[Gate-users] with and without nanoparticules -> surprising output

Mon Feb 7 12:13:11 CET 2022

Dear Sarah,

Having a quick look at your code, I believe that you could try a much
lower cut in the following commands:

/gate/physics/Gamma/SetCutInRegion      world 0.5 mm
/gate/physics/Electron/SetCutInRegion   world 0.5 mm
/gate/physics/Positron/SetCutInRegion   world 0.5 mm

0.5 mm is too large. You could maybe add a very low cut (e.g. 0.5um or
lower) in spheroide geometry:

/gate/physics/Gamma/SetCutInRegion      spheroide 0.5 mm
/gate/physics/Electron/SetCutInRegion   spheroide 0.5 mm
/gate/physics/Positron/SetCutInRegion   spheroide 0.5 mm

I hope this will help you,

Dimitris Thanasas

> Dear Gate users,
>
> I want to model a spheroid which contains 30 000 cells in each of which
> there are 10 clusters of 10 nanoparticles.
> The composition of my nanoparticles is the following
>
>
>
>
> +el: name=Gadolinium ; f=0.15
> +el: name=Silicon ; f=0.10
> +el: name=Carbon ; f=0.25
> +el: name=Nitrogen ; f=0.08
> +el: name=Oxygen ; f=0.22
> +el: name=Hydrogen ; f=0.20
>
>
>
>
> My spheroid, the cells and the clusters are all spheres full with water.
> For the moment, what I'm trying to observe is very simple : with and
> without the nanoparticles (and thus only water) I should observe a
> difference, shouldn't I ?
>
> I use Geant4-DNA; with 10 000 000 photons sent ; here is what my .hdr
> outpout file looks like
>
> Nanoparticles
> 	Average in Gy
>
> No
> 	0.002
>
> Yes
>
> 0.001
>
>
> There is almost no difference between with and without the nanoparticles,
> this surprises me.
>
>
> I'm not a physicist, do you find this normal ?
>
>
> Here is my Gate code :
>
>
>
>
> BQ_BEGIN
>
>
> ======= world.mac =======
>
>
> /gate/world/geometry/setXLength 0.5 cm
> /gate/world/geometry/setYLength 0.5 cm
> /gate/world/geometry/setZLength 0.5 cm
> /gate/world/setMaterial Air
>
>
> /gate/world/daughters/name spheroide
> /gate/world/daughters/insert sphere
> /gate/spheroide/geometry/setRmin 0.0 mm
> /gate/spheroide/geometry/setRmax 400 um
> /gate/spheroide/placement/setTranslation 0 0 0 mm
> /gate/spheroide/setMaterial G4_WATER
> /gate/spheroide/vis/setVisible 1
> /gate/spheroide/vis/setColor blue
> /gate/spheroide/vis/forceSolid false
>
>
> /gate/spheroide/daughters/name cell
> /gate/spheroide/daughters/insert sphere
> /gate/cell/geometry/setRmin 0.0 mm
> /gate/cell/geometry/setRmax 10 um
> /gate/cell/placement/setTranslation 100 0 0 um
> /gate/cell/setMaterial G4_WATER
> /gate/cell/vis/setVisible 1
> /gate/cell/vis/setColor green
> /gate/cell/vis/forceSolid false
>
> /gate/cell/daughters/name cluster
> /gate/cell/daughters/insert sphere
> /gate/cluster/geometry/setRmin 0 mm
> /gate/cluster/geometry/setRmax 0.05 um
> /gate/cluster/placement/setTranslation 0 0 0 mm
> /gate/cluster/setMaterial G4_WATER
> /gate/cluster/vis/setVisible 1
> /gate/cluster/vis/setColor yellow
> /gate/cluster/vis/forceSolid false
>
> /gate/cluster/daughters/name NP
> /gate/cluster/daughters/insert sphere
> /gate/NP/geometry/setRmin 0 mm
> /gate/NP/geometry/setRmax 0.004 um
> /gate/NP/placement/setTranslation 0 0 0 mm
> /gate/NP/setMaterial AGuIX
> /gate/NP/vis/setVisible 1
> /gate/NP/vis/setColor red
> /gate/NP/vis/forceSolid true
>
> ### repeaters ###
>
> /gate/NP/repeaters/insert genericRepeater
> /gate/NP/genericRepeater/setPlacementsFilename ../data/NP.placements
> /gate/NP/genericRepeater/useRelativeTranslation 1
>
> /gate/cluster/repeaters/insert genericRepeater
> /gate/cluster/genericRepeater/setPlacementsFilename
> ../data/cluster.placements
> /gate/cluster/genericRepeater/useRelativeTranslation 1
>
>
> /gate/cell/repeaters/insert cubicArray
> /gate/cell/cubicArray/setRepeatNumberX 32
> /gate/cell/cubicArray/setRepeatNumberY 32
> /gate/cell/cubicArray/setRepeatNumberZ 32
> /gate/cell/cubicArray/setRepeatVector 20 20 20 um
>
>
>
> ======= physics.mac =======
>
>
>
> # Geant4-DNA
> /gate/physics/addPhysicsListMixed emstandard_opt3_mixed_emdna
> /gate/physics/SetDNAInRegion spheroide
> /gate/physics/ConstructProcessMixed
>
> /gate/physics/Gamma/SetCutInRegion world 0.5 mm
> /gate/physics/Electron/SetCutInRegion world 0.5 mm
> /gate/physics/Positron/SetCutInRegion world 0.5 mm
>
> /gate/physics/displayCuts
>
> # Choice of pseudo-random number generation algorithm
> /gate/random/setEngineName MersenneTwister
>
> # Auger electron activation
> /gate/physics/addAtomDeexcitation
>
>
> /gate/physics/addProcess PhotoElectric gamma
> /gate/physics/processes/PhotoElectric/setModel LivermoreModel
> /gate/physics/processes/PhotoElectric/setAugerElectron true
> /gate/physics/processes/PhotoElectric/setDeltaRayCut 10 eV
> /gate/physics/processes/PhotoElectric/setXRayCut 10 eV
> /gate/physics/processes/PhotoElectric/setStepFunction e- 0.2 0.1 nm
>
> /gate/physics/addProcess Compton gamma
> /gate/physics/processes/Compton/setModel LivermoreModel
> /gate/physics/processes/Compton/setStepFunction e- 0.2 0.1 nm
>
> /gate/physics/addProcess RayleighScattering
> /gate/physics/processes/RayleighScattering/setModel LivermoreModel
>
> # transformation of a photon into an electron-positron pair
>
> /gate/physics/addProcess GammaConversion
> /gate/physics/processes/GammaConversion/setModel LivermoreModel
>
> /gate/physics/addProcess ElectronIonisation
> /gate/physics/processes/ElectronIonisation/setModel LivermoreModel e-
> /gate/physics/processes/ElectronIonisation/setModel PenelopeModel e+
> /gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 nm
>
> /gate/physics/addProcess Bremsstrahlung e-
> /gate/physics/addProcess Bremsstrahlung e+
> /gate/physics/processes/Bremsstrahlung/setModel LivermoreModel e-
> /gate/physics/processes/Bremsstrahlung/setModel PenelopeModel e+
>
> /gate/physics/addProcess eMultipleScattering e-
> /gate/physics/addProcess eMultipleScattering e+
> /gate/physics/processes/eMultipleScattering/setModel UrbanModel e-
> /gate/physics/processes/eMultipleScattering/setModel UrbanModel e+
>
>
>
>
> ======= detectors.mac =======
>
>
>
>
>
> /gate/actor/addActor DoseActor dose
> /gate/actor/dose/save output/dose.hdr
> /gate/actor/dose/attachTo spheroide
> /gate/actor/dose/stepHitType random
> /gate/actor/dose/setPosition 0.0 0.0 0.0 mm
> /gate/actor/dose/setSize 800 800 800 um
> /gate/actor/dose/setResolution 400 400 400
> /gate/actor/dose/enableDose true
> /gate/actor/dose/saveEveryNSeconds 30
>
>
>
>
> ======= source.mac =======
>
>
>
>
>
> /gate/source/addSource mybeam gps
> /gate/source/mybeam/gps/particle gamma
> /gate/source/mybeam/gps/pos/type Beam
> /gate/source/mybeam/gps/ene/mono 170 keV
> /gate/source/mybeam/gps/ene/type Gauss
> /gate/source/mybeam/gps/ene/sigma 1.0 keV
> /gate/source/mybeam/gps/direction 0 0 -1
>
> /gate/source/mybeam/gps/position 0 0 0.2 cm
> /gate/source/mybeam/gps/pos/type Volume
> /gate/source/mybeam/gps/pos/shape Cylinder
> /gate/source/mybeam/gps/pos/inner_radius 0 mm
> /gate/source/mybeam/gps/pos/radius 500 um
> /gate/source/mybeam/gps/pos/halfz 0.01 cm
> /gate/source/mybeam/gps/ang/type beam2d
>
>
>
> BQ_END
>
>
> Thank you for your help,
>
> Sarah Blind
>
>
>
>
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