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Geant4 - dnadamage2 example
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DNADAMAGE2
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CORRESPONDING AUTHORS
J. Naoki D. Kondo
J. Ramos-Mendez
B. Faddegon
(a) JorgeNaoki _ DominguezKondo _ ucsf _ edu
(b) Jose _ RamosMendez _ ucsf _ edu
(c) Bruce _ Faddegon _ ucsf _ edu
CONTACT EMAIL
JorgeNaoki.DominguezKondo@ucsf.edu
This example is provided by the Geant4-DNA collaboration.
(http://geant4-dna.org)
Any report or published results obtained using this example shall
cite the following publications:
[1] J.N. D-Kondo, et al., (2021) DNA damage modeled with Geant4-DNA: effects of
plasmid DNA conformation and experimental conditions.
Physics in Medicine and Biology, 66 (24). https://doi.org/10.1088/1361-6560/ac3a22
[2] J. Ramos-Méndez, et al., (2020). Independent reaction times method in Geant4-DNA:
Implementation and performance.Medical Physics, 47(11), 5919–5930.
https://doi.org/10.1002/mp.14490
In addition, cite the main Geant4-DNA collaboration publications:
[3] J. Appl. Phys. 125 (2019) 104301
[4] Med. Phys. 45 (2018) e722-e739
[5] Phys. Med. 31 (2015) 861-874
[6] Med. Phys. 37 (2010) 4692-4708
[7] Int. J. Model. Simul. Sci . Comput. 1 (2010) 157-178
0 - INTRODUCTION
This examples provides scoring of plasmid DNA strand breaks using
the IRT method [2]. The DNADAMAGE2 example extends the chem6 example
by adding DNA molecule information and the scoring of Strand Breaks.
Experimental conditions are considered such as oxygen and DMSO molar
concentrations.
The details are described in the following papers [1][2] for both
the IRT method and this example's validation.
1 - GEOMETRY DEFINITION
The geometry is composed of three main components:
- The world: A 2 um water cube which hostess the rest of the components.
- The Plasmid Envelope: A water sphere of 1 um in diameter by default.
This envelope can be resized using the "/det/setSize"
command. So users can modify their DNA concentration
without increasing the number of plasmids, but by lowering
the amount of water.
- The Plasmids: Plasmids must be supplied to the geometry. The plasmid file must
be in ASCII format. Three columns which represent the X, Y and
Z position of the plasmid vertices (bps). To control the
parameters to setup the plasmid geomtery, the following commands
shall be used:
+ /det/NbOfPlasmids :Set the number of plasmid copies. G4Box Volumes
are used to enclose the plasmid.
+ /det/OffSetFile : The file format is ASCII. It contains three columns
indicating the X, Y and Z position of the center of
the plasmid envelopes (G4Box volumes enclosing the plasmid)
+ /det/PlasmidFile : Set the ASCII file name containing the plasmid
information.
+ /det/UseDNAVolumes : Boolean to activate/deactivate the solid
volumes defining the DNA nucleotides. If set to false,
virtual molecules are created from the DNA nucleotides
position for simulating indirect strand breaks. See
reference [2].
The definition of the sensitive volumes is also made in the Geometry Definition.
Inside the method ConstructSDandField() (see section 5).
2 - PHYSICS AND CHEMISTRY LISTS
By default, if no Physics list is assigned using the "/physics/SetPhysics" the simulation
will run using:
+ G4EmDNAPhysics_option4 constructor
The full list of physics lists available for the user are:
+ G4EmDNAPhysics_option1
+ G4EmDNAPhysics_option2
+ G4EmDNAPhysics_option3
+ G4EmDNAPhysics_option4
+ G4EmDNAPhysics_option5
+ G4EmDNAPhysics_option6
+ G4EmDNAPhysics_option7
+ G4EmDNAPhysics_option8
By default, if no chemistry list is assigned using the "/physics/SetChemistry"
the simulation will run using:
+ G4EmDNAChemistry_ForPlasmids
- Custom chemistry constructor based on the G4EmDNAChemistry_option3
constructor.
- It includes DNA reactions as well as DMSO and oxygen background reactions.
- The chemistry constructor is based on the pre-chemical stage of PARTRAC
and chemical parameters of RITRACKS.
- This chemistry constructor uses the Independent Reaction Times method.
By using this Chemistry List, users can set oxygen and DMSO concentration
with the following commands "/chem/scavenger/DMSO" and "/chem/scavenger/Oxygen".
The concentrations unit must be given as molar concentaration M (mol/dm3).
*Of note, while other chemistry modules are also available, only the
G4EmDNAChemistry_ForPlasmids is capable of scoring DNA strand breaks.
3 - ACTION INITALIZATION
The class ActionInitialization instantiates and registers
to Geant4 kernel all user action classes.
While in sequential mode the action classes are instantiated just once,
via invoking the method:
ActionInitialization::Build()
In multi-threading mode the same method is invoked for each thread worker
and so all user action classes are defined thread-local.
A run action class is instantiated both thread-local
and global that's why its instance is created also in the method:
ActionInitialization::BuildForMaster()
which is invoked only in multi-threading mode.
The following actions are initialized in this example:
+ PrimaryGenerationAction: The primary particle gun.
+ RunAction: Defines the actions conducted at the start and end of each
Geant4 Run. It contains the call to the output functions of
the scorers.
+ StackingAction: Needed in order to start the chemistry (See section 7)
+ TimeStepAction: Defines actions conducted at each Step-By-Step (SBS)
Chemistry algorithm step (see section 6).
4 - AN EVENT: THE PRIMARY GENERATOR
The primary kinematic consists of N electrons with random position and
momentum in the water sphere. The kinetic energy of the electrons are
sampled from an energy spectrum suplied by the user using the "/fpGun/SourceFile"
command. The user can set the number of primary electrons per event in order
to accumulate a certain dose before running the chemistry.
This example provides the specrum of the kinetic energy of secondary electrons
at the time they were produced by cobalt-60/cesium-137 gamma rays (see section 11
and [1] for more information).
The chemistry module is triggered in the StackingAction class when all
physical tracks have been processed (see section 7).
5 - DETECTOR RESPONSE: Scorers
5.1 - Species scorer
This scorer computes the energy deposition and the number of species along
time in order to extract the radiochemical yields as in chem6 or chem4 examples.
Run::RecordEvent(), called at end of event, collects informations
event per event from the hits collections, and accumulates statistics for
RunAction::EndOfRunAction().
In multi-threading mode the statistics accumulated per worker is merged
to the master in Run::Merge().
The following macro commands can be used to control the scoring time:
/scheduler/endTime : IRT chemistry time end, must be acompanied by time units.
/scorer/species/addTimeToRecord : Adds a specific time point to report.
/scorer/species/nOfTimeBins : Sets the number of time bins separated
logaritmically even from 1 ps to the endTime
specified.
The information about all the molecular species is scored and can be saved
in a ASCII, ROOT or BINARY file, as specified by the user. The specific name
of the file can also be specified by the user by using the following commands:
-/scorer/species/OutputFile
-/scorer/species/OutputFormat
ASCII results are given in a 5 column file which are:
- Time
- GValues per 100 eV
- GValues Error
- GValues number of molecules
- Molecule name
ROOT or BINARY use the Geant4 Analysis Manager with the following columns:
- Species ID
- Number
- Number of Event
- Species Name
- Time
- Sum of G Value
- Sum of G2 Value
5.2. - LET scorer
An restricted, dose-averaged LET scorer is provided with this example,
it is the same scorer from the chem6 example. For more details visit the
chem6 example
A macro command can be used to control the energy cut of the scorer:
/scorer/LET/cutoff
5.4. - DNA Strand Break Scorer
The DNA Strand Breaks are obtained by this class, both direct and indirect.
This class needs access to the DetectorConstruction class in order to obtain
the DNA position information.
Contained within this scorer is a "MoleculeGun" as a mean to insert the DNA
molecules and keep track of them in order to know where a strand break occurs.
This helps to calculate SSBs, DSBs and other more complex DNA Strand Breaks.
The user is responsible for the Strand Break classification since this example
doesn't include any analysis tool.
Users can change the output type and output file name in the same way of the
"ScoreSpecies" scorer, with the commands:
-/scorer/StrandBreak/OutputFile
-/scorer/StrandBreak/OutputFormat
The output formats available are the same as with the ScoreSpecies scorer:
ASCII, ROOT and BINARY.
The number of direct Strand Breaks are scored when a certain energy
threshold is reached for a certain deoxyribose + phosphate geometry. Users can
change the direct energy treshold by using the following command:
-/scorer/StrandBreak/BreakEnergy
Of note, the following parameter must be set to true to score the breaks produced
by direct effect
-/det/UseDNAVolumes true
The BreakEnergy is set to 17.5 eV by default.
The "ScoreStrandBreak" class takes the LET value at the end of the simulation from
5.2 and saves it into the file of the ASCII output, so that users may get the number
of Strand Breaks as a function of LET if so they desire.
The current example only allows the use of electron sources, but the user is free to
use different electron energies.
6 - IRT specific details
The IRT is run after the few step-by-step (SBS) steps following the water dissociation
(pre-chemical) stage have finished (between 2 to 3 SBS steps), see UserPreTimeStepAction()
and UserPostTimeStepAction(). At that point,
SBS is stopped and the position of molecules and DNA molecules are passed to the IRT
method. No DNA radiolysis is considered, so every specie created inside the DNA
nucleotide territory is exclude by using the UserPreTimeStepAction as a filters, see
justification in [1]
In sumary:
The following two method are called before and after every SBS time step to pass molecules
to the IRT method:
+ TimeStepAction::UserPreTimeStepAction()
+ TimeStepAction::UserPostTimeStepAction()
7 - STACKING ACTION
StackingAction::NewStage is called when a stack of tracks has been processed
(for more details, look at the Geant4 documentation).
A verification on whether physical tracks remain to be processed is done.
If no tracks remain to be processed, the chemical module is then triggered.
8 - OUTPUT
The same output specifications from the chem6 example applies here, with the
following remarkable differences:
+ Both the ScoreSpecies and the ScoreStrandBreaks scorers have their own
output methods. Both call OutputAndClear(), which writes the output
files and cleans all the information currently stored in the scorers,
in preparation for the next run.
+ The OutputAndClear() method is called in the RunAction::EndOfRunAction()
method.
9 - RELEVANT MACRO FILES
Two user macro files can be used:
- RunExample.in
+ Single Run example.
+ 100 repetitions of 880 electrons (~5 Gys) in a 1 um diameter volume
containing 1 plasmids.
+ Caesium source.
- RunDoseDependance.in
+ This macro will repproduce results from S2 [1] (SBs Dose dependance).
+ DMSO conentration is set to 2.28E-4 M.
+ Oxygen Concentration is set to 0.27E-3 M.
+ Absorbed dose will be between ~1 - ~100 Gy.
+ 5 plasmids (28.1 ug/ml DNA concentration).
+ To reduce simulation time, the number of repetitions was lowered to 10.
+ Currently, only 1 Thread is used. Users are advised to increase the number
of threads.
+ Simulation time can take up to a couple of days depending on the specific PC.
- init_vis.in
+ Default macro file to be used if user doesn't specify any macro file at run.
+ It calls the vis.in macro which will draw the OpenGL visualizer.
- vis.in
+ Visualization parameters for the default macro file. 1 plasmid will be draw at the center.
10 - PLOT
- No PLOT/Analysis files are prodived due to the default ASCII output.
- ASCII files can be handled by most of the plot tools.
11 - EXTRA FILES
- CaesiumSource.src
+ Sample electron spectrum for the simulation.
+ Secondary electrons generated by a Caesium Gamma Source [1].
- CobaltSource.src
+ Sample electron spectrum for the simulation.
+ Secondary electrons generated by a Cobalt Gamma Source [1].
- pUC19.xyz
+ A sample pUC19 (2686 base pairs) plasmid with -0.03 super helix density generated at 20 C.
The plasmid file has the position of each individual base pair. Values are given in nm
- PlasmidOffsets.txt
+ A sample plasmid centroid file. Users can change this values manually as long
as they do not fall outside of the water sphere. In this way is possible to move
the plasmids generated in the simulation. Values are given in nm.
