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SCiMMA and SNEWS Collaborations(Baxter, A. L. et al), & Colomer, M. (2022). Collaborative experience between scientific software projects using Agile Scrum development. Softw.-Pract. Exp., 52, 2077–2096.
Abstract: Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.
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Aliaga, R. J., & Guirao, A. J. (2019). On the preserved extremal structure of Lipschitz-free spaces. Studia Math., 245(1), 1–14.
Abstract: We characterize preserved extreme points of the unit ball of Lipschitz-free spaces F (X) in terms of simple geometric conditions on the underlying metric space (X, d). Namely, the preserved extreme points are the elementary molecules corresponding to pairs of points p, q in X such that the triangle inequality d (p, q) <= d (p, r) + d (q, r) is uniformly strict for r away from p, q. For compact X, this condition reduces to the triangle inequality being strict. As a consequence, we give an affirmative answer to a conjecture of N. Weaver that compact spaces are concave if and only if they have no triple of metrically aligned points, and we show that all extreme points are preserved for several classes of compact metric spaces X, including Holder and countable compacta.
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Ferrer-Sanchez, A., Martin-Guerrero, J., Ruiz de Austri, R., Torres-Forne, A., & Font, J. A. (2024). Gradient-annihilated PINNs for solving Riemann problems: Application to relativistic hydrodynamics. Comput. Meth. Appl. Mech. Eng., 424, 116906–18pp.
Abstract: We present a novel methodology based on Physics-Informed Neural Networks (PINNs) for solving systems of partial differential equations admitting discontinuous solutions. Our method, called Gradient-Annihilated PINNs (GA-PINNs), introduces a modified loss function that forces the model to partially ignore high-gradients in the physical variables, achieved by introducing a suitable weighting function. The method relies on a set of hyperparameters that control how gradients are treated in the physical loss. The performance of our methodology is demonstrated by solving Riemann problems in special relativistic hydrodynamics, extending earlier studies with PINNs in the context of the classical Euler equations. The solutions obtained with the GA-PINN model correctly describe the propagation speeds of discontinuities and sharply capture the associated jumps. We use the relative l(2) error to compare our results with the exact solution of special relativistic Riemann problems, used as the reference ''ground truth'', and with the corresponding error obtained with a second-order, central, shock-capturing scheme. In all problems investigated, the accuracy reached by the GA-PINN model is comparable to that obtained with a shock-capturing scheme, achieving a performance superior to that of the baseline PINN algorithm in general. An additional benefit worth stressing is that our PINN-based approach sidesteps the costly recovery of the primitive variables from the state vector of conserved variables, a well-known drawback of grid-based solutions of the relativistic hydrodynamics equations. Due to its inherent generality and its ability to handle steep gradients, the GA-PINN methodology discussed in this paper could be a valuable tool to model relativistic flows in astrophysics and particle physics, characterized by the prevalence of discontinuous solutions.
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Villaescusa-Navarro, F. et al, & Villanueva-Domingo, P. (2022). The CAMELS Multifield Data Set: Learning the Universe's Fundamental Parameters with Artificial Intelligence. Astrophys. J. Suppl. Ser., 259(2), 61–14pp.
Abstract: We present the Cosmology and Astrophysics with Machine Learning Simulations (CAMELS) Multifield Data set (CMD), a collection of hundreds of thousands of 2D maps and 3D grids containing many different properties of cosmic gas, dark matter, and stars from more than 2000 distinct simulated universes at several cosmic times. The 2D maps and 3D grids represent cosmic regions that span similar to 100 million light-years and have been generated from thousands of state-of-the-art hydrodynamic and gravity-only N-body simulations from the CAMELS project. Designed to train machine-learning models, CMD is the largest data set of its kind containing more than 70 TB of data. In this paper we describe CMD in detail and outline a few of its applications. We focus our attention on one such task, parameter inference, formulating the problems we face as a challenge to the community. We release all data and provide further technical details at https://camels-multifield-dataset.readthedocs.io.
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Villaescusa-Navarro, F. et al, & Villanueva-Domingo, P. (2023). The CAMELS Project: Public Data Release. Astrophys. J. Suppl. Ser., 265(2), 54–14pp.
Abstract: The Cosmology and Astrophysics with Machine Learning Simulations (CAMELS) project was developed to combine cosmology with astrophysics through thousands of cosmological hydrodynamic simulations and machine learning. CAMELS contains 4233 cosmological simulations, 2049 N-body simulations, and 2184 state-of-the-art hydrodynamic simulations that sample a vast volume in parameter space. In this paper, we present the CAMELS public data release, describing the characteristics of the CAMELS simulations and a variety of data products generated from them, including halo, subhalo, galaxy, and void catalogs, power spectra, bispectra, Lya spectra, probability distribution functions, halo radial profiles, and X-rays photon lists. We also release over 1000 catalogs that contain billions of galaxies from CAMELS-SAM: a large collection of N-body simulations that have been combined with the Santa Cruz semianalytic model. We release all the data, comprising more than 350 terabytes and containing 143,922 snapshots, millions of halos, galaxies, and summary statistics. We provide further technical details on how to access, download, read, and process the data at .
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Liang, J., Singh, B., McCutchan, E. A., Dillmann, I., Birch, M., Sonzogni, A. A., et al. (2020). Compilation and Evaluation of Beta-Delayed Neutron Emission Probabilities and Half-Lives for Z > 28 Precursors. Nucl. Data Sheets, 168, 1–116.
Abstract: We present a compilation and evaluation of experimental beta-delayed neutron emission probabilities (P-n) and half-lives (T-1/2) for known or potential beta-delayed neutron precursors with atomic number Z > 28 (Cu-73 – Fr-233). This article includes the recommended values of both of these quantities, together with a compilation of experimental measurements when available. Some notable cases, as well as proposed standards for beta-delayed neutron measurements are also discussed. Evaluated data has also been compared to systematics using three different approaches. The literature cut-off date for this work is August 15, 2020.
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Dimitriou, P. et al, Tain, J. L., & Algora, A. (2021). Development of a Reference Database for Beta-Delayed Neutron Emission. Nucl. Data Sheets, 173, 144–238.
Abstract: Beta-delayed neutron emission is important for nuclear structure and astrophysics as well as for reactor applications. Significant advances in nuclear experimental techniques in the past two decades have led to a wealth of new measurements that remain to be incorporated in the databases. We report on a coordinated effort to compile and evaluate all the available beta-delayed neutron emission data. The different measurement techniques have been assessed and the data have been compared with semi-microscopic and microscopic-macroscopic models. The new microscopic database has been tested against aggregate total delayed neutron yields, time-dependent group parameters in 6-and 8-group re-presentation, and aggregate delayed neutron spectra. New recommendations of macroscopic delayed-neutron data for fissile materials of interest to applications are also presented.
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Valdes-Cortez, C., Niatsetski, Y., Perez-Calatayud, J., Ballester, F., & Vijande, J. (2022). A Monte Carlo study of the relative biological effectiveness in surface brachytherapy. Med. Phys., 49, 5576–5588.
Abstract: Purpose This work aims to simulate clustered DNA damage from ionizing radiation and estimate the relative biological effectiveness (RBE) for radionuclide (rBT)- and electronic (eBT)-based surface brachytherapy through a hybrid Monte Carlo (MC) approach, using realistic models of the sources and applicators. Methods Damage from ionizing radiation has been studied using the Monte Carlo Damage Simulation algorithm using as input the primary electron fluence simulated using a state-of-the-art MC code, PENELOPE-2018. Two Ir-192 rBT applicators, Valencia and Leipzig, one Co-60 source with a Freiburg Flap applicator (reference source), and two eBT systems, Esteya and INTRABEAM, have been included in this study implementing full realizations of their geometries as disclosed by the manufacturer. The role played by filtration and tube kilovoltage has also been addressed. Results For rBT, an RBE value of about 1.01 has been found for the applicators and phantoms considered. In the case of eBT, RBE values for the Esteya system show an almost constant RBE value of about 1.06 for all depths and materials. For INTRABEAM, variations in the range of 1.12-1.06 are reported depending on phantom composition and depth. Modifications in the Esteya system, filtration, and tube kilovoltage give rise to variations in the same range. Conclusions Current clinical practice does not incorporate biological effects in surface brachytherapy. Therefore, the same absorbed dose is administered to the patients independently on the particularities of the rBT or eBT system considered. The almost constant RBE values reported for rBT support that assumption regardless of the details of the patient geometry, the presence of a flattening filter in the applicator design, or even significant modifications in the photon energy spectra above 300 keV. That is not the case for eBT, where a clear dependence on the eBT system and the characteristics of the patient geometry are reported. A complete study specific for each eBT system, including detailed applicator characteristics (size, shape, filtering, among others) and common anatomical locations, should be performed before adopting an existing RBE value.
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Assam, I., Vijande, J., Ballester, F., Perez-Calatayud, J., Poppe, B., & Siebert, F. A. (2022). Evaluation of dosimetric effects of metallic artifact reduction and tissue assignment on Monte Carlo dose calculations for I-125 prostate implants. Med. Phys., 49, 6195–6208.
Abstract: Purpose Monte Carlo (MC) simulation studies, aimed at evaluating the magnitude of tissue heterogeneity in I-125 prostate permanent seed implant brachytherapy (BT), customarily use clinical post-implant CT images to generate a virtual representation of a realistic patient model (virtual patient model). Metallic artifact reduction (MAR) techniques and tissue assignment schemes (TAS) are implemented on the post-implant CT images to mollify metallic artifacts due to BT seeds and to assign tissue types to the voxels corresponding to the bright seed spots and streaking artifacts, respectively. The objective of this study is to assess the combined influence of MAR and TAS on MC absorbed dose calculations in post-implant CT-based phantoms. The virtual patient models used for I-125 prostate implant MC absorbed dose calculations in this study are derived from the CT images of an external radiotherapy prostate patient without BT seeds and prostatic calcifications, thus averting the need to implement MAR and TAS. Methods The geometry of the IsoSeed I25.S17plus source is validated by comparing the MC calculated results of the TG-43 parameters for the line source approximation with the TG-43U1S2 consensus data. Four MC absorbed dose calculations are performed in two virtual patient models using the egs_brachy MC code: (1) TG-43-based D-w,w-TG(43), (2) D-w,D-w-MBDC that accounts for interseed scattering and attenuation (ISA), (3) D-m,D-m that examines ISA and tissue heterogeneity by scoring absorbed dose in tissue, and (4) D-w,D-m that unlike D-m,D-m scores absorbed dose in water. The MC absorbed doses (1) and (2) are simulated in a TG-43 patient phantom derived by assigning the densities of every voxel to 1.00 g cm(-3) (water), whereas MC absorbed doses (3) and (4) are scored in the TG-186 patient phantom generated by mapping the mass density of each voxel to tissue according to a CT calibration curve. The MC absorbed doses calculated in this study are compared with VariSeed v8.0 calculated absorbed doses. To evaluate the dosimetric effect of MAR and TAS, the MC absorbed doses of this work (independent of MAR and TAS) are compared to the MC absorbed doses of different I-125 source models from previous studies that were calculated with different MC codes using post-implant CT-based phantoms generated by implementing MAR and TAS on post-implant CT images. Results The very good agreement of TG-43 parameters of this study and the published consensus data within 3% validates the geometry of the IsoSeed I25.S17plus source. For the clinical studies, the TG-43-based calculations show a D-90 overestimation of more than 4% compared to the more realistic MC methods due to ISA and tissue composition. The results of this work generally show few discrepancies with the post-implant CT-based dosimetry studies with respect to the D-90 absorbed dose metric parameter. These discrepancies are mainly Type B uncertainties due to the different I-125 source models and MC codes. Conclusions The implementation of MAR and TAS on post-implant CT images have no dosimetric effect on the I-125 prostate MC absorbed dose calculation in post-implant CT-based phantoms.
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Peppa, V., Thomson, R. M., Enger, S. A., Fonseca, G. P., Lee, C. N., Lucero, J. N. E., et al. (2023). A MC-based anthropomorphic test case for commissioning model-based dose calculation in interstitial breast 192-Ir HDR brachytherapy. Med. Phys., 50(7), 4675–4687.
Abstract: PurposeTo provide the first clinical test case for commissioning of Ir-192 brachytherapy model-based dose calculation algorithms (MBDCAs) according to the AAPM TG-186 report workflow. Acquisition and Validation MethodsA computational patient phantom model was generated from a clinical multi-catheter Ir-192 HDR breast brachytherapy case. Regions of interest (ROIs) were contoured and digitized on the patient CT images and the model was written to a series of DICOM CT images using MATLAB. The model was imported into two commercial treatment planning systems (TPSs) currently incorporating an MBDCA. Identical treatment plans were prepared using a generic Ir-192 HDR source and the TG-43-based algorithm of each TPS. This was followed by dose to medium in medium calculations using the MBDCA option of each TPS. Monte Carlo (MC) simulation was performed in the model using three different codes and information parsed from the treatment plan exported in DICOM radiation therapy (RT) format. Results were found to agree within statistical uncertainty and the dataset with the lowest uncertainty was assigned as the reference MC dose distribution. Data Format and Usage NotesThe dataset is available online at ,. Files include the treatment plan for each TPS in DICOM RT format, reference MC dose data in RT Dose format, as well as a guide for database users and all files necessary to repeat the MC simulations. Potential ApplicationsThe dataset facilitates the commissioning of brachytherapy MBDCAs using TPS embedded tools and establishes a methodology for the development of future clinical test cases. It is also useful to non-MBDCA adopters for intercomparing MBDCAs and exploring their benefits and limitations, as well as to brachytherapy researchers in need of a dosimetric and/or a DICOM RT information parsing benchmark. Limitations include specificity in terms of radionuclide, source model, clinical scenario, and MBDCA version used for its preparation.
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