Attention
Attention
Physics Processes
The physical processes of the Geant4-DNA toolkit [Incerti2010] [Bernal2015] [Incerti2018]
can be used in TOPAS-nBio to perform track-structure simulations via the modules
g4em-dna and g4em-dna_optN with N = 1,…,8. To use any of these lists, users need to include one of
these modules in the modular physics list, e.g.:
sv:Ph/Default/Modules = 1 "g4em-dna_opt2"
We provide a tested physics list, which also can be configurable:
sv:Ph/Default/Modules = 1 "TsEmDNAPhysics"
List of Available Modules
It is not trivial to set a default physics list for track-structure Monte Carlo simulations. The lack of experimental measurements at nanoscopic scales makes it difficult to validate of the existing physics models. Typically, experiments are performed in water-gas, allowing detectors to be 1000 times larger than for liquid water, however, with potentially different interaction between the water molecules. New measurements for liquid water at nanoscales as well as a for few other materials are now available and implemented in Geant4-DNA.
Geant-DNA provides several constructors which contain a variety of physics models for scattering processes. Hence, the selection of a suitable physics list is delegated to the users judgment according to the problem they want to tackle. A detailed description of each process and associated model available in Geant4-DNA is shown here. These models are condensed into several Geant4 constructors as shown here The correspondence between the Geant4-DNA physics constructors and the TOPAS modules is shown in the table below. Users who are advanced experts in Geant4 physics can also write their own Geant4 physics modules and plug these into TOPAS through the extensions interface, see OpenTOPAS physics list.
TOPAS Module Name |
Geant4 Class Name |
Notes |
TsEmDNAPhysics |
N/A |
Allows to customize physics models per process |
TsEmDNAChemistry |
N/A |
Includes revised chemistry parameters |
TsEmDNAChemistryExtended |
N/A |
Includes revised chemistry parameters and an extended set of reactions |
g4em-dna |
G4EmDNAPhysics |
Default Geant4-DNA constructor |
g4em-dna_opt1 |
G4EmDNAPhysics_option1 |
|
g4em-dna_opt2 |
G4EmDNAPhysics_option2 |
Accelerated default Geant4-DNA constructor |
g4em-dna_opt3 |
G4EmDNAPhysics_option3 |
|
g4em-dna_opt4 |
G4EmDNAPhysics_option4 |
|
g4em-dna_opt5 |
G4EmDNAPhysics_option5 |
|
g4em-dna_opt6 |
G4EmDNAPhysics_option6 |
|
g4em-dna_opt7 |
G4EmDNAPhysics_option7 |
|
g4em-dna_opt8 |
G4EmDNAPhysics_option8 |
|
g4em-dna-stationary |
G4EmDNAPhysics_stationary |
The kinetic energy of the particle is set to its incident value in inelastic processes |
g4em-dna-stationary_opt2 |
G4EmDNAPhysics_stationary_opt2 |
The kinetic energy of the particle is set to its incident value in inelastic processes |
g4em-dna-stationary_opt4 |
G4EmDNAPhysics_stationary_opt4 |
The kinetic energy of the particle is set to its incident value in inelastic processes |
g4em-dna-stationary_opt6 |
G4EmDNAPhysics_stationary_opt6 |
The kinetic energy of the particle is set to its incident value in inelastic processes |
g4em-dna-chemistry |
G4EmDNAChemistry |
Default Geant4-DNA constructor |
g4em-dna-chemistry_opt1 |
G4EmDNAChemistry_opt1 |
Includes revised chemistry parameters |
Physics models per region
A region is a Geant4 concept that allows the use of different production cuts of secondary particles in different parts of the simulated geometry/world. Geant4-DNA extended that capability to use different physical models in different geometry components [Ivanchenko2011]. This allows to delegate the more computationally expensive tracking of detailed particle interactions to specific components while using the condensed-history approach elsewhere. In this way, the simulation can be sped up without compromising accuracy, if the setup is carefully designed. This feature is also available in TOPAS-nBio. In order to use this capability, the first step is to assign all the components where simulations using the Geant4-DNA physics processes are wanted, to a region, e.g.:
s:Ge/MyComponent1/AssignToRegionNamed = "DetailedTransport"
s:Ge/AnotherComponent/AssignToRegionNamed = "DetailedTransport"
Subsequently, an electromagnetic standard physics list is defined in a modular way and the Geant4-DNA physics is activated in the region of interest (DetailedTransport in this example) by the following parameter:
sv:Ph/Default/Modules = 1 "g4em-penelope"
s:Ph/Default/ForRegion/DetailedTransport/ActiveG4EmModelFromModule = "g4em-dna"
The example G4DNAModelPerRegion.txt shows a complete implementation of this capability.
Customizable Physics models
TOPAS-nBio provides the flexibility to control the model type involved in each process
provided by Geant4-DNA through the module TsEmDNAPhysics. To accomplish this task,
the energy cut for applying electron capture or electron solvation is automatically
readjusted according to the lower energy limit of the physical models. In this way,
it is possible, for example, to combine the elastic models from the CPA100 implementation available
in g4em-dna_opt6 with the inelastic models from the Emfietzoglou-based implementation
available in g4em-dna_opt4:
sv:Ph/Default/Modules = 1 "TsEmDNAPhysics"
s:Ph/Default/Electron/SetElasticScatteringModel = "CPA100"
s:Ph/Default/Electron/SetExcitationModel = "Emfietzoglou"
s:Ph/Default/Electron/SetIonisationModel = "Emfietzoglou"
b:Ph/Default/Electron/ActiveVibExcitation = "True"
b:Ph/Default/Electron/ActiveAttachment = "True"
This feature is supported for mainly for electrons and in a restricted way for protons
(only the elastic scattering model WentzelVI can be chosen instead of the default one). The
example ActiveCustomizablePhysics.txt shows a complete implementation of this capability.
Physics models for Gold material
The Geant4-DNA physics process for interactions of electrons and gammas with Gold can be activated
with TsEmDNAPhysics. It requires the creation of a geometry region for the components made of gold
material:
s:Ge/MyGNP/AssignToRegionNamed = "goldregion"
Current implementation is case-sensitive, and is preferable to use lower-case naming for the region. The next step is to activate the processes:
sv:Ph/Default/Modules = 1 "TsEmDNAPhysics"
b:Ph/Default/PhysicsForGold/Active = "True"
s:Ph/Default/PhysicsForGold/Region = "goldregion"
Note
Only electrons and gammas are supported.
Variance reduction for e- ionization events
Another capability included in the module TsEmDNAPhysics is a variance reduction named
flagged uniform particle split. This technique performs uniform splitting to secondary
electrons produced in ionization events at strategically located regions (defined by
the user) within the geometry and assigns a unique flag number, which is inherited by
their progeny. The flag permits reclassification of each split event as if they were
produced by independent histories. This method reduces the variance by improving the
statistics of secondary electrons, while keeping the time increase small compared to
the generation of additional particles, by only producing additional electrons in strategically selected
regions [RamosMendez2017]. To use this technique, as a first step, the volumes of interest
(where the split will occur) must be assigned to a common region:
s:Ge/MySplitRegion/AssignToRegionNamed = "SplitRegion"
Then, the variance reduction has to be activated and the region and the number of particle splits must be defined, in the example below, 100 electrons will be propagated for every 1 electron entering the region:
b:Vr/UseG4DNAVarianceReduction = "True"
s:Vr/ParticleSplit/SplitElectronsInRegionNamed = "SplitRegion"
i:Vr/ParticleSplit/NumberOfSplit = 100
The scorers used with this technique must be modified to register the contribution of each split
particle independent from other particles using a flag. Two concrete scorers that show how to
use this option are TsScoreDBSCAN.cc and TsScorePDB4DNA.cc. The associated examples are
DBSCAN_VRT.txt and PDB4DNA_VRT.txt. These examples show the implementation of this technique
for the calculation of DNA strand breaks.
References
- Ivanchenko2011
Ivanchenko V, Apostolakis J, Bagulya a., et al., 2011 Recent Improvements in Geant4 Electromagnetic Physics Models and Interfaces 3th Monte Carlo Conf. MC2010 2 898–903 http://hal.in2p3.fr/in2p3-00658779
- RamosMendez2017
Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R and Faddegon B 2017 Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations Phys. Med. Biol. 62 5908–25 http://iopscience.iop.org/0031-9155/62/15/5908
- Incerti2010
Incerti S, Ivanchenko A, Karamitros M, et al., 2010 Comparison of GEANT4 very low energy cross section models with experimental data in water. Med. Phys. 37 4692–708. https://pubmed.ncbi.nlm.nih.gov/20964188/
- Bernal2015
Bernal M A, Bordage M C, Brown J M C, et al., 2015 Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. Phys. Med. 31 861–74 http://www.sciencedirect.com/science/article/pii/S1120179715010042
- Incerti2018
Incerti S, Kyriakou I, Bernal M A, et al., 2018 Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project Med. Phys. 45 e722–39 http://doi.wiley.com/10.1002/mp.13048