[Simulation question]:Example IRTcummulative simulation on e_aq^-1

[mmvs-j]

Simulation question

Hi,
I am attempting to use the TsIRTcummulative example to reproduce the results seen in the attached paper by Ramos-Méndez et al, specifically the figure 2 and 4 graph corresponding to 100MeV protons and a 1 ns pulse width, as a starting point for my simulations.

For the hydroxyl radical the yield as well as the G-value is similar to the literature results, but for the hydronium radical it was found to fall faster than expected to the point that it is different from the literature results, see attached figure. What is the reason for this, is there any reaction process missing and what should I change to get the correct results?

Many thanks for any assistance with this problem.
I have attached a sample script and the results.
With best regards
Mao

PlanteReactions.txt
PlanteTypeVI.txt
TsIRTCummulativecopy.txt

TOPAS-nBio category

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[WKjie]

Dear Sir,

In the configuration file you provided, I found the following chemical stage parameter settings:

b:Ch/Plante/ChemicalStageTransportActive = "True"
d:Ch/Plante/ChemicalStageTimeEnd = 1.00001 ps
dv:Ch/Plante/ChemicalStageTimeStepsHighEdges = 1 999999 ps
dv:Ch/Plante/ChemicalStageTimeStepsResolutions = 1 0.5 ps
The relevant literature describes:

"To simulate the radiolysis of water, three distinct stages defined by their time duration with respect to each particle traversing the irradiated volume are considered. The first is the physical stage, which begins from the incidence of radiation to about 10⁻¹⁵ s. In this stage, the radiation traversing the aqueous environment excites water molecules (H₂O*) or ionizes them (H₂O⁺) through energy transfer events to the medium. Subsequently, the physico-chemical stage takes place from about 10⁻¹⁵ to 10⁻¹² s, where those excited and ionized water molecules dissociate into the so-called primary chemical species (e⁻ₐq, H₂, H•, •OH, and H₃O⁺). Finally, the chemical stage (from about 10⁻¹² to 10⁻⁶ s) occurs where the primary chemical species, initially non-homogeneously distributed in the medium, diffuse through the environment following Brownian dynamics, reacting with each other, reducing the yield of primary species, and producing secondary chemical species. After 10⁻⁵ s, the cloud of species is sufficiently sparse (homogeneous) so that no further reactions between primary chemical species are likely (Sanguanmith et al., 2012). The models used by Geant4-DNA and TOPAS-nBio to simulate these three stages have been reported in detail elsewhere (Karamitros et al., 2011, 2014; Ramos-Méndez et al., 2018; Schuemann et al., 2019; Shin et al., 2019; Ramos-Méndez et al., 2020a, 2021)."

Does this mean the parameter should be set to d:Ch/Plante/ChemicalStageTimeEnd = 1 μs (i.e., 0.000001 s)? Additionally, what is the basis for the following parameter settings?

dv:Ch/Plante/ChemicalStageTimeStepsHighEdges = 1 999999 ps
dv:Ch/Plante/ChemicalStageTimeStepsResolutions = 1 0.5 ps
I saw these settings in the user guide but didn't fully understand their physical or computational significance.