| Home | << 1 2 3 4 5 6 7 8 9 >> |
|
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).
Keywords: proton therapy; GATE; Monte Carlo simulations; J-PET; medical imaging
|
|
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.
|
|
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.
|
|
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.
|
|
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.
Keywords: Quantum walks; Quantum simulation; Lattice field theory
|
|
ATLAS Collaboration(Aad, G. et al), Aparisi Pozo, J. A., Bailey, A. J., Cabrera Urban, S., Cardillo, F., Castillo, F. L., et al. (2021). Measurements of sensor radiation damage in the ATLAS inner detector using leakage currents. J. Instrum., 16(8), P08025–46pp.
Abstract: Non-ionizing energy loss causes bulk damage to the silicon sensors of the ATLAS pixel and strip detectors. This damage has important implications for data-taking operations, charged-particle track reconstruction, detector simulations, and physics analysis. This paper presents simulations and measurements of the leakage current in the ATLAS pixel detector and semiconductor tracker as a function of location in the detector and time, using data collected in Run 1 (2010-2012) and Run 2 (2015-2018) of the Large Hadron Collider. The extracted fluence shows a much stronger vertical bar z vertical bar-dependence in the innermost layers than is seen in simulation. Furthermore, the overall fluence on the second innermost layer is significantly higher than in simulation, with better agreement in layers at higher radii. These measurements are important for validating the simulation models and can be used in part to justify safety factors for future detector designs and interventions.
|
|
Asai, M., Cortes-Giraldo, M. A., Gimenez-Alventosa, V., Gimenez, V., & Salvat, F. (2021). The PENELOPE Physics Models and Transport Mechanics. Implementation into Geant4. Front. Physics, 9, 738735–20pp.
Abstract: A translation of the penelope physics subroutines to C++, designed as an extension of the Geant4 toolkit, is presented. The Fortran code system penelope performs Monte Carlo simulation of coupled electron-photon transport in arbitrary materials for a wide energy range, nominally from 50 eV up to 1 GeV. Penelope implements the most reliable interaction models that are currently available, limited only by the required generality of the code. In addition, the transport of electrons and positrons is simulated by means of an elaborate class II scheme in which hard interactions (involving deflection angles or energy transfers larger than pre-defined cutoffs) are simulated from the associated restricted differential cross sections. After a brief description of the interaction models adopted for photons and electrons/positrons, we describe the details of the class-II algorithm used for tracking electrons and positrons. The C++ classes are adapted to the specific code structure of Geant4. They provide a complete description of the interactions and transport mechanics of electrons/positrons and photons in arbitrary materials, which can be activated from the G4ProcessManager to produce simulation results equivalent to those from the original penelope programs. The combined code, named PenG4, benefits from the multi-threading capabilities and advanced geometry and statistical tools of Geant4.
|
|
Etxebeste, A., Dauvergne, D., Fontana, M., Letang, J. M., Llosa, G., Muñoz, E., et al. (2020). CCMod: a GATE module for Compton camera imaging simulation. Phys. Med. Biol., 65(5), 055004–17pp.
Abstract: Compton cameras are gamma-ray imaging systems which have been proposed for a wide variety of applications such as medical imaging, nuclear decommissioning or homeland security. In the design and optimization of such a system Monte Carlo simulations play an essential role. In this work, we propose a generic module to perform Monte Carlo simulations and analyses of Compton Camera imaging which is included in the open-source GATE/Geant4 platform. Several digitization stages have been implemented within the module to mimic the performance of the most commonly employed detectors (e.g. monolithic blocks, pixelated scintillator crystals, strip detectors...). Time coincidence sorter and sequence coincidence reconstruction are also available in order to aim at providing modules to facilitate the comparison and reproduction of the data taken with different prototypes. All processing steps may be performed during the simulation (on-the-fly mode) or as a post-process of the output files (offline mode). The predictions of the module have been compared with experimental data in terms of energy spectra, angular resolution, efficiency and back-projection image reconstruction. Consistent results within a 3-sigma interval were obtained for the energy spectra except for low energies where small differences arise. The angular resolution measure for incident photons of 1275 keV was also in good agreement between both data sets with a value close to 13 degrees. Moreover, with the aim of demonstrating the versatility of such a tool the performance of two different Compton camera designs was evaluated and compared.
Keywords: Monte Carlo; simulation; gamma imaging; Compton camera
|
|
Mertsch, P., Parimbelli, G., de Salas, P. F., Gariazzo, S., Lesgourgues, J., & Pastor, S. (2020). Neutrino clustering in the Milky Way and beyond. J. Cosmol. Astropart. Phys., 01(1), 015–23pp.
Abstract: The standard cosmological model predicts the existence of a Cosmic Neutrino Background, which has not yet been observed directly. Some experiments aiming at its detection are currently under development, despite the tiny kinetic energy of the cosmological relic neutrinos, which makes this task incredibly challenging. Since massive neutrinos are attracted by the gravitational potential of our Galaxy, they can cluster locally. Neutrinos should be more abundant at the Earth position than at an average point in the Universe. This fact may enhance the expected event rate in any future experiment. Past calculations of the local neutrino clustering factor only considered a spherical distribution of matter in the Milky Way and neglected the influence of other nearby objects like the Virgo cluster, although recent N-body simulations suggest that the latter may actually be important. In this paper, we adopt a back-tracking technique, well established in the calculation of cosmic rays fluxes, to perform the first three-dimensional calculation of the number density of relic neutrinos at the Solar System, taking into account not only the matter composition of the Milky Way, but also the contribution of the Andromeda galaxy and the Virgo cluster. The effect of Virgo is indeed found to be relevant and to depend non-trivially on the value of the neutrino mass. Our results show that the local neutrino density is enhanced by 0.53% for a neutrino mass of 10 meV, 12% for 50 meV, 50% for 100 meV or 500% for 300 meV.
|
|
Arnault, P., Macquet, A., Angles-Castillo, A., Marquez-Martin, I., Pina-Canelles, V., Perez, A., et al. (2020). Quantum simulation of quantum relativistic diffusion via quantum walks. J. Phys. A, 53(20), 205303–39pp.
Abstract: Two models are first presented, of a one-dimensional discrete-time quantum walk (DTQW) with temporal noise on the internal degree of freedom (i.e., the coin): (i) a model with both a coin-flip and a phase-flip channel, and (ii) a model with random coin unitaries. It is then shown that both these models admit a common limit in the spacetime continuum, namely, a Lindblad equation with Dirac-fermion Hamiltonian part and, as Lindblad jumps, a chirality flip and a chirality-dependent phase flip, which are two of the three standard error channels for a two-level quantum system. This, as one may call it, Dirac Lindblad equation, provides a model of quantum relativistic spatial diffusion, which is evidenced both analytically and numerically. This model of spatial diffusion has the intriguing specificity of making sense only with original unitary models which are relativistic in the sense that they have chirality, on which the noise is introduced: the diffusion arises via the by-construction (quantum) coupling of chirality to the position. For a particle with vanishing mass, the model of quantum relativistic diffusion introduced in the present work, reduces to the well-known telegraph equation, which yields propagation at short times, diffusion at long times, and exhibits no quantumness. Finally, the results are extended to temporal noises which depend smoothly on position.
|