The present contribution introduces an automated procedure for estimating the size and the shape of the effective focal spot of an X-ray source using a single 2D experimental image of a tungsten sphere. The proposed procedure is based on an iterative deconvolution scheme where the effective focal spot is estimated from an experimental image and a Digitally Reconstructed Radiography (DRR) model. The iterative scheme is only applied on small, automatically selected, regions of interest; allowing a dramatic reduction of the computation time. Moreover, another iterative scheme is used for accurately estimating the position of the sphere in the DRR model. This allows a simpler experimental setup for the acquisition of a 2D experimental image, as the position of the sphere need only to be known approximately. In order to assess the accuracy of the proposed procedure, sizes and shapes of effective focal spots were extracted from experimentally acquired cone-beam computed radiography (CR) images using X-ray sources with different focal spot sizes. These effective focal spots were subsequently used to deblur real-world radiographies using a fast deconvolution algorithm; showing that the proposed approach could significantly improve the resolution of CR images.

gVirtualXray (gVXR) is an open-source framework that relies on the Beer-Lambert law to simulate X-ray images in real time on a graphics processor unit (GPU) using triangular meshes. A wide range of programming languages is supported (C/C++, Python, R, Ruby, Tcl, C#, Java, and GNU Octave). Simulations generated with gVXR have been benchmarked with clinically realistic phantoms (i.e. complex structures and materials) using Monte Carlo (MC) simulations, real radiographs and real digitally reconstructed radiographs (DRRs), and X-ray computed tomography (CT). It has been used in a wide range of applications, including real-time medical simulators, proposing a new densitometric radiographic modality in clinical imaging, studying noise removal techniques in fluoroscopy, teaching particle physics and X-ray imaging to undergraduate students in engineering, and XCT to masters students, predicting image quality and artifacts in material science, etc. gVXR has also been used to produce a high number of realistic simulated images in optimisation problems and to train machine learning algorithms. This paper presents a comprehensive review of such applications of gVXR.

gVirtualXray (gVXR) is an open-source framework that relies on the Beer-Lambert law to simulate X-ray images in real time on a graphics processor unit (GPU) using triangular meshes. A wide range of programming languages is supported (C/C++, Python, R, Ruby, Tcl, C#, Java, and GNU Octave). Simulations generated with gVXR have been benchmarked with clinically realistic phantoms (i.e. complex structures and materials) using Monte Carlo (MC) simulations, real radiographs and real digitally reconstructed radiographs (DRRs), and X-ray computed tomography (CT). It has been used in a wide range of applications, including real-time medical simulators, proposing a new densitometric radiographic modality in clinical imaging, studying noise removal techniques in fluoroscopy, teaching particle physics and X-ray imaging to undergraduate students in engineering, and XCT to masters students, predicting image quality and artifacts in material science, etc. gVXR has also been used to produce a high number of realistic simulated images in optimization problems and to train machine learning algorithms. This paper presents applications of gVXR related to XCT.

Experimental ion mobility-mass spectrometry (IM-MS) results are often correlated to three-dimensional structures owing to theoretical chemistry calculations. The bottleneck of this approach is the need for accurate values, both experimentally and theoretically predicted. Here, we analyze experimental and theoretical collision cross-section (CCS) evolutions instead of interpreting absolute CCS values. Experimentally, the CCS trends of synthetic homopolymers are analyzed as a function of increasing degrees of polymerization (DP) for different charge states. Then, shape evolutions of modeled shape deformations yield theoretical CCS trends, calculated using new software called MoShade (projected area calculations). The shapes are modeled using computer-aided design software where we considered only geometric factors: no atoms, chemical potentials or interactions are taken into consideration to make the method orthogonal to classical methods for 3D shape assessments using time-consuming computational chemistry. We are able to correlate modeled shape evolutions to experimentally-obtained polymer CCS trends. We thus modeled the apparent volume or envelope of their ion-drift gas interactions as sampled by IM-MS. Moreover, the CCS of convex shapes could be directly related to their surface area. The relation seems to hold even for concave shapes which could be correlated to geometry-optimized structures of ions obtained by conventional computational chemistry methods. Modeling beads-on-a-string shape evolutions allows extracting precise dimension relations between two homopolymers, without modeling any chemical interactions.

The present article introduces an automated procedure to construct geometrical representative volume elements (RVE) of open‐foam cellular materials from computerized tomography (CT) images, with the final aim of generating meshable geometries usable in the finite element method (FEM) used in order to analyse their mechanical behavior. The methodology consists in growing and fitting a set of ellipsoids to each of the foam cells. These ellipsoids are seeded by local maxima of the distance to the struts obtained from computer tomography images. This methodology is thus fully voxel‐based and does not depend on any assumption about statistical distributions of the foam cells. Therefore, it is able to reproduce an accurate geometrical model of the foam's microstructure and its possible irregularities. Moreover, this procedure allows the processing of large 3D data sets that do not fit the random access memory (RAM) by slicing it into smaller independent chunks. The effectiveness of the proposed approach is illustrated by comparing it to FEM simulations for which meshes are obtained from a feature reconstruction approach. Both FEM simulations are then compared with experimental results of uniaxial compressions of an open foam.

It is well-known that the convergence rate of non-overlapping domain decomposition methods (DDMs) applied to the parallel finite-element solution of large-scale time-harmonic wave problems strongly depends on the transmission condition enforced at the interfaces between the subdomains. Transmission operators based on perfectly matched layers (PMLs) have proved to be well-suited for configurations with layered domain partitions. They are shown to be a good compromise between basic impedance conditions, which can lead to slow convergence, and computational expensive conditions based on the exact Dirichlet-to-Neumann (DtN) map related to the complementary of the subdomain. Unfortunately, the extension of the PML-based DDM for more general partitions with cross-points (where more than two subdomains meet) is rather tricky and requires some care. In this work, we present a non-overlapping substructured DDM with PML transmission conditions for checkerboard (Cartesian) decompositions that takes cross-points into account. In such decompositions, each subdomain is surrounded by PMLs associated to edges and corners. The continuity of Dirichlet traces at the interfaces between a subdomain and PMLs is enforced with Lagrange multipliers. This coupling strategy offers the benefit of naturally computing Neumann traces, which allows to use the PMLs as discrete operators approximating the exact Dirichlet-to-Neumann maps. Two possible Lagrange multiplier finite element spaces are presented, and the behavior of the corresponding DDM is analyzed on several numerical examples. (C) 2022 Elsevier B.V. All rights reserved.

GmshFem is an open source C++ finite element library based on the application programming interface of Gmsh. Both share the same design philosophy: to be fast, light and user-friendly. This paper presents the main principles of GmshFem, as well as some scalability results for high-order scalar and vector finite element assembly on multi-core architectures.

Disulfide bonds between cysteine residues are commonly involved in the stability of numerous peptides and proteins and are crucial for providing biological activities. In such peptides, the appropriate cysteine connectivity ensures the proper conformation allowing an efficient binding to their molecular targets. Disulfide bond connectivity characterization is still challenging and is a critical issue in the analysis of structured peptides/proteins targeting pharmaceutical or pharmacological utilizations. This study describes the development of new and fast gas-phase and in-solution electrophoretic methods coupled to mass spectrometry to characterize the cysteine connectivity of disulfide bonds. For this purpose, disulfide isomers of three peptides bearing two intramolecular disulfide bonds but different cysteine connectivity have been investigated. Capillary zone electrophoresis and ion mobility both coupled to mass spectrometry were used to perform the separation in both aqueous and gas phases, respectively. The separation efficiency of each technique has been critically evaluated and compared. Finally, theoretical calculations were performed to support and explain the experimental data based on the predicted physicochemical properties of the different peptides.

To alleviate the computational burden of the finite element method for thermal analyses involving conduction and radiation, this paper proposes an automatic conductive-radiative reduction process based on the clustering of a detailed mesh coming from a structural model for instance. The proposed method leads to a significant reduction of the number of radiative exchange factors (REFs) to compute and size of the corresponding matrix. It further keeps accurate conduction information by introducing the concept of physically meaningful super nodes. The REFs between the super nodes are computed through Monte Carlo ray-tracing on the partitioned mesh, preserving the versatility of the method. The resulting conductive-radiative reduced model is solved using standard iterative techniques and the detailed mesh temperatures can be recovered from the super nodes temperatures for further thermo-mechanical analysis. The proposed method is applied to a structural component of the Meteosat Third Generation mission and is benchmarked against ESATAN-TMS, the standard thermal analysis software used in the European aerospace industry.

The eXtended Finite Element Method (X-FEM), developed intensively in the past 15 years has become a competitive tool for the solution of problems with evolving discontinuities and singularities. In the present study, we focus on the application of X-FEM on frictionless contact problems in the context of fracture mechanics. A promising approach in the literature counting for this problem consists in applying Lagrangian multipliers. Meanwhile, as pointed out in Ji and Dolbow (Int J Numer Methods Eng 61: 2508-2535, 2004), a naive choice for Lagrangian multiplier space leads to oscillatory multipliers on the contact surface. This oscillation results from a non-uniform but mesh-dependent inf-sup condition. In this work, we adapt the algorithm proposed in Bechet et al. (Int J Numer Methods Eng 78: 931-954, 2009) on crack lip contact by discretizing the displacement field with both scalar and vector tip enrichment functions (Chevaugeon et al., Int J Multiscale Comput Eng 11: 597-631, 2013). The influence of the tip enrichment functions on the stability of the formulation is addressed. We show evidences that the vector enrichment functions can improve the conditioning of the problem without jeopardizing the simulation accuracy in the presence of contact.

This work deals with the various issues to keep all the capabilities of the CAE, with non-matching meshes. The geometric representation, the design of the functional space and the enforcement of boundary conditions are covered in the context the X-FEM, especially with solids embedded in a space of higher dimension. Several numerical examples are provided to illustrate the accuracy of the proposed approach.