"Physical determinants of vesicle mobility and supply at a central synapse"
Rothman et al. 2016
Figures 2C, 4D
Source Data

Title: Parameters file for best-match finite-difference FRAP simulation

Dlong = 0.028 um^2/s
Immobile vesicles = 29%

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#D3D Parameter File v1.6
#Sat, 7 Nov 2015 14:53:51 +0000

Class=Project
name=Finite Difference FRAP
initClassAndFunction=InitFrapJason.initFiniteDifferenceFrap
simTime=10100.0
dt=0.05505952380952383
dx=0.05
stability=0.00185
maxD=2.8E-5
maxC0=0.71
saveRate=20.0
saveDT=0.05
printRate=0.0010
printDT=1000.0
batchNum=0
timeUnits=ms
freqUnits=kHz
spaceUnits=um
concUnits=mM
directory=/cluster/project3/silverlab1/d3d/jason/FD/
folder=K2_d028_im29_0
date=Sat, 7 Nov 2015 14:53:04 +0000

Class=RunFiniteDifference
useCompactArrays=true
fastArrayAccess=true
singleCompartment=false

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

Class=Geometry
name=Cuboid
voxelPriority=true
xWidth=1.0
yWidth=1.0
zWidth=2.0
volume=2.0
x1=-0.5
y1=-0.5
z1=-1.0
x2=0.5
y2=0.5
z2=1.0
xCenter=0.0
yCenter=0.0
zCenter=0.0
xVoxels=20
yVoxels=20
zVoxels=40
voxels=16000
spaceVoxels=16000
spaceVolume=2.0
xVoxel1=0
yVoxel1=0
zVoxel1=0
xVoxel2=19
yVoxel2=19
zVoxel2=39
xVoxelCenter=9.5
yVoxelCenter=9.5
zVoxelCenter=19.5
xScale=1
yScale=1
zScale=1
simpleCuboid=true
forceEvenVoxels=true
forceOddVoxels=false

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

Class=DiffusantPhoto
name=Mobile
C0=0.71
D=2.8E-5
h=6.166666666666667E-4
reaction=true
saveConc=false
useGeometryCoordinates=true
displaySelect=C0
kPhoto=2.0

Class=PSFtorok
name=Illumination PSF
arbitraryVoxelCenter=true
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=0.17793985979606772
sum=0.0
avg=0.0
dx=0.05
computedValues=0
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
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=100.0
duration=0.5
amplitude=1.0

Class=Pulse
time=30.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=60.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=90.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=120.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=150.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=180.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=210.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=250.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=300.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=360.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=410.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=490.0
duration=2.0
amplitude=0.0014

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

Class=Pulse
time=910.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1210.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1810.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=2810.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=4010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=4980.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=6010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=7010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=8010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=9010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=9980.0
duration=2.0
amplitude=0.0014

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

Class=DiffusantPhoto
name=Immobile
C0=0.29
D=0.0
h=0.0
reaction=true
saveConc=false
numSubRegions=0
useGeometryCoordinates=true
displaySelect=C0
kPhoto=2.0

Class=PSFtorok
name=Illumination PSF
arbitraryVoxelCenter=true
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=0.9686775824816585
sum=435.6731213580531
avg=0.027229570084878318
dx=0.05
computedValues=16000
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
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=100.0
duration=0.5
amplitude=1.0

Class=Pulse
time=30.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=60.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=90.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=120.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=150.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=180.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=210.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=250.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=300.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=360.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=410.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=490.0
duration=2.0
amplitude=0.0014

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

Class=Pulse
time=910.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1210.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=1810.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=2810.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=4010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=4980.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=6010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=7010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=8010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=9010.0
duration=2.0
amplitude=0.0014

Class=Pulse
time=9980.0
duration=2.0
amplitude=0.0014

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

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

Class=Save
outputFile=Detector0_Mobile_0
dataPoints=1
sampleRate=18.162162162162154
sampleInterval=0.05505952380952383
samples2save=183438
skipSamples=0
save2TextFile=false
save2BinaryFile=true
saveWhileComputing=false
save2array=true
xdim=ms
ydim=Fluorescence
autoDimensions=false
skipCounter=0
dataCounter=0

Class=PSFgauss
name=Gaussian PSF
arbitraryVoxelCenter=true
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=1.0
sum=0.0
avg=0.0
dx=0.05
computedValues=0
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
normalize=true
zCount=50
xSTDV=0.10833099562673683
ySTDV=0.10833099562673683
zSTDV=0.3888619862618695
xFWHM=0.2551
yFWHM=0.2551
zFWHM=0.9157

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

Class=DetectorPSF
name=Detector1
diffusantName=Immobile
diffusantNum=1
useGeometryCoordinates=true

Class=ColorD3D
name=Detector1_color
colorRGB=Heat
gradientRGB=
invert=false

Class=Save
outputFile=Detector1_Immobile_0
dataPoints=1
sampleRate=18.162162162162154
sampleInterval=0.05505952380952383
samples2save=183438
skipSamples=0
save2TextFile=false
save2BinaryFile=true
saveWhileComputing=false
save2array=true
xdim=ms
ydim=Fluorescence
autoDimensions=false
skipCounter=0
dataCounter=0

Class=PSFgauss
name=Gaussian PSF
arbitraryVoxelCenter=true
xVoxelCenter=19.5
yVoxelCenter=19.5
zVoxelCenter=19.5
max=0.9461791526563695
sum=142.29995610304888
avg=0.008893747256440555
dx=0.05
computedValues=16000
useGeometryCoordinates=true
rotateXY=0.0
rotateYZ=0.0
rotateZX=0.0
normalize=true
zCount=50
xSTDV=0.10833099562673683
ySTDV=0.10833099562673683
zSTDV=0.3888619862618695
xFWHM=0.2551
yFWHM=0.2551
zFWHM=0.9157

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

Class=InitFrapJason
stabilityFD=0.00185
quarter_geometry=true
FRAP_on=true
FRAP_kPhoto=2.0
FRAP_onset=100.0
FRAP_bleach_length=0.5
FRAP_bleach_on=true
FRAP_small_length=2.0
FRAP_small_amp_ratio=0.0014
FRAP_small_on=true

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