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Geant4 extended examples - medical
Specific examples for medical physics applications are demonstarted in this directory.
DICOM

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Geant4 - AuNP example
README file
CORRESPONDING AUTHOR
Should you have any enquiry, please do not hesitate to contact: D. Sakata National Institute of Radiological Science * e-mail:sakata.dousatsu@qst.go.jp, dosatsu.sakata@cern.ch

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
chem1
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
chem2
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
Chem3
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
Chem4
CORRESPONDING AUTHORS P. Piersimoni (a), M. Karamitros (b) (a) pierluigi.piersimoni _ gmail _ com (b) matkara _ gmail _ com

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
Chem5
Jose Ramos-Mendez(a) and Bruce Faddegon Department of Radiation Oncology, University of California San Francisco.

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$Id: $
Geant4 - an Object-Oriented Toolkit for Simulation in HEP
Chem6

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Geant4 - clustering
Authors: Y. Perrot (a), H. Payno (b)
(a) ysperrot@gmail.com (b) henri.payno@gmail.com
Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org
Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications: Phys. Med. 31 (2015) 861-874 Med. Phys. 37 (2010) 4692-4708
---> 1. Introduction
The clustering example simulates protons tracks in liquid water using Geant4-DNA processes and models. Energy deposit are clustered with a dedicated clustering algorithm to assess strand breaks. The default parameters of the clustering algorithm have been tuned to reproduce data published by Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3)
Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publication: Med. Phys. 37 (2010) 4692-4708
----> 2. Set-up
It is similar to the geometry set-up proposed in Francis et al. 2011 Comput. Meth. Programs. Biomed. 2011 101(3). It consists in a World volume containing a Target box made of liquid water of 1µm x 1µm x 0.5 µm. Energy deposits in the Target are registered (see SteppingAction.cc) and the clustering algorithm is run at the end of each event (see EventAction.cc)
----> 3. How to run the example
To get help, run:
> ./clustering -h
In interactive mode, run:
> ./clustering -gui
In batch mode , run:
> ./clustering [-mac run.in] [-mt numberofThreads]
Two macros are available:
run.in: shoots 1000 protons of 500 keV
runOneEvent.in: shoots one proton of 500 keV
All UI clustering commands in these macros are described below in section 5.
----> 4. Simulation output
The output results consists in a clusters_output.root file, containing for each event: - the number of single strand break - the number of complex single strand break - the number of double strand break - the cluster size distribution - the absorbed dose in the Target
----> 5. More information
Specific classes are available in this example:
* ClusteringAlgo: contains the core clustering algorithm
* ClusteringAlgoMessenger: defines all UI commands to tune the clustering algorithm
/clustering/algo/setMinPts: Minimal number of points to create a cluster
/clustering/algo/setSelectionProb: Probability to select potential damage according to the geometry
/clustering/algo/setEps: Maximal distance between points to create a cluster
/clustering/algo/setEmin: Energy to have a probability to create a strand break = 0
/clustering/algo/setEmax: Energy to have a probability to create a strand break = 1 allow * ClusterSBPoints: defines a cluster of strand break points
* CommandLineParser: defines a parser for command line control as in other Geant4-DNA examples
* RunInitObserver: allows initializations at new run (as in pdb4dna and microdosimetry)
* SBPoint: defines a class for point of energy deposition
----> Acknowledgments :
Ziad Francis for discussion about clustering algorithm. ...

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Geant4 - dnadamage1 example
README file
This is a new example and it may contain bugs. It was developed by Hoang Tran. Damage analysis was developed by Le Tuan Anh. If you find a bug, please contact IRSN: yann.perrot@irsn.fr or carmen.villagrasa@irsn.fr

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$Id: $
Geant4 - dnadamage2 example
DNADAMAGE2

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Geant4 - dnaphysics example
README file
CORRESPONDING AUTHOR
S. Incerti (a, *), H. Tran (a, *), V. Ivantchenko (b), M. Karamitros a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France b. G4AI Ltd., UK * e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
icsd
Authors: Sylvain Meylan, Yann Perrot and Carmen Villagrasa (IRSN, France) Marcin Pietrzak (NCBJ, Poland) For any question, please contact: carmen.villagrasa@irsn.fr

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Geant4 - Jet Counter nanodosemeter example
README file
Authors: M. Pietrzak, M. Mietelska, A. Bancer, A. Rucinski and B. Brzozowska For any question, please contact the developer: marcin.pietrzak@fuw.edu.pl or marcin.pietrzak@ncbj.gov.pl

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Geant4 - mfp example
README file
CORRESPONDING AUTHOR
S. Incerti et al. (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France * e-mail: incerti@lp2ib.in2p3.fr

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Geant4 - microdosimetry example
README file
CORRESPONDING AUTHOR
S. Incerti (a, *), H. Tran (a, *), V. Ivantchenko (b), M. Karamitros a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France b. G4AI Ltd., UK * e-mail: incerti@lp2ib.in2p3.fr or tran@lp2ib.in2p3.fr

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*** microprox example ***
Author: S. Incerti et al. Date: March 2nd, 2019 Email: incerti@lp2ib.in2p3.fr
(c) The Geant4-DNA collaboration.

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*** microyz example ***
Author: S. Incerti et al. Date: 1 June 2017 Email: incerti@lp2ib.in2p3.fr
(c) The Geant4-DNA collaboration.

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
moleculardna
A Geant4-DNA application for simulating DNA damage.
AUTHORS

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Geant4 - NEURON
README file
Authors: M. Batmunkh *(a,b), O.V. Belov *(a), L. Bayarchimeg (a), O. Lkhagva (b)
(a) Laboratory of Radiation Biology, Joint Institute for Nuclear Research (JINR), 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia (b) Division of Natural Sciences, National University of Mongolia (NUM), 1 University St., 210646 Ulaanbaatar, Mongolia * Corresponding authors, email to batmunkh@jinr.ru, dem@jinr.ru

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Geant4 - pdb4dna
Authors: E. Delage *(a), Y. Perrot *(a), Q.T. Pham (a)
(a) Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France * Corresponding authors, email to delage@clermont.in2p3.fr, perrot@clermont.in2p3.fr
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org
Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications: Phys. Med. 31 (2015) 861-874 Med. Phys. 37 (2010) 4692-4708
---> 1. A brief description
The PDB4DNA example simulates energy deposits in a target volume generated from a PDB file representing DNA geometry. Position of energy deposits are used to compute strand breaks in the DNA geometry. Geant4-DNA processes are used.
The example package contains: - source files (src, include, pdb4dna.cc) - README - .in, analysis.C and visualization macro files - 1ZBB.pdb (di nucleosome is loaded by default)
To run the example: see section 4 of this README To analyze output: see section 6 of this README
----> 2. Set-up.
The geometry is a 1000 angstrom side cube (World) made of galactic material. Before a computation, user loads a PDB file and generates a target volume (the bounding volume) of liquid water, which dimensions are extrapolated from PDB file atom 3D coordinates.
----> 3. Some main features
| MESSENGER LIST |
[1] Load a PDB file (The default atoms visualization is done by sphere that are parametrized with the van der Waals radius). CPK coloring. - Hydrogen(H) => white sphere, - Carbon(C) => gray sphere, - Oxygen(O) => red sphere, - Nitrogen(N) => dark blue sphere, - Sulfur(S) => yellow sphere, - Phosphorus(P) => orange sphere, - others/undefined => pink sphere. /PDB4DNA/det/loadPDB filename.pdb
[2] Build only a bounding volume for computation and draw it : /PDB4DNA/det/buildBoundingV
[3] Draw Atoms : /PDB4DNA/det/drawAtoms [4] Draw Nucleotids (sphere representing nucleotids) : /PDB4DNA/det/drawNucleotides [5] Draw Residues - Base => blue sphere, - Sugar => yellow sphere, - Phosphate => red sphere. Spheres are linked by cylinders: /PDB4DNA/det/drawResidues [6] Draw Atoms with bounding volume : /PDB4DNA/det/drawAtomsWithBounding [7] Draw Nucleotides with bounding volume : /PDB4DNA/det/drawNucleotidesWithBounding [8] Draw Residues with bounding volume : /PDB4DNA/det/drawResiduesWithBounding
[9] Set energy treshold to compute SSB : /PDB4DNA/event/setEnergyThres 8.22 eV (default value set to 8.22 eV) [10] Set distance treshlod to compute DSB : /PDB4DNA/event/setDistanceThres 10 (default value set to 10)
Notes: [1] is mandatory for visualization and simulation. [2] is needed for simulation.
----> 4. How to run the example.
To get help, run:
> ./pdb4dna(.exe) -h
In interactive mode, run:
> ./pdb4dna(.exe) -gui
"1ZBB.pdb" is the default file and it should be placed into same directory as the executable. You can download it here: www.rcsb.org/pdb/download/downloadFile.do">http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZBB
In batch mode , run:
> ./pdb4dna(.exe) [-mac pdb4dna.in] [-mt numberofThreads]
To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
----> 5. The physics
This example shows how to use the Geant4-DNA processes from constructor
Look at the PhyscisList.cc file.
----> 6. Simulation output
The output results consists in a pdb_dna.root file, containing for each event: - the energy deposit in the bounding box (in electronVolt) - the number of single strand break (SSB) - the number of double strand break (DSB)
This file can be easily analyzed using for example the provided ROOT macro file analysis.C; to do so : * be sure to have ROOT installed on your machine * be sure to be in the example directory * launch ROOT by typing root * under your ROOT session, type in : .X analysis.C to execute the macro file * alternatively you can type directly under your session : root analysis.C
----> 7. Contacts
If you have any questions or wish to notify of updates and/or modification please contact:
E. Delage (geometry and visualization referee) at delage@clermont.in2p3.fr Y. Perrot (physics and simulation referee) at perrot@clermont.in2p3.fr
----> Acknowledgments :
Jean Orloff (LPC, Clermont-Ferrand, France) for 3D rotation implementation, Michel Maire (G4AI) for /extended/geometry/transforms example, Laurent Garnier (LAL, Orsay, France) for Qt visualisation. ...

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Geant4 - range example
README file
CORRESPONDING AUTHOR
S. Incerti et al. (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France e-mail: incerti@lp2ib.in2p3.fr

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
scavenger
CORRESPONDING AUTHORS F. Chappuis (a), L. Desorgher (b), H. Tran (c) (a) flore.chappuis@chuv.ch (b) laurent.desorgher@chuv.ch (c) tran@cenbg.in2p3.fr

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Geant4 - slowing example
README file
CORRESPONDING AUTHOR
S. Incerti (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France * e-mail: incerti@lp2ib.in2p3.fr

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Geant4 - splitting
Authors: J. A. Ramos-Mendez*, B. A. Faddegon
Department of Radiation Oncology, University of California San Francisco * Corresponding author, email to joserm84@gmail.com
This example is provided by the Geant4-DNA collaboration.
These processes and models are further described at: geant4-dna.org">http://geant4-dna.org
Any report or published results obtained using the Geant4-DNA software shall cite the following Geant4-DNA collaboration publications: Phys. Med. 31 (2015) 861-874 Med. Phys. 37 (2010) 4692-4708
If use this example, please cite J Ramos-Mendez, et. Al. Phys. Med. Biol. 62(15), 5908-5925, (2017) DOI: 10.1088/1361-6560/aa7831
---> 1. A brief description
The splitting example uses variance reduction to improve the computational efficiency of calculations of ionization cluster size distributions. Ionization events are scored in a nanoscaled cylinder. Ionized electrons generated by the first generation of secondary electrons are split, i.e. new clone electrons are generated, labeled and propagated. The label is used to classify those new particles as if they were produced by independent histories to avoid overlapping of tracks at final analysis. The splitting is performed only if the ionization event occurred in the cylinder.
Geant4-DNA processes are used.
The example package contains: - source files (src, include) - README - .in, plot.C and visualization macro files
**** 2. Set-up.
The geometry is a nanoscaled cylinder centered in the world. The medium is water everywhere. The dimensions can be defined with /detector/diameter 6 nm /detector/length 10 nm
User can define the split number (default is 1, i.e. no split) with:
/vrt/numberOfSplit 10
**** 3. How to run the example. In interactive mode, run: ./splitting Idle> /control/execute vis.mac
In batch mode , run:
./splitting run.mac
To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
**** 4. The physics
This example shows: - how to use the Geant4-DNA processes, - how to implement the splitting via G4WrappedProcess - how to set the splitting in specific region - how to propagate new track information to secondary particles
A simple electron capture process is also provided in order to kill electrons below a chosen energy threshold, set in the Physics list.
Look at the PhyscisList.cc file.
**** 5. Simulation output
The output results consists in two histograms in root format
- the energy deposit in the cylindrical target - the frequency distribution of ionization cluster size
NOTE: Every time a value is added to a ROOT histogram, it contributes to the statistics. For this example, to correct estimate the uncertainties is recommended to split the simulation into several jobs and to calculate the statistics from them: batch mode. Otherwise, the statistical uncertainty may be underestimated.
**** 6. Contacts
If you have any questions or wish to notify of updates and/or modification please contact:
J. Ramos-Mendez at joserm84@gmail.com
**** Acknowledgments :
Sebastien Incerti (CNRS) for its guidance ...

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Geant4 - spower example
README file
CORRESPONDING AUTHOR
S. Incerti et al. (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France * e-mail: incerti@lp2ib.in2p3.fr

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Geant4 - svalue example
README file
CORRESPONDING AUTHOR
S. Incerti (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France * e-mail: incerti@lp2ib.in2p3.fr

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Geant4 - an Object-Oriented Toolkit for Simulation in HEP
UHDR (Ultra High Dose Rate)
This example is provided by the Geant4-DNA collaboration (geant4-dna.org">http://geant4-dna.org).

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Geant4 - wholenucleardna example
README file
CORRESPONDING AUTHOR
For any question, please contact: C. Villagrasa email: carmen.villagrasa@irsn.fr
This example is provided by the Geant4-DNA collaboration Any report or published results obtained using the Geant4-DNA software and the DNA geometry given in the Geom_DNA example shall cite the following Geant4-DNA collaboration publications: [1] NIM B 298 (2013) 47-54 [2] Med. Phys. 37 (2010) 4692-4708 [3] Phys. Med. 31 (2015) 861-874
---->0. INTRODUCTION.
The wholenucleardna example offers the basic tools to simulate the track structure of different charge particles within a simplified geometrical model of the DNA molecule contained in a cell nucleus. In this example, the DetectorConstruction file contains the placement of the 6 Gbp (base-pairs) of a human cell respecting five compaction levels in the structure of the DNA molecule: double helix, nucleosome, chromatin fiber, simple chromatin fiber loop and complex chromatin fiber loops. These complex chromatin fiber loops are then used to fill the chromosome territories using a constant density (~30-31 kbp/µm3. Even though this geometry defines different volumes for the DNA base, the back-bone region or the histone proteins, the material filling all these volumes in the simulation is liquid water ("G4_WATER")
In order to simulate all the energy transfer points of the track at nanometric level, the Geant4-DNA physics processes and models are used. These processes and models are further described at: geant4-dna.org">http://geant4-dna.org
---->1. GEOMETRY SET-UP.
As indicated in the introduction, the whole DNA molecule contained in a human cell with 5 different compaction levels is described in this geometry. In order to place the complex chromatin loops in each of the 43 chromosome territories, the files called "chromo-number.dat" are needed. These 43 chromosome territories are then placed in an ellipsoid that has the typical dimensions of a human fibroblast cell nucleus. All the volumes in the geometry are made of liquid water (G4_WATER material) despite of what they geometrically represent. Particles are shot from a random (x,y)position covering the main central part of the cell nucleus and at z=2.99 µm from the center of the nucleus. This value allows the primary particle to be either inside the cell nucleus, either not far from the entrance surface so its energy loss before the cell nucleus entrance is negligible.
WARNING: By default, the bases are not built. To build the whole geometry, set the flag fBuildBases in DetectorConstruction to true.
---->2. SET-UP
Make sure G4LEDATA points to the low energy electromagnetic data files.
The variable G4ANALYSIS_USE must be set to 1.
The code can be compiled with gmake.
---->3. HOW TO RUN THE EXAMPLE
In normal mode, without interactivity:
> wholeNuclearDNA
In interactive mode, run:
> wholeNuclearDNA -gui -out
The -gui option launches a user interface for interactivity The -out option create a root file (can be changed for other format). This option may also take argument to set the name of the file (name of the application by default):
> wholeNuclearDNA -gui -out MyFile
The macro wholenucleardna.in is executed by default. A proton of 0.1 MeV is shot. This energy has been chosen because only a few minutes are needed for the proton to lose all its energy and thus the event to finish. Nevertheless, one should keep in mind that for this energy, protons do not traverse the whole cell nucleus width.
Visualization (DAWN) is not activated by default in wholenucleardna.mac. To get visualization, make sure to uncomment the #/control/execute vis.mac. We would like to warn the users that the time to visualize the whole DNA structure is extremely long.
To build the whole geometry, set the flag fBuildBases in DetectorConstruction to true.
---->4. PHYSICS
This example uses the Geant4-DNA processes, using the G4EmDNAPhysics constructor as in the dnaphysics example.
---->5. SIMULATION OUTPUT AND RESULT ANALYSIS
The output results consist in a wholenucleardna.root file, containing only the information about the energy transfers located in the backbone region of the DNA double helix. Both strands are distinguished with different flags (1 or 2): - the type of particle for the current step - the type of process for the current step - the flag of the strand (1 or 2) - the track position of the current energy transfer (in nanometers) - the energy deposit corresponding to the energy transfer (in eV) - the total energy loss along the current step (in eV) - the step length (in nm)
This file can be easily analyzed using for example the provided ROOT macro file plot.C; to do so : * be sure to have ROOT installed on your machine * be sure to be in the directory containing the ROOT files created by wholenucleardna * copy plot.C into this directory * from there, launch ROOT by typing root * under your ROOT session, type in : .X plot.C to execute the macro file * alternatively you can type directly under your session : root plot.C
The naming scheme on the displayed ROOT plots can be seen in the SteppingAction.cc file. ...

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Geant4 - wvalue example
README file
CORRESPONDING AUTHOR
S. Incerti (a, *) a. LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France * e-mail: incerti@lp2ib.in2p3.fr

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