Proton Track Overlap Model

TOPAS-nBio 1.0 (TOPAS 3.6.1) parameter files and MATLAB R2020a analysis codes used to model the distribution and yield of chemical species after proton irradiation, to investigate the possibility of physico-chemical inter-track interactions within ultra-high dose-rate proton therapy. Files are separated into two folders, the AnalyticTrackModel and the InstantaneousDeliveryModel, which are summarised below. The AnalyticTrackModel simulates proton tracks through a shallow cylindrical water phantom, recording the radial position of physical and chemical interactions around the track to estimate track dimensions for a geometric track overlap model. The InstantaneousDeliveryModel simulates independently and instantaneously delivered proton tracks to a small water phantom, recording the energy-averaged G-Values of chemical species to compare any changes in yields across the chemical stage.

Analytic Track Model

Topas-nBio Parameter Files

ProtonTrackRadius_Physics.txt This parameter file simulates proton irradiation through the centre of a shallow cylindrical water phantom, outputting the positional and energy deposition information of physical interactions around the track.

ProtonTrackRadius_Chemistry.txt This parameter files simulates proton irradiation through the centre of a shallow cylindrical water phantom, outputting the positional information of chemical species around the track at given timepoints.

TopasChemistry.txt This file defines the standard rate constants for relevant chemical processes.

Bragg_Peak_Profile.txt This file simulates proton irradiation in a 10 cm water phantom, outputting the dose deposition profile data.

MATLAB Analysis Codes

Physics_TrackRadius_LET.m This code analyses pTuple data from ProtonTrackRadius_Physics.txt, outputting an energy-weighted histogram of the physical interactions as a function of radial distance around the proton track. The LET is also calculated using the total energy deposited and cylinder depth.

Chemistry_TrackRadius_SpeciesSpecific.m This code analyses pTuple data from ProtonTrackRadius_Chemistry.txt, outputting an histogram of the chemical species as a function of radial distance around the proton track. The code can be used for specific species or at the 1 ps timepoint to exclude any excited or ionised water molecules which are still present.

Chemistry_TrackRadius.m This code analyses pTuple data from ProtonTrackRadius_Chemistry.txt, outputting an histogram of the chemical species as a function of radial distance around the proton track. The code was used for all species for timepoints after 1 ps.

Instantaneous Delivery Model

TOPAS-nBio Setup

MultipleSources.m This tool generates multiple beam sources (to produce a single Geant4 event) to create parameter file Source_Simultaneous.txt for an instantaneous proton delivery.

TOPAS-nBio Parameter Files

Independent_Delivery.txt File for water phantom proton irradiation for independently delivered proton tracks, reads in Source_Independent.txt.

Simultaneous_Delivery.txt File for water phantom proton irradiation for simultaneously delivered proton tracks, reads in Source_Simultaneous.txt.

Source_Independent.txt File of the beam delivery information, using a single source with multiple tracks for individually delivered protons.

Source_Simultaneous.txt File of the beam delivery information, using multiple sources each with an individual proton for instantaneously delivered protons.

TOPAS-nBio Extensions

ScoreGValueEnergy.hh

ScoreGValueEnergy.cc Scoring extension files which calculate the G-Value of each chemical species, weighting by the total energy deposited.

Contact

For any questions or comments please contact sthompson76 (at) qub.ac.uk.