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 \page Examplednadamage2 Example dnadamage2
 
 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.perrot@irsn.fr, carmen.villagrasa@irsn.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:
 - PrimaryGeneratorAction: 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:
 - dnadamage2.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 provided 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.

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