# New TOPAS documentation website goes live!

I have moved our documentation from the old PDF document to a website hosted by ReadTheDocs: http://topas.readthedocs.org

From the user perspective, I hope that this will help to discover features of TOPAS more easily and find solutions to their problems more quickly. Hyperlinks now connect related sections.

From the developer perspective, this should make collaboration… Read more about New TOPAS documentation website goes live!

# Syntax highlighting for TOPAS parameter files

I wrote a package for the Sublime Text editor that understands the grammar of a TOPAS parameter file and will enable syntax highlighting (see image below).
Although it is by no means perfect, it should only be confused by non-standard files. I thought I'd share it, in case it helps TOPAS users who like this text editor: https://github.com/davidchall/topas-syntax

# Generating random directions in a beam model

As described here, I'm a developer of the TOPAS Monte Carlo simulation tool for radiotherapy research. To improve our beam source model, I wanted a method to randomly generate uniformly distributed directions that are constrained to a certain region of the unit sphere, centered upon the z-axis (the beam direction). Generated particles are assigned these random directions before they are transported through the simulated geometry, in order to account for beam divergence.

# Predicting patient-specific dosimetric benefits of proton therapy for skull-base tumors using a geometric knowledge-based method

DC Hall, AV Trofimov, BA Winey, NJ Liebsch, and H Paganetti. 2017. “Predicting patient-specific dosimetric benefits of proton therapy for skull-base tumors using a geometric knowledge-based method.” International Journal of Radiation Oncology • Biology • Physics, 5, 97: 1087-1094. Publisher's Version Abstract

Purpose: To predict the organ at risk (OAR) dose levels achievable with proton beam therapy (PBT), solely based on the geometric arrangement of the target volume in rela- tion to the OARs. A comparison with an alternative therapy yields a prediction of the patient-specific benefits offered by PBT. This could enable physicians at hospitals without proton capabilities to make a better-informed referral decision or aid patient selection in model-based clinical trials.

Methods and Materials: Skull-base tumors were chosen to test the method, owing to their geometric complexity and multitude of nearby OARs. By exploiting the correla- tions between the dose and distance-to-target in existing PBT plans, the models were independently trained for 6 types of OARs: brainstem, cochlea, optic chiasm, optic nerve, parotid gland, and spinal cord. Once trained, the models could estimate the feasible doseevolume histogram and generalized equivalent uniform dose (gEUD) for OAR structures of new patients. The models were trained using 20 patients and validated using an additional 21 patients. Validation was achieved by comparing the predicted gEUD to that of the actual PBT plan.

Results: The predicted and planned gEUD were in good agreement. Considering all OARs, the prediction error was þ1.4  5.1 Gy (mean  standard deviation), and Pearson’s correlation coefficient was 93%. By comparing with an intensity modulated photon treatment plan, the model could classify whether an OAR structure would experience a gain, with a sensitivity of 93% (95% confidence interval: 87%-97%) and specificity of 63% (95% confidence interval: 38%-84%).

Conclusions: We trained and validated models that could quickly and accurately pre- dict the patient-specific benefits of PBT for skull-base tumors. Similar models could be developed for other tumor sites. Such models will be useful when an estimation of the feasible benefits of PBT is desired but the experience and/or resources required for treatment planning are unavailable.

# Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors

TSA Underwood, W Sung, CH McFadden, SJ McMahon, DC Hall, AL McNamara, H Paganetti, GO Sawakuchi, and J Schuemann. 2017. “Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors.” Physics in Medicine and Biology, 8, 62: 3237. Publisher's Version Abstract

Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al2O3:C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated $8\times 4\times 0.5$  mm3 FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm. MC simulations were implemented in two stages: (1) using TOPAS to model the beam properties within a water phantom and (2) using TOPAS-nBio with Geant4-DNA physics to score particle interactions through a water surrogate of Al2O3:C,Mg. The measured median track integrated brightness (IB) was observed to be strongly correlated to both (i) voxelized track-averaged linear energy transfer (LET) and (ii) frequency mean microdosimetric lineal energy, $\overline{{{y}_{F}}}$ , both simulated in pure water. Histograms of FNTD track IB were compared against TOPAS-nBio histograms of the number of terminal electrons per proton, scored in water with mass-density scaled to mimic Al2O3:C,Mg. Trends between exposure depths observed in TOPAS-nBio simulations were experimentally replicated in the study of FNTD track IB. Our results represent an important first step towards the experimental validation of MC simulations on the sub-cellular scale and suggest that FNTDs can enable experimental study of the microdosimetric properties of individual proton tracks.

# Measurement of fiducial differential cross sections of gluon-fusion production of Higgs bosons decaying to WW∗→eνμν with the ATLAS detector at √s=8 TeV

This paper describes a measurement of fiducial and differential cross sections of gluon-fusion Higgs boson production in the HWWeνμν channel, using 20.3 fb1 of proton-proton collision data. The data were produced at a centre-of-mass energy of √s=8 TeV at the CERN Large Hadron Collider and recorded by the ATLAS detector in 2012. Cross sections are measured from the observed HWWeνμν signal yield in categories distinguished by the number of associated jets. The total cross section is measured in a fiducial region defined by the kinematic properties of the charged leptons and neutrinos. Differential cross sections are reported as a function of the number of jets, the Higgs boson transverse momentum, the dilepton rapidity, and the transverse momentum of the leading jet. The jet-veto efficiency, or fraction of events with no jets above a given transverse momentum threshold, is also reported. All measurements are compared to QCD predictions from Monte Carlo generators and fixed-order calculations, and are in agreement with the Standard Model predictions.

# Validation of nuclear models in Geant4 using the dose distribution of a 177 MeV proton pencil beam

DC Hall, A Makarova, H Paganetti, and B Gottschalk. 2016. “Validation of nuclear models in Geant4 using the dose distribution of a 177 MeV proton pencil beam.” Physics in Medicine and Biology, 1, 61: N1-10. Publisher's Version Abstract

A proton pencil beam is associated with a surrounding low-dose envelope, originating from nuclear interactions. It is important for treatment planning systems to accurately model this envelope when performing dose calculations for pencil beam scanning treatments, and Monte Carlo (MC) codes are commonly used for this purpose. This work aims to validate the nuclear models employed by the Geant4 MC code, by comparing the simulated absolute dose distribution to a recent experiment of a 177 MeV proton pencil beam stopping in water.

Striking agreement is observed over five orders of magnitude, with both the shape and normalisation well modelled. The normalisations of two depth dose curves are lower than experiment, though this could be explained by an experimental positioning error. The Geant4 neutron production model is also verified in the distal region. The entrance dose is poorly modelled, suggesting an unaccounted upstream source of low-energy protons. Recommendations are given for a follow-up experiment which could resolve these issues.

# Observation and measurement of Higgs boson decays to WW* with the ATLAS detector

We report the observation of Higgs boson decays to WW based on an excess over background of 6.1 standard deviations in the dilepton final state, where the Standard Model expectation is 5.8 standard deviations. Evidence for the vector-boson fusion (VBF) production process is obtained with a significance of 3.2 standard deviations. The results are obtained from a data sample corresponding to an integrated luminosity of 25fb1 from √s=7 and 8 TeV pp collisions recorded by the ATLAS detector at the LHC. For a Higgs boson mass of 125.36 GeV, the ratio of the measured value to the expected value of the total production cross section times branching fraction is 1.09+0.160.15(stat)+0.170.14(syst). The corresponding ratios for the gluon fusion and vector-boson fusion production mechanisms are 1.02±0.19(stat)+0.220.18(syst) and 1.27+0.440.40(stat)+0.300.21(syst), respectively. At √s=8TeV, the total production cross sections are measured to be σ(ggHWW)=4.6±0.9(stat)+0.80.7(syst)pb and σ(VBHWW)=0.51+0.170.15(stat)+0.130.08(syst)pb. The fiducial cross section is determined for the gluon-fusion process in exclusive final states with zero or one associated jet.