAxialRatio=8.0
setMitoVolumeFraction=0.28
mitoShape=cylinder
mito_ijkselect=-2
hydrodynamicsLocalD=false
hydrodynamicsDscale=false
hydroWallZ=false
overlapTrialLimit=10000
absLimit=1000000

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

Class=Geometry
name=Cuboid
voxelPriority=true
xWidth=2.0
yWidth=2.0
zWidth=2.0
volume=8.0
x1=-1.0
y1=-1.0
z1=-1.0
x2=1.0
y2=1.0
z2=1.0
xCenter=0.0
yCenter=0.0
zCenter=0.0
xVoxels=40
yVoxels=40
zVoxels=40
voxels=64000
spaceVoxels=47056
spaceVolume=5.8820000000000014
xVoxel1=0
yVoxel1=0
zVoxel1=0
xVoxel2=39
yVoxel2=39
zVoxel2=39
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
xScale=1
yScale=1
zScale=1
simpleCuboid=false
forceEvenVoxels=true
forceOddVoxels=false
cubeWidth=2.0

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

Class=DiffusantVesicles
name=Vesicles
C0=0.0
D=5.999999999997713E-5
h=2.6666666666666657E-4
reaction=true
saveConc=false
numSubRegions=0
useGeometryCoordinates=true
displaySelect=C0
minRadius=0.0245
maxRadius=0.0245
meanRadius=0.024499999999993378
setMeanRadius=0.0245
meanVolume=6.160087235038299E-5
totalVolume=0.9999053599914167
meanFluorescence=1.0
meanStep3=0.0011547005383792499
maxX0=0.9754847666090609
maxY0=0.9754121184045996
maxZ0=0.9754973342243294
setVolumeFraction=0.17
density=2759.6055763345794
volumeFraction=0.1699941108451915
numVesicles=16232
mobileVesicles=12174
immobileVesicles=4058
immobileVesicleFraction=0.25
setImmobileVesicleFraction=0.25
kPhoto=2.0

Class=PSFtorok
name=Illumination PSF
arbitraryVoxelCenter=false
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=0.9686775824816585
sum=1407.8397059655947
avg=0.029918388855100193
dx=0.05
computedValues=16000
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
xySymmetric=true
normalize=true
zCount=50
integrationSteps=1000
numericalAperture=0.90643
waveLength=0.488
refractiveIndex=1.338
ab1=-0.15507
ab2=13.488
ab3=-154.08
ab4=839.65
ab5=-2324.9
ab6=2568.2
ab7=1049.8
ab8=-3276.1
ab9=0.0
ab10=0.0
abZoff=0.0
zFxnOffset=0.0
rscale=1.0

Class=PulseTimer
numPulses=25
impulse=false

Class=Pulse
time=570.0
duration=0.5
amplitude=1.0

Class=Pulse
time=500.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=530.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=560.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=590.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=620.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=650.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=680.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=720.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=770.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=830.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=880.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=960.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1060.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1380.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1680.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=2280.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=3280.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=4480.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=5450.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=6480.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=7480.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=8480.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=9480.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=10450.0
duration=2.0
amplitude=0.0014

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

Class=DetectorPSF
name=Detector0
diffusantName=Vesicles
diffusantNum=0
useGeometryCoordinates=true

Class=Save
outputFile=Detector0_Vesicles_0
dataPoints=1
sampleRate=22.49999999999143
sampleInterval=0.04444444444446137
samples2save=237825
skipSamples=3
save2TextFile=false
save2BinaryFile=true
saveWhileComputing=false
save2array=true
xdim=ms
ydim=Fluorescence
autoDimensions=false
skipCounter=0
dataCounter=0

Class=PSFgauss
name=Gaussian PSF
arbitraryVoxelCenter=false
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=0.9461791526563695
sum=396.83290135748035
avg=0.008433205146155226
dx=0.05
computedValues=16000
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
xySymmetric=true
normalize=true
zCount=50
xSTDV=0.10833099562673683
ySTDV=0.10833099562673683
zSTDV=0.3888619862618695
xFWHM=0.2551
yFWHM=0.2551
zFWHM=0.9157

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

Class=InitFrapJason
vesicleRadius=0.0245
d1_name=Vesicles
d1_C=1.0
d1_D=6.0E-5
FRAP_on=true
FRAP_kPhoto=2.0
FRAP_onset=570.0
FRAP_bleach_length=0.5
FRAP_bleach_on=true
FRAP_small_length=2.0
FRAP_small_amp_ratio=0.0014
FRAP_small_on=true
mitoNonSpaceVoxels=true
mitoRadius=0.1404494382022472
mitoAxialRatio=8.0
mitoVolumeFraction=0.28
mitoVolumeFractionTolerance=0.02
mitoVolumeFractionActual=0.26475
mitoVolumeFractionExact=false
mitoPreset=false
mitoCylinder=true
mito_ijkselect=1
psf_file=D3D_Wilson_PSF.d3d
refrac_water=1.338
lambda_illum=0.488
NA=0.9
rscale=1.0
detect_fwhm_xy=0.2551
detect_fwhm_z=0.9157
xvcenter=19.5
yvcenter=19.5
zvcenter=19.5

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