Gabriele Cosmo
127 lines
3.3 KiB
Plaintext
127 lines
3.3 KiB
Plaintext
### MCF7 cell line - irradiation with He4 ions
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#
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# See more details on moleculardna specific UI commands:
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
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# - the README file
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# - the messenger classes of the moleculardna example
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#
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# Physics: choice of thermalization model
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/process/dna/e-SolvationSubType Meesungnoen2002
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#/process/dna/e-SolvationSubType Ritchie1994
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#/process/dna/e-SolvationSubType Terrisol1990
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# Verbosity: settings
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/run/verbose 1
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/control/verbose 1
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# Chemistry: selection of IRT_syn
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/process/chem/TimeStepModel IRT_syn
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# Chemistry: verbosity
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/scheduler/verbose 0
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# Chemistry: end time of chemistry stage
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/scheduler/endTime 5.0 ns
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# Chemistry: set maximum allowed zero time steps
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/scheduler/maxNullTimeSteps 10000000
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# Geometry: size of World volume
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/world/worldSize 50 um
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# Geometry: shape of the cell
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/cell/radiusSize 14 2.5 11 um
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# Geometry: creation
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
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# - Side length for each placement
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/dnageom/placementSize 64 64 64 nm
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# - Scaling of XYZ in fractal definition file
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/dnageom/fractalScaling 64 64 64 nm
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# - Path to file that defines placement locations
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/dnageom/definitionFile geometries/cube-centred-X-8.txt
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# - Set placement volumes
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/dnageom/placementVolume turn geometries/turned_solenoid_640_withHistone.txt
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/dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_640_withHistone.txt true
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/dnageom/placementVolume straight geometries/straight_solenoid_640_withHistone.txt
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# Geometry: distance from base pairs at which radicals are killed
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/dnageom/radicalKillDistance 9 nm
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# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
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/dnageom/interactionDirectRange 2.0 angstrom
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# Damage: model settings
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/dnadamage/directDamageLower 5 eV
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/dnadamage/directDamageUpper 37.5 eV
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/dnadamage/indirectOHBaseChance 1.0
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/dnadamage/indirectOHStrandChance 0.405
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/dnadamage/inductionOHChance 0.0
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/dnadamage/indirectHBaseChance 1.0
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/dnadamage/indirectHStrandChance 0.0
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/dnadamage/inductionHChance 0.0
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/dnadamage/indirectEaqBaseChance 1.0
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/dnadamage/indirectEaqStrandChance 0.0
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/dnadamage/inductionEaqChance 0.0
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# Analysis: add ellipsoid chromosomal region of interest, with the name "cell"
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/chromosome/add cell ellipse 7005 2500 5300 0 0 0 nm 0 0 0
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# Run: initialization
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/run/initialize
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# Run: print progress
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/run/printProgress 1
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# Source geometry
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/gps/pos/type Plane
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/gps/pos/shape Circle
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/gps/pos/centre 0 3000 0 nm
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/gps/pos/rot1 0 0 1
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/gps/pos/rot2 1 0 0
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/gps/pos/radius 7005 nm
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/gps/direction 0 -1 0
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# Source particle
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/gps/particle ion
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/gps/ion 2 4 2 ### Helium
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# Analysis ROOT output file name, particle energy, beam on
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/analysisDNA/fileName MCF5MeV #LET 80.3
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/gps/energy 5 MeV
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/run/beamOn 150
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/analysisDNA/fileName MCF7p5MeV #65.9
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/gps/energy 7.5 MeV
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/run/beamOn 180
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/analysisDNA/fileName MCF10MeV #53.3
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/gps/energy 10 MeV
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/run/beamOn 220
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/analysisDNA/fileName MCF15MeV #39.2
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/gps/energy 15 MeV
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/run/beamOn 300
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/analysisDNA/fileName MCF20MeV #31.4
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/gps/energy 20 MeV
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/run/beamOn 390
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/analysisDNA/fileName MCF30MeV #22.8
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/gps/energy 30 MeV
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/run/beamOn 550
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/analysisDNA/fileName MCF60MeV #13
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/gps/energy 60 MeV
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/run/beamOn 930
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/analysisDNA/fileName MCF261MeV #4
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/gps/energy 261 MeV
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/run/beamOn 3000
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