[Simulation question]:Changing Scavenger Concentration in TOPAS-nBio Does Not Significantly Affect /Gy/Da and umol/J Metrics

[WKjie]

Simulation question

Here’s the English version of your question, focusing on the scavenger (DMSO in the code) and highlighting the /Gy/Da and umol/J metrics:

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Title: Changing Scavenger Concentration in TOPAS-nBio Does Not Significantly Affect /Gy/Da and umol/J Metrics

Description:

Hello everyone,

I am using TOPAS-nBio to study the scavenging effect of hydroxyl radicals, referencing the TOPAS-nBio User Guide. I modified the scavenger concentration (DMSO in the example code) in the provided script (TsScoreDNADamage.txt) to observe its impact on SSB (single-strand break) yield. Specifically, I focused on the /Gy/Da and umol/J metrics, but I noticed that these metrics did not show significant or consistent changes despite varying the scavenger concentration. Here are the steps I followed:

1. I modified the d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Concentration parameter, setting it to 0.001, 0.01, 0.1, 1, and 10 M.
2. I ran simulations for each concentration and observed the /Gy/Da and umol/J metrics.

Here is the relevant part of the code:

#############################

Scavenger Molecules

#############################

s:Mo/DMSO/Symbol = "DMSO"
d:Mo/DMSO/DiffusionCoefficient = 0 nm2/s
u:Mo/DMSO/Charge = 0
d:Mo/DMSO/Radius = 0.3 nm

s:Mo/OHDMSOProduct/Symbol = "OHDMSOProduct"
d:Mo/OHDMSOProduct/DiffusionCoefficient = 0 nm2/s
u:Mo/OHDMSOProduct/Charge = 0
d:Mo/OHDMSOProduct/Radius = 0.3 nm

d:Ch/TOPASChemistry/Reaction/Hydroxyl/Deoxyribose/ReactionRate = 4.8689e9 /M/s

sv:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Products = 1 "OHDMSOProduct"
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ReactionRate = 7.1e9 /M/s
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Concentration = 1e-1 M # Modified this line
s:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ScavengingModel = "ExponentialSingleFactor"
b:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/CompatibleWithStepByStep = "False"

Here are the /Gy/Da and umol/J metrics for different scavenger concentrations:

Scavenger Concentration (M)	SSB in Plasmid (/Gy/Da)	SSB in Plasmid (umol/J)
0.001	5.2478e+18	0.21675
0.01	5.2478e+18	0.21675
0.1	5.2417e+18	0.21650
1	5.1358e+18	0.21213
10	5.1604e+18	0.21314

From the results, it appears that the /Gy/Da and umol/J metrics do not show a clear trend as the scavenger concentration increases. Given the scavenging effect, I expected these metrics to exhibit more significant changes.

Questions:

1. Have I missed any critical points in the setup or interpretation of the results, particularly regarding the /Gy/Da and umol/J metrics?
2. Could the ScavengingModel or other parameters have influenced the results in a way I haven’t considered?
3. Are there additional steps or considerations I should take to properly observe the scavenger’s effect on these metrics?

Thank you very much for your help and guidance!

Best regards,
Wei Kaijie

TOPAS-nBio category

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