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

Wed Feb 9 10:09:21 CET 2022

Hi Sarah,

What values did you put in the cuts?
Based on a previous email of Olie you could change the material of the
nanoparticles to a metal (like Pb, Au) to see if there is a difference in
the dose.
Moreover to reduce the statistical uncertainty of the dose
(you can record the relative uncertainty with the command
/gate/actor/xxxxxxxxxx/enableUncertaintyDose true),
increase the simulated time of the run (e.g. ten times increase, it
depends on the real duration of the simulation).

I hope this will help you,

Regards,
Dimitris

> 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
>
> _______________________________________________
> Gate-users mailing list
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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
>