Non-overlapping domain decomposition methods for three-dimensional cardiac reaction-diffusion models and applications

Recent advances in biotechnology and the availability of ever more powerful computers have led to the formulation of increasingly complex models at all levels of life sciences, in particular of cardiac electrophysiology. Multiscale modeling of the bioelectric activity of the heart, taking into account macroscopic (fiber architecture and anisotropy) and microscopic (cellular) features of the tissue, aim to develop predictive tools for future drug design and patient-specific therapies, using detailed and efficient three-dimensional solvers for the governing equations of tissue electrophysiology

Parallel accelerated cyclic reduction preconditioner for three-dimensional elliptic PDEs with variable coefficients

We present a robust and scalable preconditioner for the solution of large-scale linear systems that arise from the discretization of elliptic PDEs amenable to rank compression. The preconditioner is based on hierarchical low-rank approximations and the cyclic reduction method. The setup and application phases of the preconditioner achieve log-linear complexity in memory footprint and number of operations, and numerical experiments exhibit good weak and strong scalability at large processor counts in a distributed memory environment. Numerical experiments with linear systems that feature symmetry and nonsymmetry, definiteness and indefiniteness, constant and variable coefficients demonstrate the preconditioner applicability and robustness. Furthermore, it is possible to control the number of iterations via the accuracy threshold of the hierarchical matrix approximations and their arithmetic operations, and the tuning of the admissibility condition parameter. Together, these parameters allow for optimization of the memory requirements and performance of the preconditioner.Comment: 24 pages, Elsevier Journal of Computational and Applied Mathematics, Dec 201

KSPHPDDM and PCHPDDM: Extending PETSc with advanced Krylov methods and robust multilevel overlapping Schwarz preconditioners

[EN] Contemporary applications in computational science and engineering often require the solution of linear systems which may be of different sizes, shapes, and structures. The goal of this paper is to explain how two libraries, PETSc and HPDDM, have been interfaced in order to offer end-users robust overlapping Schwarz preconditioners and advanced Krylov methods featuring recycling and the ability to deal with multiple right-hand sides. The flexibility of the implementation is showcased and explained with minimalist, easy-to-run, and reproducible examples, to ease the integration of these algorithms into more advanced frameworks. The examples provided cover applications from eigenanalysis, elasticity, combustion, and electromagnetism.Jose E. Roman was supported by the Spanish Agencia Estatal de Investigacion (AEI) under project SLEPc-DA (PID2019-107379RB-I00)Jolivet, P.; Roman, JE.; Zampini, S. (2021). KSPHPDDM and PCHPDDM: Extending PETSc with advanced Krylov methods and robust multilevel overlapping Schwarz preconditioners. Computers & Mathematics with Applications. 84:277-295. https://doi.org/10.1016/j.camwa.2021.01.0032772958

BDDC preconditioners for virtual element approximations of the three-dimensional Stokes equations

The Virtual Element Method (VEM) is a novel family of numerical methods for approximating partial differential equations on very general polygonal or polyhedral computational grids. This work aims to propose a Balancing Domain Decomposition by Constraints (BDDC) preconditioner that allows using the conjugate gradient method to compute the solution of the saddle-point linear systems arising from the VEM discretization of the three-dimensional Stokes equations. We prove the scalability and quasi-optimality of the algorithm and confirm the theoretical findings with parallel computations. Numerical results with adaptively generated coarse spaces confirm the method's robustness in the presence of large jumps in the viscosity and with high-order VEM discretizations

Posterior Lamellar Graft Preparation: A Prospective Review from an Eye Bank on Current and Future Aspects

Descemet membrane endothelial keratoplasty (DMEK) is a corneal surgical technique which selectively replaces the damaged posterior part of the cornea with a healthy donor graft retaining the rest of the tissue intact. There is a need to validate and standardize the donor tissue before grafting due to certain issues that can lead to consequences such as graft failure due to poor endothelial cell count, higher mortality, detachment of the graft, or increased surgical expenses, time, and effort. Thus, prospective potential surgeons and eye banks should now aim at developing new improved surgical techniques in order to prepare the best suited, validated, precut, preloaded, and easy to transplant tissue to reduce pre- and postsurgical complications. This could be achieved by defining parameters like graft thickness, accepted mortality threshold of the endothelial cells, and behavior of grafts during preservation and transportation along with using more sophisticated instruments like microkeratome and femtosecond lasers for graft preparation. Thus, a rapport between the eye banks and the surgeons along with the advanced instruments can overcome this challenge to find the best possible solution for endothelial keratoplasty (EK)

Toward Performance-Portable PETSc for GPU-based Exascale Systems

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization.The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.Comment: 15 pages, 10 figures, 2 table

Substrate reduction therapy with Miglustat in pediatric patients with GM1 type 2 gangliosidosis delays neurological involvement: A multicenter experience

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The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5–11 December, to 17.5% (25/143 samples) in the week 12–18, to 65.9% (89/135 samples) in the week 19–25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased fromone in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons