[Simulation question]:Setting up 0.27 mM oxygen and IRT temperature functionality causes SSB to become 0

[WKjie]

Simulation question

Hi!everyone:

I’m trying to set up a solution with 0.27 mM oxygen in TOPAS-nBio. Additionally, I want to use the IRT temperature functionality based on the example PlasmidIrradiation.

I added the following parameters to enable IRT temperature:

u:Ch/TOPASChemistry/Temperature = 20
b:Ch/TOPASChemistry/ApplyCorrectionScalingForTemperature = "True"
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity = 0.9984371 g/cm3

And modified:

Ge/World/Material = "G4_WATER_MODIFIED"
However, this causes SSB (Single-Strand Breaks) to become 0. The user guide only mentions modifying temperature and water density.

How do I correctly set up a solution with 0.27 mM oxygen?
Why does enabling IRT temperature cause SSB to become 0, and how can I fix it?
Any help would be appreciated!

TOPAS-nBio category

Chemistry

Code of Conduct

• I agree to follow this project's Code of Conduct

Attestation

• I testify that I have fully read the bug reporting guideline beforehand.

[wgshin]

Hi,
That because there is material filter in the DNA scorer (https://github.com/topas-nbio/TOPAS-nBio/blob/master/scorers/TsScoreDNADamageWithIRT.cc#L111).
BTW, it seems like the radicals will be not simulated in the recent version. Is there any reason why, @tmasilela ?

[tmasilela]

Hey WG,
I'm not sure - the only change I made to this example within the last year was updating some of the rate constants in TOPASDefaultReactions.txt.
I'll take a look

[alfiafazimah]

Mine also have problems in simulating the PlasmidIrradiation, resulting in SSB=0. Even without any changes of the example, the SSB still not calculated from my Linux machine both in Mint and Ubuntu system.
But, on my iOs system (M3), the same code counting the SSB.
Is this the problem of recent version?
I installed the nbio on mac earlier (on June, 2025) while on the Linux was installed around july-august.

[tmasilela]

Hi,

I haven't had any spare time but taking a look at the SBS/IRT plasmid examples is on my to-do list. Will try and provide more details by the end of this week/early next week.

All the best,
Thongchai

[wgshin]

There are two bugs in this issue.

1. IRT takes over "H2O^0" and "H2O^1" before they're dissociated.
2. AssignMoleculeID command in TsIRTConfiguration is missing.
   Let me prepare a merge request for that.