Chemistry



1 keV electron track evolution in 150 nm liquid water sphere
http://dx.doi.org/10.6084/m9.figshare.978887



Geant4-DNA released features to simulate water radiolysis for the first time in 2014 (in Geant4 10.1), following the modeling of physical interactions described in the Physics section. These features include the production of chemical species, the simulation of their diffusion, and chemical reactions.

A full review of these features is available in the following publication:

Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project, H. N. Tran, J. Archer, G. Baldacchino, J. M. C. Brown, F. Chappuis, G. A. P. Cirrone, L. Desorgher, N. Dominguez, S. Fattori, S. Guatelli, V. Ivantchenko, J.-R. Méndez, P. Nieminen, Y. Perrot, D. Sakata, G. Santin, W.-G. Shin, C. Villagrasa, S. Zein, S. Incerti, Med. Phys. 51 (2024) 5873-5889 (link) - free access

Today, Geant4-DNA adopts several approaches for the simulation of water radiolysis:
  • A Step-By-Step approach (SBS): Brownian transport of molecules is simulated using the Smoluchowski model. Chemical species are represented as point objects diffusing in the (continuum) liquid medium. Chemical reactions are « controlled by diffusion ». This approach enables chemical species to be tracked in space and time but requires computer resources. See references: 1, 2, 3, 4, 5.
  • The Independent Reaction Time method (IRT): in this approach, the « independent pairs » approximation is assumed: it calculates the reaction times between all possible pairs of reactive species as if they were isolated. Then, reactions occur one by one, starting with the pairs with the shortest reaction times. It is no longer necessary to diffuse the chemical species and calculate the possible reactions between the species at each time step. As this approach excludes the diffusion of chemical species, it is significantly faster. See references: 6, 7, 8
  • A synchronized version of the IRT (IRT-sync): this approach synchronizes the positions of chemical species with each shortest reaction time calculated by the IRT method. This implementation provides users with spatio-temporal information on the species, which can then be coupled with information on the geometric boundaries or geometry of a biological target. See reference 9.
  • A mesoscopic approach: this approach uses a compartment-based representation that describes the evolution of species through the alteration of species concentrations in different compartments. These compartments are created by voxelizing the simulation volume, where species can react with each other within the same voxels. Diffusion is modeled by jumps between adjacent voxels. This approach is suitable for a larger number of species in a limited volume. See reference 10.

The examples section includes several extended examples explaining how to simulate water radiolysis:
  • « chem1 » to « chem5 »: SBS-based, including the calculation of radiochemical yields (G-values) versus time (chem4, chem5)
  • « chem6 »: IRT-based, including the calculation of radiochemical yields (G-values) versus time or LET. Note that SBS and IRT-sync approaches can also be used.
  • « scavenger »: simulation of scavenging using IRT
  • « UHDR »: mesoscopic approach fur ultra-high-dose-rate simulations (in combination with SBS)

Dedicated documentation is provided in the Geant4 Book For Application Developers, in the Geant4-DNA: Physico-chemical and chemical processes in liquid water section.