\ This example is provided by the Geant4-DNA collaboration (http://geant4-dna.org).

Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications:
Med. Phys. 45 (2018) e722-e739
Phys. Med. 31 (2015) 861-874
Med. Phys. 37 (2010) 4692-4708
Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178

INTRODUCTION

This example shows how to activate the mesoscopic model in chemistry and combine with SBS model (Tran et al.,Int. J. Mol. Sci. 22 (2021) 6023). It allows to simulate chemical reactions longtime (beyond 1 us) of post-irradiation.

To run the example:

mkdir UHRD-build
cd UHRD-build
cmake ../pathToExamples/UHRD
make

In batch mode, the macro beam.in can be used as follows:

./UHRD beam.in

or

./UHRD beam.in 123
   # 123 is the user's seed number

GEOMETRY DEFINITION

The world volume is a simple water box 3.2 x 3.2 x 3.2 um3 for 0.01 Gy of cut-off absorbed dose and 1.6 x 1.6 x 1.6 um3 for 1 Gy. This example is limited to these geometries. The choice of simulation volume is a compromise between a sufficient number of chemical species a nd an achievable computation time.

Two parameters define the geometry :

the material of the box for the physical stage is water.
for the chemistry stage, the concentration of scavengers in [mole/l] is added. This concentration is supposed to have no effect on the physical stage. pH is defined as scavengers of H3O^1, OH^-1. In this example, we consider that chemical molecules diffuse and react in a bounded volume (that is, limited by geometrical boundaries) which is also the irradiated water box volume of the physical stage. The bouncing of chemical molecules on the volume border is applied for both SBS and mesoscopic models. The bouncing is not applied for physical stage.

PHYSICS LIST

PhysicsList is Geant4 modular physics list using G4EmDNAPhysics_option2 and EmDNAChemistry constructors (the chemistry constructor uses the Step-by-step method).

CHEMISTRY WORLD

This object is controlled by DetectorContruction. It defines the chemistry volume, scavengers and pH of water.

AN EVENT: PRIMARY GENERATOR

This example utilizes the G4SingleParticleSource. Each event consists of multiple incident particles. A large number has been chosen to ensure that the stack remains non-empty until the desired energy deposition is achieved (which is then converted to a cutoff dose). With each /run/beamOn command, a group of particles is emitted. The cutoff dose (dose threshold) determined by users. The actual dose is calculated based on the real energy deposited in the volume.

DETECTOR RESPONSE : Scorer

There is one G4MultiFunctionalDetector object which computes the energy deposition and the number of species along time in order to extract the G-value: (Number of species X) / (100 eV of deposited energy).

These two macro commands can be used to control the scoring time:

/scorer/species/addTimeToRecord 1 ps
   # user can select time bin to score G values.
/scorer/species/nOfTimeBins
   # or user can automatically select time bin logarithmically.

PULSE ACTION

This functionality is not available for this version.

OUTPUT

G-value

RELEVANT MACRO COMMANDS AND MACRO FILE

The user macro file is: beam.in

REACTION BUILDER

Reaction lists are collected by builders for specific applications. ChemNO2_NO3ScavengerBuilder is to build the reaction list with NO2-/NO3-. ChemPureWaterBuilder is to build the reaction list with pH. ChemOxygenWaterBuilder is to build the reaction list with ROS. ChemFrickeReactionBuilder is to build the reaction list of Fricke Dosimeter.

PLOT

The information about all the molecular species is scored in a ROOT (https://root.cern) ntuple file Dose_xxx.root (xxx is seed number). The ROOT program plot_time.C can be used to plot the G values vs time for each species.

Execute plot_time as:

root plot_time.C

or print G values to scorer.txt

root plot_time.C > scorer.txt

The results show the molecular species (G values) as a function of time (ns). Please correct the dose in the

TTree *tree = (TTree *) dir->Get("0.010000");

Funding: FNS Synergia grant MAGIC-FNS CRSII5_186369. Contact: H. Tran (tran@.nosp@m.cenb.nosp@m.g.in2.nosp@m.p3.f.nosp@m.r) CNRS, lp2i, UMR 5797, Université de Bordeaux, F-33170 Gradignan, France