Geant4 Cross Reference

Cross-Referencing   Geant4
Geant4/examples/advanced/dna/moleculardna/human_cell_MCF7.mac

Version: [ ReleaseNotes ] [ 1.0 ] [ 1.1 ] [ 2.0 ] [ 3.0 ] [ 3.1 ] [ 3.2 ] [ 4.0 ] [ 4.0.p1 ] [ 4.0.p2 ] [ 4.1 ] [ 4.1.p1 ] [ 5.0 ] [ 5.0.p1 ] [ 5.1 ] [ 5.1.p1 ] [ 5.2 ] [ 5.2.p1 ] [ 5.2.p2 ] [ 6.0 ] [ 6.0.p1 ] [ 6.1 ] [ 6.2 ] [ 6.2.p1 ] [ 6.2.p2 ] [ 7.0 ] [ 7.0.p1 ] [ 7.1 ] [ 7.1.p1 ] [ 8.0 ] [ 8.0.p1 ] [ 8.1 ] [ 8.1.p1 ] [ 8.1.p2 ] [ 8.2 ] [ 8.2.p1 ] [ 8.3 ] [ 8.3.p1 ] [ 8.3.p2 ] [ 9.0 ] [ 9.0.p1 ] [ 9.0.p2 ] [ 9.1 ] [ 9.1.p1 ] [ 9.1.p2 ] [ 9.1.p3 ] [ 9.2 ] [ 9.2.p1 ] [ 9.2.p2 ] [ 9.2.p3 ] [ 9.2.p4 ] [ 9.3 ] [ 9.3.p1 ] [ 9.3.p2 ] [ 9.4 ] [ 9.4.p1 ] [ 9.4.p2 ] [ 9.4.p3 ] [ 9.4.p4 ] [ 9.5 ] [ 9.5.p1 ] [ 9.5.p2 ] [ 9.6 ] [ 9.6.p1 ] [ 9.6.p2 ] [ 9.6.p3 ] [ 9.6.p4 ] [ 10.0 ] [ 10.0.p1 ] [ 10.0.p2 ] [ 10.0.p3 ] [ 10.0.p4 ] [ 10.1 ] [ 10.1.p1 ] [ 10.1.p2 ] [ 10.1.p3 ] [ 10.2 ] [ 10.2.p1 ] [ 10.2.p2 ] [ 10.2.p3 ] [ 10.3 ] [ 10.3.p1 ] [ 10.3.p2 ] [ 10.3.p3 ] [ 10.4 ] [ 10.4.p1 ] [ 10.4.p2 ] [ 10.4.p3 ] [ 10.5 ] [ 10.5.p1 ] [ 10.6 ] [ 10.6.p1 ] [ 10.6.p2 ] [ 10.6.p3 ] [ 10.7 ] [ 10.7.p1 ] [ 10.7.p2 ] [ 10.7.p3 ] [ 10.7.p4 ] [ 11.0 ] [ 11.0.p1 ] [ 11.0.p2 ] [ 11.0.p3, ] [ 11.0.p4 ] [ 11.1 ] [ 11.1.1 ] [ 11.1.2 ] [ 11.1.3 ] [ 11.2 ] [ 11.2.1 ] [ 11.2.2 ] [ 11.3.0 ] 

  1 ### MCF7 cell line - irradiation with He4 ions
  2 
  3 #
  4 # See more details on moleculardna specific UI commands:
  5 # - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
  6 # - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
  7 # - the README file
  8 # - the messenger classes of the moleculardna example
  9 #
 10 
 11 # Physics: choice of thermalization model
 12 /process/dna/e-SolvationSubType Meesungnoen2002
 13 #/process/dna/e-SolvationSubType Ritchie1994
 14 #/process/dna/e-SolvationSubType Terrisol1990
 15 
 16 # Verbosity: settings
 17 /run/verbose 1
 18 /control/verbose 1
 19 
 20 # Chemistry: selection of IRT_syn
 21 /process/chem/TimeStepModel IRT_syn
 22 
 23 # Chemistry: end time of chemistry stage
 24 /scheduler/endTime 5.0 ns
 25 
 26 # Chemistry: set maximum allowed zero time steps
 27 /scheduler/maxNullTimeSteps 10000000
 28 
 29 # Geometry: size of World volume
 30 /world/worldSize 50 um
 31 
 32 # Geometry: shape of the cell
 33 /cell/radiusSize 14 2.5 11 um
 34 
 35 # Geometry: creation
 36 # See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
 37 #  - Side length for each placement
 38 /dnageom/placementSize 64 64 64 nm
 39 #  - Scaling of XYZ in fractal definition file
 40 /dnageom/fractalScaling 64 64 64 nm
 41 #  - Path to file that defines placement locations
 42 /dnageom/definitionFile geometries/cube-centred-X-8.txt
 43 #  - Set placement volumes
 44 /dnageom/placementVolume turn geometries/turned_solenoid_640_withHistone.txt
 45 /dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_640_withHistone.txt true
 46 /dnageom/placementVolume straight geometries/straight_solenoid_640_withHistone.txt
 47 
 48 # Geometry: distance from base pairs at which radicals are killed
 49 /dnageom/radicalKillDistance 9 nm
 50 
 51 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
 52 /dnageom/interactionDirectRange 2.0 angstrom
 53 
 54 # Damage: model settings
 55 /dnadamage/directDamageLower 5 eV
 56 /dnadamage/directDamageUpper 37.5 eV
 57 
 58 /dnadamage/indirectOHBaseChance 1.0
 59 /dnadamage/indirectOHStrandChance 0.405
 60 /dnadamage/inductionOHChance 0.0
 61 
 62 /dnadamage/indirectHBaseChance 1.0
 63 /dnadamage/indirectHStrandChance 0.0
 64 /dnadamage/inductionHChance 0.0
 65 
 66 /dnadamage/indirectEaqBaseChance 1.0
 67 /dnadamage/indirectEaqStrandChance 0.0
 68 /dnadamage/inductionEaqChance 0.0
 69 
 70 # Analysis: add ellipsoid chromosomal region of interest, with the name "cell"
 71 /chromosome/add cell ellipse 7005 2500 5300 0 0 0 nm 0 0 0
 72 
 73 # Run: initialization
 74 /run/initialize
 75 
 76 # Run: print progress
 77 /run/printProgress 1
 78 
 79 # Source geometry
 80 /gps/pos/type Plane
 81 /gps/pos/shape Circle
 82 /gps/pos/centre 0 3000 0 nm
 83 /gps/pos/rot1 0 0 1
 84 /gps/pos/rot2 1 0 0
 85 /gps/pos/radius 7005 nm
 86 /gps/direction 0 -1 0
 87 
 88 # Source particle
 89 /gps/particle ion
 90 /gps/ion 2 4 2 ### Helium
 91 
 92 # Analysis ROOT output file name, particle energy, beam on
 93 /analysisDNA/fileName MCF5MeV #LET 80.3
 94 /gps/energy 5 MeV
 95 /run/beamOn 150
 96 
 97 /analysisDNA/fileName MCF7p5MeV #65.9
 98 /gps/energy 7.5 MeV
 99 /run/beamOn 180
100 
101 /analysisDNA/fileName MCF10MeV #53.3
102 /gps/energy 10 MeV
103 /run/beamOn 220
104 
105 /analysisDNA/fileName MCF15MeV #39.2
106 /gps/energy 15 MeV
107 /run/beamOn 300
108 
109 /analysisDNA/fileName MCF20MeV #31.4
110 /gps/energy 20 MeV
111 /run/beamOn 390
112 
113 /analysisDNA/fileName MCF30MeV #22.8
114 /gps/energy 30 MeV
115 /run/beamOn 550
116 
117 /analysisDNA/fileName MCF60MeV #13
118 /gps/energy 60 MeV
119 /run/beamOn 930
120 
121 /analysisDNA/fileName MCF261MeV #4
122 /gps/energy 261 MeV
123 /run/beamOn 3000