| Geant4 Cross Reference |
1 ### MCF7 cell line - irradiation with He4 ions
2
3 #
4 # See more details on moleculardna specific UI
5 # - https://geant4-dna.github.io/molecular-doc
6 # - https://geant4-dna.github.io/molecular-doc
7 # - the README file
8 # - the messenger classes of the moleculardna
9 #
10
11 # Physics: choice of thermalization model
12 /process/dna/e-SolvationSubType Meesungnoen200
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 ste
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-d
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 locat
42 /dnageom/definitionFile geometries/cube-centre
43 # - Set placement volumes
44 /dnageom/placementVolume turn geometries/turne
45 /dnageom/placementVolume turntwist geometries/
46 /dnageom/placementVolume straight geometries/s
47
48 # Geometry: distance from base pairs at which
49 /dnageom/radicalKillDistance 9 nm
50
51 # Geometry: deposited energy accumulation rang
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 o
71 /chromosome/add cell ellipse 7005 2500 5300 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 ene
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