This is a new dnadamage example and it may contain bugs. It was developed by J. Naoki D-Kondo. If you find a bug, please contact IRSN: yann..nosp@m.perr.nosp@m.ot@ir.nosp@m.sn.f.nosp@m.r, carme.nosp@m.n.vi.nosp@m.llagr.nosp@m.asa@.nosp@m.irsn..nosp@m.fr

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.

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

GEOMETRY SET-UP

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).

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.

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).

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).

SCORERS

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

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

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.

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()

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.

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.

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.

PLOT

No PLOT/Analysis files are prodived due to the default ASCII output. ASCII files can be handled by most of the plot tools.

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.