Attention
Attention
Chemistry
TOPAS-nBio Default chemistry list
We recommend the following chemistry parameters which include changes that allowed to reconcile the experimental and simulated yields of chemical species at the picosecond level as shown in [RamosMendez2021].
The default chemistry list for TOPAS-nBio can be found at topas-nBio/examples/processes/TOPASDefaultReactions.txt.
To use the default chemistry parameters from TOPAS-nBio, users should specify TsEmDNAChemistry
as the chemistry module. In addition, add the following parameter:
includeFile = TOPASDefaultReactions.txt
The example topas-nBio/examples/scorers/IRTGetGValue/TsIRTGvalue.txt shows how to properly use this chemistry list
and recreate the validation results from [RamosMendez2021].
Geant4 Default chemistry list
TOPAS-nBio [Schuemann2019a] can inherit the parameters (reactions, reaction rates, etc.) provided by the Geant4-DNA toolkit to perform radiolysis simulations via the modules g4em-dna-chemistry and g4em-dna-chemistry_opt1. The chemistry parameters provided in the first module are reported in [Karamitros2012] [Incerti2016]. The chemistry parameters provided in the second module are reported in [RamosMendez2018].
The activation of the chemical stage is performed by including a chemistry model in the modular physics list, for example using the following parameter:
sv:Ph/Default/Modules = 2 "g4em-dna" "g4em-dna-chemistry"
The order of these modules must be consistent with the occurrence of the
physical and chemical processes. Thus, the module for the physical process
must be followed by the module for the chemical process. By default, the
pre-chemical and chemical stages are activated, but no explicit step-by-step
transport is performed. This is useful only for the scoring of the G-value
(the yield of chemical species per 100 eV of energy deposit) as a function
of time. A scorer that retrieves this quantity is the GValue scorer.
The example topas-nBio/examples/scorers/SBSGetGValue/GvalueG4DNADefault.txt shows a complete implementation of this
scorer.
Actvating the Chemistry of TOPAS-nBio
Simulation of chemical species reactions can be activated by
using a set of parameters associated with a chemistry name (analogous to the physics list Ph/ListName).
Different sets of parameters can be associated to different chemistry names, and only those assigned to the
chemistry name defined by the following parameter will be used (e.g.
TOPASChemistry:
s:Ch/ChemistryName = "TOPASChemistry"
The configuration of parameters for the chemistry stage requires the user to define an end time
and (in the case of the Step-By-Step method) a time resolution. The end time must be larger
than 1 ps (i.e. the time where the chemical stage begins). The time resolution can be defined piecewise.
For example, to set the transport of chemical species up to 15 ns with time step resolution of
1 ns from 1 ps to 10 ns and 10 ps from 10 ns to 15 ns, the following parameters must be set
(assuming the chemistry name TOPASChemistry):
# Activate Chemistry and Set Chemistry End Time
b:Ch/TOPASChemistry/ChemicalStageTransportActive = "True"
d:Ch/TOPASChemistry/ChemicalStageTimeEnd = 15.0 ns
# Only for Step-By-Step Chemistry
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsHighEdges = 2 10.0 15.0 ns
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsResolutions = 2 1.0 10.0 ps
After these parameters have been set, the spatio-temporal information of the
chemical species is available and can be visualized using the
TOPAS graphics for Step-By-Step chemistry only. A scorer example to retrieve the track information (physical
and chemical) is particleTuple.txt. A graphics example to visualize the transport
of chemical species is ActiveChemistryDefault.txt.
Configurable chemistry list
Simulation of the water radiolysis process requires the setup of a
large set of parameters: branching ratios, dissociation schemes,
reaction rates, types of chemical species and diffusion coefficients.
Advanced users that require to activate or deactivate reactions, change the
reaction rates or diffusion coefficients, etc., have that flexibility
provided by TOPAS-nBio. This can be done by including TsEmDNAChemistry
instead of the Geant4DNA chemistry module as follows:
sv:Ph/Default/Modules = 2 "TsEmDNAPhysics" "TsEmDNAChemistry"
Instead of the TsEmDNAPhysics physics module, one of the other options described in the
Physics Processes can be used.
In this way, a whole set of parameters can be customized by using the following
conventions. Chemical species are named using full names without separation
spaces, for example, H2O2 is HydrogenPeroxide (case
insensitive). The list of available molecules and diffusion coefficients
customizable via TsEmDNAChemistry are shown in the following table:
Molecule |
TOPAS name |
D (10–9m2/s) at 25oC |
e–aq |
SolvatedElectron |
4.9 |
•OH |
Hydroxyl |
2.2 |
H• |
Hydrogen |
7.0 |
H3O+ |
Hydronium |
9.46 |
H2 |
Dyhydrogen |
4.8 |
OH– |
Hydroxide |
5.3 |
H2O2 |
HydrogenPeroxide |
2.3 |
O2 |
Oxygen |
2.4 |
O2– |
SuperoxideAnion |
1.75 |
HO2 |
HydroPeroxy |
2.3 |
HO–2 |
Dioxidanide |
1.4 |
O3P |
AtomicOxygen |
2.0 (only for IRT) |
O– |
Oxyde |
2.0 (only for IRT) |
O3 - |
Trioxide |
2.0 (only for IRT) |
O3 |
Ozone |
2.0 (only for IRT) |
Prechemical stage
The dissociation schemes and branching ratios are inherited from Geant4-DNA. In general, users do not need to change or set these values. Users can select different branching ratio models as follows:
s:Ch/TOPASChemistry/BranchingRatiosModel = "topasnbio" # "g4dna" "experimental"
The default branching ratios in TOPAS-nBio are specified by topasnbio.
The default branching ratios from Geant4-DNA are specified by g4dna. And experimental
can be used if you are interested in testing different ratios. Modification of these branching ratios can
be accomplished as follows (assuming s:Ch/ChemistryName = "TOPASChemistry"):
s:Ch/TOPASChemistry/BranchingRatiosModel = "experimental"
u:Ch/TOPASChemistry/BranchingRatios/IonizationState/DissociativeDecay = 1.00
u:Ch/TOPASChemistry/BranchingRatios/A1B1/DissociativeDecay = 0.65
u:Ch/TOPASChemistry/BranchingRatios/A1B1/Relaxation = 0.35
u:Ch/TOPASChemistry/BranchingRatios/B1A1/AutoIonization = 0.55
u:Ch/TOPASChemistry/BranchingRatios/B1A1/DissociativeDecay = 0.15
u:Ch/TOPASChemistry/BranchingRatios/B1A1/Relaxation = 0.30
u:Ch/TOPASChemistry/BranchingRatios/RydbergStatesAndDiffuseBands/AutoIoinization = 0.5
u:Ch/TOPASChemistry/BranchingRatios/RydbergStatesAndDiffuseBands/Relaxation = 0.5
Note
Users should avoid filling the entire world with water. When radiolysis happens close to the world edge the pre-chemical displacements can sometimes create species that are outside the world, leading to segmentation faults. The solution is to have a small air gap between your target and world edge.
Chemical stage
For the chemical stage, the number of reactions and reaction rates are also
inherited from Geant4-DNA. Additional reactions can be defined using the molecules
from the previous table, and the reaction rates can also be overwritten for the
existing reactions. The way the reactions are defined is the following, let us
assume we have two molecules named SolvatedElectron and Oxygen. After
their reaction, they produce the product SuperoxideAnion. Then, two
parameters are required to define that reaction: one parameter to
associate the pair of molecules and define the products, one parameter to
assigns the reaction rate (with units of /M/s), e.g:
# Define the products:
sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/Products = 1 "SuperoxideAnion"
# Assign a reaction rate value:
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/ReactionRate = 1.9e10 /M/s
# Assign the Reaction Type
i:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/ReactionRate = 2
# SBS Compatible Reactions
b:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/CompatibleWithStepByStep = "True"
Reaction types can be 1, 2, 3, 4 or 5 depending on the reactants charge and mode of reaction (totally diffusion controlled or partially diffusion controlled) [Plante2017]. Background reactions (type 6) are threated separetedly for either Step-By-Step or IRT simulations, as it will be discussed in a following section.
If the reaction does not produce any product or the product won’t react further, for
example, the product from •OH + H• –> H 2O, then the name None
must be used, e.g:
# Define the reaction without products:
sv:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydrogen/Products = 1 "None"
TOPAS-nBio provides a set of chemical parameters in the file TOPASChemistry.txt to be used with TsEmDNAChemistry.
These files (available in examples/processes) should be included in the usual way
with includeFile = "TOPASChemistry.txt". This set of reactions and reaction rates reproduces
experimental data from the literature, as reported in [RamosMendez2018]. The example
ActiveChemistryRevised.txt shows how to define the new reaction capability.
Truncation transport for chemical stage
An additional feature is the capability to terminate the transport of chemical species in volumes
having a user defined material. In that case, the species are terminated once they come in contact
with the volume (at the boundary or the first step within the volume). To use that capability, a new
material must be cloned from the G4_WATER material:
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity = 1.0 g/cm3
Then call the following parameters (also, see example RemoveChemicalSpeciesInVolume.txt):
s:Ch/TOPASChemistry/RemoveInMaterial = "G4_WATER_MODIFIED"
sv:Ch/TOPASChemistry/RemoveInMaterialTheseMolecules = 2 "SolvatedElectron" "Hydrogen"
Chemical Diffusion-Reaction Algorithms
TOPAS-nBio incorporates two different methods for the diffusion and reaction of chemical species, the Step-By-Step (SBS) [Turner1983] and Independent Reaction Times (IRT) [Clifford1986] methods. Either method can be invoked by means of specific scorers. Main differences between both methods are the following:
SBS simulates the spatial and temporal evolution of the chemical species and thus is slower than IRT.
SBS allows to visualize chemical evolution.
IRT can reach up to two or three orders of magnitude shorter times than SBS.
Further chemical species can be defined only in IRT using parameters starting with ‘’Mo’’, see below.
Reactions between chemical species and background are defined in a different way between both methods.
Products from background reactions can be simulated only with IRT.
Step-By-Step
For the SBS method, TOPAS-nBio inherits the reactions and molecules from Geant4-DNA.
This is done automatically when using the default Geant4-DNA chemistry list g4em-dna-chemistry.
When using the configurable chemistry list of TOPAS-nBio TsEmDNAChemistry, the set of diffusion coefficients
and reaction rates to be used can be found in the GvalueRevisedPhysicsChemistry.txt example.
To incorporate reactions with the background (scavenging) in TOPAS-nBio, the following structure must be used:
# The Reactant: Scavenged Molecules
sv:Sc/SBSGValue/Scavenger/Molecules = 2 "SolvatedElectron" "Hydroxyl"
# The Scavenger concentrations
dv:Sc/SBSGValue/Scavenger/Concentrations = 2 1e-2 1e-2 M
# The Scavenger reaction rate
dv:Sc/SBSGValue/Scavenger/ReactionRates = 2 5e10 2.7e9 /M/s
# Confirm if there are products: Must be set to False.
bv:Sc/SBSGValue/Scavenger/HasProducts = 2 "False" "False"
where M = 1 mol/dm3.
In the previous example solvated electrons and Hydroxyl radicals will be scavenged at a rate (scavenging capacity) of \(5 \times 10^{8} s^{-1}\) for the solvated electrons and \(2.7 \times 10^{7} s^{-1}\) for the hydroxyl radical, respectively. Current version of TOPAS-nBio does not produces any product from background reaction. This capability will be added in a future release of TOPAS-nBio.
Independent Reaction Times
For IRT we provide a revisited reaction kinetics model (reaction and reaction rates) reported in [RamosMendez2021] which reconciliated simulated and measured G values at the picosecond range. This model is provided in the TsIRTGvalue.txt example.
The user can define new molecules by using the parameter system by using the Mo prefix as follows:
# Define the internal Symbol of the Molecule
s:Mo/DMSO/Symbol = "DMSO^0"
# Define the Diffussion Coefficient
d:Mo/DMSO/DiffusionCoefficient = 0 nm2/s
# Define the Charge of the Molecule
u:Mo/DMSO/Charge = 0
# Define the reaction radius
d:Mo/DMSO/Radius = 0.3 nm
New molecules defined with the previous method are not compatible with the StepByStep method. In IRT, the declaration of background reactions follows the same convention from the regular reactions:
sv:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Products = 1 "OHDMSOProduct^0"
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ReactionRate = 7.1e9 /M/s
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Concentration = 1e-1 M
Two models for simulating background reactions are provided, and can be selected as follows:
# Either ExponentialSingleFactor or ExponentialDoubleFactor s:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ScavengingModel = “ExponentialSingleFactor”
Where ExponentialSingleFactor refers to method described in [Plante2017] and ExponentialDoubleFactor
is the method described in [Pimblott1991].
TOPAS-nBio IRT allows for the activation and deactivation of reactions. This allows users to define a list of chemical reactions and pick and choose which ones of them will be active during the simulation without the need to introduce or delete the whole reaction:
# Deactivate an already existing Chemical Reaction
b:Ch/TOPASChemistry/Reaction/hydrogen/hydroxyl/Active = "False"
# Deactivate an already existing Background Reaction
b:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Active = "False"
The section up to this point describes the pure IRT, which can be enabled as follows:
s:Ch/TOPASChemistry/IRTProcedure = "pure"
Note
the pure IRT is default in TOPAS-nBio and will be used if no other IRT procedure is specified.
In order to simulate the dose and dose rate dependency of long-term chemistry for continuous and quasi-continuous beam structures,
the continuous IRT can be used instead. This IRT modality is described in detail in [Shin2025]:
s:Ch/TOPASChemistry/IRTProcedure = "continuous"
Simulations considering pH
The IRT method of TOPAS-nBio allows the user to scale the pH value of the medium. This can be usefull to model the physical conditions of experimental setups in more detail. The pH scalling was developed following the work of [Autsavapromporn2007] and [Plante2011]. To change the pH of the medium the following parameters are used:
# Modeling acid properties can be set to "H2SO4" or "Generic"
# "Generic" is an artifical PH scalling in which no acid is present
s:Ch/TOPASChemistry/ModelAcidPropertiesFromSubstance = "H2SO4"
# Use acid concentration to change pH, not available with "Generic" solvent
s:Ch/TOPASChemistry/ModelAcidPropertiesWithConcentration = 0.4 M
# Use a specific pH and calculate acid concentration
s:Ch/TOPASChemistry/ModelAcidPropertiesWithpH = 4.6
The last two parameters; ModelAcidPropertiesWithConcentration and ModelAcidPropertiesWithpH canot be
used at the same time, if the user attemps to do so TOPAS will exit and an error message displayed. TOPAS-nBio will
automatically scale reaction rates for reactions between two charged chemical species based on the ionic strength
of the medium. An example is provide shown this capability throught the Fricke dosimeter, see example TOPAS-nBio/example/scorers/FrickeIRT
IRT Automatic Temperature Scalling
TOPAS-nBio provides its users with a built-in temperature scalling algorithm compatible with IRT.
It is based on the work of [Elliot1994] and [DuPenhoat200].
Specif details regarding the implementation can be found in [RamosMendez2022]. To use the temperature scaling of reaction rates and
diffusion coefficients, the users must the parameter u:Ch/TOPASChemistry/Temperature and setting it to the temperature in Celsius.
For the best results, it is recommended to also change the water density to the value that corresponds with the desired temperature.
We provide users with two examples that showcase this TOPAS-nBio IRT feature in the folder /examples/scorers/Temperatures: TemperatureExample_20C.txt and TemperatureExample_90C.txt.
We remind users that this specific implementation is only valid between 0 and 90 degrees Celsius.
References
- Karamitros2012
Karamitros M, Mantero A, Incerti S, Friedland W, Baldacchino G, Barberet P, Bernal M, Capra R, Champion C, El Bitar Z, Francis Z, Gueye P, Ivanchenko A, Ivanchenko V, Kurashige H, Mascialino B, Moretto P, Nieminen P, Santin G, Seznec H, Tran H N, Villagrasa C and Zacharatou C 2011 Modeling Radiation Chemistry in the Geant4 Toolkit Prog. Nucl. Sci. Technol. 2 503–8 http://www.aesj.or.jp/publication/pnst002/data/503-508.pdf
- Incerti2016
Incerti S, Douglass M, Penfold S, Guatelli S and Bezak E 2016 Review of Geant4-DNA applications for micro and nanoscale simulations Phys. Medica 32 1187–200 http://www.physicamedica.com/article/S1120-1797(16)30927-9/pdf
- RamosMendez2018(1,2)
Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H and Faddegon B 2018 Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio Phys. Med. Biol. 63 105014 http://iopscience.iop.org/article/10.1088/1361-6560/aac04c
- RamosMendez2021(1,2,3)
Ramos-Méndez J, LaVerne J, D-Kondo J, et. al. 2021 TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys. Med. Biol. https://iopscience.iop.org/article/10.1088/1361-6560/ac1f39
- RamosMendez2022
Ramos-Méndez, J., García-García, O., Domínguez-Kondo, J., Laverne, J. A., Schuemann, J., Moreno-Barbosa, E., Faddegon, B. (2022). TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Physics in Medicine and Biology. https://doi.org/10.1088/1361-6560/ac79f9
- Clifford1986
Clifford P, Green N J B, Oldfield M J, Pilling M J and Pimblott S M 1986 Stochastic Models of Multi-species Kinetics in Radiation-induced Spurs J. Chem. Soc., Faraday Trans. 1 82 2673–89 http://doi.org/10.1039/F19868202673
- Turner1983
Turner JE, Magee JL, Wright HA, Chatterjee A, Hamm RN, RitchieRH 1983 Physical and chemical development of electron tracksin liquid water. Radiat Res 96:437–449 https://www.jstor.org/stable/3576111
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Plante I and Devroye L 2017 Considerations for the independent reaction times and step-by-step methods for radiation chemistry simulations” Radiat. Phys. Chem. 139 157-172 http://dx.doi.org/10.1016/j.radphyschem.2017.03.021
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Pimblott SM, Pilling MJ, and Green NJB 1991 Stochastic Models of Sput Kinetics In Water. Radiat. Phys. Chem. 37 (3) 377-388 https://doi.org/10.1016/1359-0197(91)90006-N
- Schuemann2019a
Schuemann, J, McNamara, A L, Ramos-Méndez, J, Perl, J, Held, K D, Paganetti, H, Incerti, S, Faddegon, B 2019 TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology Radiation Research, 191(2), 125–138 https://pubmed.ncbi.nlm.nih.gov/30609382/
- Autsavapromporn2007
Autsavapromporn N, Meesungnoen J, Plante I, Jay-Gerin J-P 2007. Monte Carlo simulation study of the effects of acidity and LET on the primary free-radical and molecular yields of water radiolysis — Application to the Fricke dosimeter. Canadian Journal of Chemistry, 85(3), 214–229. https://doi.org/10.1139/v07-021
- Plante2011
Plante I 2011. A Monte-Carlo step-by-step simulation code of the non-homogeneous chemistry of the radiolysis of water and aqueous solutions-Part II: Calculation of radiolytic yields under different conditions of LET, pH, and temperature. Radiation and Environmental Biophysics, 50(3), 405–415. https://doi.org/10.1007/s00411-011-0368-7
- Elliot1994
Elliot A J 1994. Rate Constants and G-Values for the Simulation of the Radiolysis of Light Water over the Range 0-300°C. https://inis.iaea.org/records/1964r-srn97
- DuPenhoat200
Du Penhoat M-A H, Goulet T, Frongillo Y, Fraser M J, Bernat P, Jay-Gerin J P 2000. Radiolysis of liquid water at temperatures up to 300 °c: A Monte Carlo simulation study. Journal of Physical Chemistry A, 104(50), 11757–11770. https://doi.org/10.1021/jp001662d
- Shin2025
Wook-Geun Shin, J Naoki D-Kondo, José Ramos-Méndez, Jay A LaVerne, Bethany Rothwell, Alejandro Bertolet, Aimee McNamara, Bruce Faddegon, Harald Paganetti and Jan Schuemann 2025. Investigation of hydrogen peroxide yields and oxygen consumption in high dose rate irradiation: a TOPAS-nBio Monte Carlo study. Phys. Med. Biol. 70 (2025) 015012. https://iopscience.iop.org/article/10.1088/1361-6560/ad9ce2