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DNAParameters.txt
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#---------------------------------------------------------------------------------------------------
# Program control
#---------------------------------------------------------------------------------------------------
# Pauses
Ts/PauseBeforeInit = "False" # This allows checking memory use before any physics tables are loaded
Ts/PauseBeforeSequence = "False" # This allows checking memory use before any histories are run
Ts/PauseBeforeQuit = "True" # This allows visualizing graphics before exiting
# Verbosity
i:Ts/RunVerbosity = 0
i:Ts/EventVerbosity = 0
i:Ts/TrackingVerbosity = 0
i:Ts/SequenceVerbosity = 0
i:Ts/ChemistryVerbosity = 0
#---------------------------------------------------------------------------------------------------
# Geometry
#---------------------------------------------------------------------------------------------------
# World
d:Ge/World/HLX=10. um
d:Ge/World/HLY=10. um
d:Ge/World/HLZ=10. um
s:Ge/World/Material = "Vacuum"
# Spherical cell with volume ~2000 um^3, filled with water
s:Ge/Cell/Type="TsSphere"
s:Ge/Cell/Parent="World"
d:Ge/Cell/RMax = 7.8 um
d:Ge/Cell/RMin = 0. um
s:Ge/Cell/Material = "G4_WATER"
# DNA
s:Ge/MyDNA/Type="VoxelizedNuclearDNA"
s:Ge/MyDNA/Parent="Cell"
s:Ge/MyDNA/Material="G4_WATER"
b:Ge/MyDNA/BuildNucleus = "True" # If true, build voxelized cubic nucleus. If false, build single chromatin fiber
i:Ge/MyDNA/NumVoxelsPerSide = 26 # Number of voxels per side of cubic nucleus
d:Ge/MyDNA/VoxelSideLength = 150 nm # Modifying this value may break the geometry
b:Ge/MyDNA/FillFibersWithDNA = "True" # Either fill chromatin fibers with DNA or generate empty fibers
i:Ge/MyDNA/DnaNumNucleosomePerFiber = 90 # Max 90
i:Ge/MyDNA/DnaNumBpPerNucleosome = 200 # Max 200
b:Ge/MyDNA/CutVolumes = "True" # cut DNA residues to prevent overlaps
# Materials
s:Ge/MyDNA/DNAMaterialName = "G4_WATER_DNA"
s:Ge/MyDNA/HistoneMaterialName = "G4_WATER_HISTONE"
s:Ma/G4_WATER_DNA/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_DNA/CloneWithDensity = 1.407 g/cm3
s:Ma/G4_WATER_HISTONE/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_HISTONE/CloneWithDensity = 1.0 g/cm3
i:Ma/Verbosity = 1
b:Ge/CheckForOverlaps = "False"
b:Ge/CheckForUnusedComponents = "False"
# Overall Visualization control
b:Gr/Enable = "False"
# Ts/UseQt = "True"
#---------------------------------------------------------------------------------------------------
# Physics
#---------------------------------------------------------------------------------------------------
# sv:Ph/Default/Modules = 2 "g4em-dna_opt2and4" "TsEmDNAChemistryExtended"
sv:Ph/Default/Modules = 2 "g4em-dna_opt2and4" "TsEmDNAChemistry"
# sv:Ph/Default/Modules = 2 "g4em-dna_opt2and4" "g4em-dna-chemistry"
d:Ph/Default/EMRangeMin = 10. eV # minimum for EM tables
b:Ph/Default/Fluorescence = "True"
b:Ph/Default/Auger = "True"
b:Ph/Default/AugerCascade = "True"
b:Ph/Default/DeexcitationIgnoreCut = "True"
#---------------------------------------------------------------------------------------------------
# Chemistry
#---------------------------------------------------------------------------------------------------
# includeFile = supportFiles/TOPASChemistry_Extended.txt
includeFile = supportFiles/TOPASChemistry.txt
#---------------------------------------------------------------------------------------------------
# Particle source (volumetric or surface based)
#---------------------------------------------------------------------------------------------------
s:So/Example/Type = "VolumeOrSurface"
s:So/Example/Component = "Cell"
s:So/Example/DistributePrimariesAtVolumeRegion = "volume"
s:So/Example/DirectPrimariesTo = "isotropic"
ic:So/Example/NumberOfHistoriesInRun = 100000
i:Ts/ShowHistoryCountAtInterval = 100
s:So/Example/BeamEnergySpectrumType = "Discrete"
# Example: irradiation using the electron component of 100 keV neutrons in the intermediate scoring volume
includeFile = spectra/energy_bins.txt
includeFile = spectra/spectrum_n100keV_inter_electron.txt
# Specify the relative dose of the secondary particle species if relevant:
# If using secondary particle spectra:
includeFile = relative_doses/reldose_n100keV_inter_electron.txt # defines Sc/ClusterScorer/RelativeDose
# If not using secondary particle spectra:
# u:Sc/ClusterScorer/RelativeDose = 1.0
#---------------------------------------------------------------------------------------------------
# Clustered DNA damage scorer
#---------------------------------------------------------------------------------------------------
s:Sc/ClusterScorer/Quantity = "ClusteredDNADamage"
s:Sc/ClusterScorer/Component = "MyDNA"
b:Sc/ClusterScorer/PropagateToChildren = "True"
sv:Sc/ClusterScorer/Modules = Ph/Default/Modules
sv:Sc/ClusterScorer/OnlyIncludeIfInMaterial = 3 "G4_WATER_HISTONE" "G4_WATER_DNA" "G4_WATER"
includeFile = supportFiles/DNADamageParameters.txt # defines parameters related to direct and indirect action
# Provide scorer with access to some geometry parameters
s:Sc/ClusterScorer/DNAMaterialName = Ge/MyDNA/DNAMaterialName
s:Sc/ClusterScorer/HistoneMaterialName = Ge/MyDNA/HistoneMaterialName
i:Sc/ClusterScorer/DnaNumNucleosomePerFiber = Ge/MyDNA/DnaNumNucleosomePerFiber
i:Sc/ClusterScorer/DnaNumBpPerNucleosome = Ge/MyDNA/DnaNumBpPerNucleosome
i:Sc/ClusterScorer/NumVoxelsPerSide = Ge/MyDNA/NumVoxelsPerSide
d:Sc/ClusterScorer/VoxelSideLength = Ge/MyDNA/VoxelSideLength nm
b:Sc/ClusterScorer/BuildNucleus = Ge/MyDNA/BuildNucleus
# Specify whether to terminate simulation once a dose threshold has been exceeded (otherwise use NumberOfHistoriesInRun)
b:Sc/ClusterScorer/UseDoseThreshold = "True"
d:Sc/ClusterScorer/TotalDose = 1 Gy # Total dose to be delivered across all secondary particles
d:Sc/ClusterScorer/DoseThreshold = Sc/ClusterScorer/TotalDose Gy * Sc/ClusterScorer/RelativeDose
# Options to modify how damage yields are recorded
b:Sc/ClusterScorer/IncludeDirectDamage = "True"
b:Sc/ClusterScorer/IncludeIndirectDamage = "True"
b:Sc/ClusterScorer/ScoreClusters = "True" # toggle whether or not to record clustered DNA damage
b:Sc/ClusterScorer/RecordDamagePerEvent = "False" # record damage per run or per event
b:Sc/ClusterScorer/RecordDamagePerFiber= "False" # record damage for all fibres together or per fibre
# Output files
s:Sc/ClusterScorer/OutputType = "ASCII" # Applies to main output file (damage yields) only
b:Sc/ClusterScorer/OutputToConsole = "True"
s:Sc/ClusterScorer/IfOutputFileAlreadyExists = "Overwrite"
b:Sc/ClusterScorer/OutputHeaders = "False" # Applies to additional output files
s:Sc/ClusterScorer/OutputFile = "damage_yields" # Main output file with DNA damage yields
s:Sc/ClusterScorer/FileRunSummary = "data_run_summary" # Output file containing run details: dose delivery, etc.
s:Sc/ClusterScorer/FileComplexDSB = "data_comp_dsb_cluster" # Output file containing complex-DSB cluster properties
s:Sc/ClusterScorer/FileNonDSBCluster = "data_non_dsb_cluster" # Output file containing non-DSB cluster properties
i:Ts/NumberOfThreads = 4
i:Ts/Seed = 1234