[Simulation question]: How to set up parameters for compounds like DMSO, Tris, WR-1065 in TOPAS-nBio simulations?

[WKjie]

Simulation question

Hi all,

I’ve been reviewing several papers that utilize TOPAS-nBio to simulate plasmid irradiation experiments, and I noticed that some setups include compounds like DMSO, Tris, and WR-1065. These compounds seem to be primarily considered for their ability to scavenge •OH (hydroxyl radicals). However, I noticed that other potential effects of these compounds, such as pH regulation, appear not to be included in the simulations.

So, my questions are:

Should I focus only on the hydroxyl radical scavenging properties (e.g., reaction rates, concentrations) when setting up these compounds, or are there other properties (e.g., pH regulation) that I should take into account in the simulation?

I am trying to define new compound parameters in TOPAS-nBio and wanted to ask if the approach below (from this example: Plasmid Irradiation Example) can be directly adapted for other compounds:

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
s:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ScavengingModel = "ExponentialSingleFactor"
b:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/CompatibleWithStepByStep = "False"
Specifically:

When adding compounds like WR-1065 or Tris, should I follow a similar parameterization structure as shown in the DMSO example above?
How do I determine proper values for parameters like diffusion coefficient, charge, radius, reaction rate, etc., for new compounds such as WR-1065?
I’d appreciate any insights, especially for defining compound-specific parameters and understanding whether additional properties (beyond •OH scavenging) need to be modeled for these compounds.

Thank you in advance for your help!

TOPAS-nBio category

Geometry

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