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

Tue Feb 8 16:57:12 CET 2022

Dear Gate users, 

I followed David and Dimitrios advices and reduced the SetCutInRegion values in my code. 
David, thank you, I deleted the range cut for positrons and I defined different range cuts for the volumes. 

I still obtain no significant Gy values differences as output with and without nanoparticles... 

I'm searching, but if someone as any idea, I would be very grateful for the help or any advice! 

Best regards, 
Sarah Blind 

De: "Sarah Blind" <sarah.blind at univ-lorraine.fr> 
À: "David Leibold" <D.Leibold at tudelft.nl> 
Cc: "gate-users" <gate-users at lists.opengatecollaboration.org> 
Envoyé: Lundi 7 Février 2022 17:27:59 
Objet: Re: [Gate-users] with and without nanoparticules -> surprising output 

Dear David, dear Dimitrios, 

Thank you very much for your quick responses! 
I'm testing your advices, I will keep you informed of the result. 

Regards, 
Sarah Blind 

----- Le 7 Fév 22, à 16:51, David Leibold <D.Leibold at tudelft.nl> a écrit : 

Dear Sarah, 

while I do not have the knowledge to tell you whether your result makes sense or not, I had the same thought as Dimitris. A colleague once told me to choose a range cut that is about a fourth or fifth of the smallest dimension involved in your simulation. I am not sure whether this also holds true at the very small length scales that you are using in your simulation; others might shed more light on this topic. 

You probably know that decreasing the range cut increases the simulation time, too. You might want to decrease the the range cut in small steps (factors of 10) and check both the simulation time and whether the results still change noticeably below a certain range cut. 

It might also make sense to set different range cuts for your various volumes, so the smaller your structure, the smaller the range cut. By doing so, you help keeping the computation time as low as possible. 

Last but not least, I noticed that you set a range cut for positrons. If you use X-ray energies as specified in your Gate macro (170 keV) then you don’t have to care about positrons, since the energy is too small to create them in the first place. 

Kind regards, 
David Leibold 

BQ_BEGIN

On 7 Feb2022, at 10:15, Sarah Blind < [ mailto:sarah.blind at univ-lorraine.fr | sarah.blind at univ-lorraine.fr ] > wrote: 

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 

BQ_BEGIN

+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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BQ_END

BQ_END

-- 
Sarah Blind 
Ingénieure de recherche - CNRS 
Centre de Recherche en Automatique de Nancy (CRAN) 
Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS) 
Site de la faculté de médecine 
9, Avenue de la Forêt de Haye 
54505 Vandoeuvre les Nancy 
Tél : 03.72.74.61.13 

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-- 
Sarah Blind 
Ingénieure de recherche - CNRS 
Centre de Recherche en Automatique de Nancy (CRAN) 
Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS) 
Site de la faculté de médecine 
9, Avenue de la Forêt de Haye 
54505 Vandoeuvre les Nancy 
Tél : 03.72.74.61.13 
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