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Borys, D. et al, & Brzezinski, K. (2022). ProTheRaMon-a GATE simulation framework for proton therapy range monitoring using PET imaging. Phys. Med. Biol., 67(22), 224002–15pp.
Abstract: Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user's needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022).
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Poley, L., Stolzenberg, U., Schwenker, B., Frey, A., Gottlicher, P., Marinas, C., et al. (2021). Mapping the material distribution of a complex structure in an electron beam. J. Instrum., 16(1), P01010–33pp.
Abstract: The simulation and analysis of High Energy Physics experiments require a realistic simulation of the detector material and its distribution. The challenge is to describe all active and passive parts of large scale detectors like ATLAS in terms of their size, position and material composition. The common method for estimating the radiation length by weighing individual components, adding up their contributions and averaging the resulting material distribution over extended structures provides a good general estimate, but can deviate significantly from the material actually present. A method has been developed to assess its material distribution with high spatial resolution using the reconstructed scattering angles and hit positions of high energy electron tracks traversing an object under investigation. The study presented here shows measurements for an extended structure with a highly inhomogeneous material distribution. The structure under investigation is an End-of-Substructure-card prototype designed for the ATLAS Inner Tracker strip tracker – a PCB populated with components of a large range of material budgets and sizes. The measurements presented here summarise requirements for data samples and reconstructed electron tracks for reliable image reconstruction of large scale, inhomogeneous samples, choices of pixel sizes compared to the size of features under investigation as well as a bremsstrahlung correction for high material densities and thicknesses.
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Valdes-Cortez, C., Mansour, I., Rivard, M. J., Ballester, F., Mainegra-Hing, E., Thomson, R. M., et al. (2021). A study of Type B uncertainties associated with the photoelectric effect in low-energy Monte Carlo simulations. Phys. Med. Biol., 66(10), 105014–14pp.
Abstract: Purpose. To estimate Type B uncertainties in absorbed-dose calculations arising from the different implementations in current state-of-the-art Monte Carlo (MC) codes of low-energy photon cross-sections (<200 keV). Methods. MC simulations are carried out using three codes widely used in the low-energy domain: PENELOPE-2018, EGSnrc, and MCNP. Three dosimetry-relevant quantities are considered: mass energy-absorption coefficients for water, air, graphite, and their respective ratios; absorbed dose; and photon-fluence spectra. The absorbed dose and the photon-fluence spectra are scored in a spherical water phantom of 15 cm radius. Benchmark simulations using similar cross-sections have been performed. The differences observed between these quantities when different cross-sections are considered are taken to be a good estimator for the corresponding Type B uncertainties. Results. A conservative Type B uncertainty for the absorbed dose (k = 2) of 1.2%-1.7% (<50 keV), 0.6%-1.2% (50-100 keV), and 0.3% (100-200 keV) is estimated. The photon-fluence spectrum does not present clinically relevant differences that merit considering additional Type B uncertainties except for energies below 25 keV, where a Type B uncertainty of 0.5% is obtained. Below 30 keV, mass energy-absorption coefficients show Type B uncertainties (k = 2) of about 1.5% (water and air), and 2% (graphite), diminishing in all materials for larger energies and reaching values about 1% (40-50 keV) and 0.5% (50-75 keV). With respect to their ratios, the only significant Type B uncertainties are observed in the case of the water-to-graphite ratio for energies below 30 keV, being about 0.7% (k = 2). Conclusions. In contrast with the intermediate (about 500 keV) or high (about 1 MeV) energy domains, Type B uncertainties due to the different cross-sections implementation cannot be considered subdominant with respect to Type A uncertainties or even to other sources of Type B uncertainties (tally volume averaging, manufacturing tolerances, etc). Therefore, the values reported here should be accommodated within the uncertainty budget in low-energy photon dosimetry studies.
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Gimenez-Alventosa, V., Gimenez, V., & Oliver, S. (2021). PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE. Comput. Phys. Commun., 267, 108065–12pp.
Abstract: Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, standalone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming language and takes advantage of modern object-oriented technologies. In addition, PenRed offers the capability to read and process DICOM images as well as to construct and simulate image-based voxelized geometries, so as to facilitate its usage in medical applications. Our framework has been successfully verified against the original PENELOPE Fortran code. Furthermore, the implemented parallelism has been tested showing a significant improvement in the simulation time without any loss in precision of results. Program summary Program title: PenRed: Parallel Engine for Radiation Energy Deposition. CPC Library link to program files: https://doi .org /10 .17632/rkw6tvtngy.1 Licensing provision: GNU Affero General Public License (AGPL). Programming language: C++ standard 2011. Nature of problem: Monte Carlo simulations usually require a huge amount of computation time to achieve low statistical uncertainties. In addition, many applications necessitate particular characteristics or the extraction of specific quantities from the simulation. However, most available Monte Carlo codes do not provide an efficient parallel and truly modular structure which allows users to easily customise their code to suit their needs without an in-depth knowledge of the code system. Solution method: PenRed is a fully parallel, modular and customizable framework for Monte Carlo simulations of the passage of radiation through matter. It is based on the PENELOPE [1] code system, from which inherits its unique physics models and tracking algorithms for charged particles. PenRed has been coded in C++ following an object-oriented programming paradigm restricted to the C++11 standard. Our engine implements parallelism via a double approach: on the one hand, by using standard C++ threads for shared memory, improving the access and usage of the memory, and, on the other hand, via the MPI standard for distributed memory infrastructures. Notice that both kinds of parallelism can be combined together in the same simulation. Moreover, both threads and MPI processes, can be balanced using the builtin load balance system (RUPER-LB [30]) to maximise the performance on heterogeneous infrastructures. In addition, PenRed provides a modular structure with methods designed to easily extend its functionality. Thus, users can create their own independent modules to adapt our engine to their needs without changing the original modules. Furthermore, user extensions will take advantage of the builtin parallelism without any extra effort or knowledge of parallel programming. Additional comments including restrictions and unusual features: PenRed has been compiled in linux systems withg++ of GCC versions 4.8.5, 7.3.1, 8.3.1 and 9; clang version 3.4.2 and intel C++ compiler (icc) version 19.0.5.281. Since it is a C++11-standard compliant code, PenRed should be able to compile with any compiler with C++11 support. In addition, if the code is compiled without MPI support, it does not require any non standard library. To enable MPI capabilities, the user needs to install whatever available MPI implementation, such as openMPI [24] or mpich [25], which can be found in the repositories of any linux distribution. Finally, to provide DICOM processing support, PenRed can be optionally compiled using the dicom toolkit (dcmtk) [32] library. Thus, PenRed has only two optional dependencies, an MPI implementation and the dcmtk library.
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Jay, G., Arnault, P., & Debbasch, F. (2021). Dirac quantum walks with conserved angular momentum. Quantum Stud. Math. Found., 8, 419–430.
Abstract: A quantum walk (QW) simulating the flat (1+2)D Dirac equation on a spatial polar grid is constructed. Because fermions are represented by spinors, which do not constitute a representation of the rotation group SO(3), but rather of its double cover SU(2), the QW can only be defined globally on an extended spacetime where the polar angle extends from 0 to 4 pi. The coupling of the QW with arbitrary electromagnetic fields is also presented. Finally, the cylindrical relativistic Landau levels of the Dirac equation are computed explicitly and simulated by the QW.
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