Multiblock High Order Large Eddy Simulation of Powered Fontan Hemodynamics: Towards Computational Surgery

Children born with only one functional ventricle must typically undergo a series of three surgeries to obtain the so-called Fontan circulation in which the blood coming from the body passively flows from the Vena Cavae (VCs) to the Pulmonary Arteries (PAs) through the Total Cavopulmonary Connection (TCPC). The circulation is inherently inefficient due to the lack of a subpulmonary ventricle. Survivors face the risk of circulatory sequelae and eventual failure for the duration of their lives. Current efforts are focused on improving the outcomes of Fontan palliation, either passively by optimizing the TCPC, or actively by using mechanical support. We are working on a chronic implant that would be placed at the junction of the TCPC, and would provide the necessary pressure augmentation to re-establish a circulation that recapitulates a normal two-ventricle circulation. This implant is based on the Von Karman viscous pump and consists of a vaned impeller that rotates inside the TCPC. To evaluate the performance of such a device, and to study the flow features induced by the presence of the pump, Computational Fluid Dynamics (CFD) is used. CFD has become an important tool to understand hemodynamics owing to the possibility of simulating quickly a large number of designs and flow conditions without any harm for patients. The transitional and unsteady nature of the flow can make accurate simulations challenging. We developed and in-house high order Large Eddy Simulation (LES) solver coupled to a recent Immersed Boundary Method (IBM) to handle complex geometries. Multiblock capability is added to the solver to allow for efficient simulations of complex patient specific geometries. Blood simulations are performed in a complex patient specific TCPC geometry. In this study, simulations without mechanical assist are performed, as well as after virtual implantation of the temporary and chronic implants being developed. Instantaneous flow structures, hepatic factor distribution, and statistical data are presented for all three cases

accelerating wrf i/o performance with adios2 and network-based streaming

With the approach of Exascale computing power for large-scale High Performance Computing (HPC) clusters, the gap between compute capabilities and storage systems is growing larger. This is particularly problematic for the Weather Research and Forecasting Model (WRF), a widely-used HPC application for high-resolution forecasting and research that produces sizable datasets, especially when analyzing transient weather phenomena. Despite this issue, the I/O modules within WRF have not been updated in the past ten years, resulting in subpar parallel I/O performance. This research paper demonstrates the positive impact of integrating ADIOS2, a next-generation parallel I/O framework, as a new I/O backend option in WRF. It goes into detail about the challenges encountered during the integration process and how they were addressed. The resulting I/O times show an over tenfold improvement when using ADIOS2 compared to traditional MPI-I/O based solutions. Furthermore, the study highlights the new features available to WRF users worldwide, such as the Sustainable Staging Transport (SST) enabling Unified Communication X (UCX) DataTransport, the node-local burst buffer write capabilities and in-line lossless compression capabilities of ADIOS2. Additionally, the research shows how ADIOS2's in-situ analysis capabilities can be smoothly integrated with a simple WRF forecasting pipeline, resulting in a significant improvement in overall time to solution. This study serves as a reminder to legacy HPC applications that incorporating modern libraries and tools can lead to considerable performance enhancements with minimal changes to the core application.Comment: arXiv admin note: text overlap with arXiv:2201.0822

High order Large Eddy Simulation of unpowered and powered Fontan hemodynamics in idealized and patient specific geometries

Children born with univentricular heart disease typically must undergo three open heart surgeries within the first 2-3 years of life to eventually establish the Fontan circulation. In that case the single working ventricle pumps oxygenated blood to the body and blood returns to the lungs flowing passively through the Total Cavopulmonary Connection (TCPC) rather than being actively pumped by a subpulmonary ventricle. A mechanical pump inserted into this circulation providing a 3-5 mmHg pressure augmentation would reestablish bi-ventricular physiology serving as a bridge-to-recovery, bridge-to-transplant or destination therapy as a biventricular Fontan circulation. A Viscous Impeller Pump (VIP) situated in the center of the 4-way TCPC intersection is studied here. We hypothesized that Large Eddy Simulation (LES) using high-order numerical methods is needed to capture unsteady powered and unpowered Fontan hemodynamics. Inclusion of a mechanical pump into the CFD further complicates matters due to the need to account for rotating machinery. Validation of the code is provided for an Idealized Medical Device, as well as for idealized TCPC simulations. Multiblock capabilities are added to the solver to allow for easier setup of complex geometries. Fontan hemodynamics is studied for both Unpowered and Powered cases on both Idealized and Patient specific geometries. Models to estimate blood damage and improve boundary conditions are also proposed

Large eddy simulation of FDA’s idealized medical device

A hybrid large eddy simulation and immersed boundary method (IBM) computational approach is used to make quantitative predictions of flow field statistics within the Food and Drug Administration’s idealized medical device. An in-house code is used, hereafter (WenoHemo™), that combines high-order finite-difference schemes on structured staggered Cartesian grids with an IBM to facilitate flow over or through complex stationary or rotating geometries and employs a subgrid-scale turbulence model that more naturally handles transitional flows (Delorme et al., J Biomech 46:207–436, 2013). Predictions of velocity and wall shear stress statistics are compared with previously published experimental measurements from Hariharan et al. (J Biomech Eng 133:041002, 2011) for the four Reynolds numbers considered

A novel multiblock immersed boundary method for large eddy simulation of complex arterial hemodynamics

Computational fluid dynamics (CFD) simulations are becoming a reliable tool to understand hemodynamics, disease progression in pathological blood vessels and to predict medical device performance. Immersed boundary method (IBM) emerged as an attractive methodology because of its ability to efficiently handle complex moving and rotating geometries on structured grids. However, its application to study blood flow in complex, branching, patient-specific anatomies is scarce. This is because of the dominance of grid nodes in the exterior of the fluid domain over the useful grid nodes in the interior, rendering an inevitable memory and computational overhead. In order to alleviate this problem, we propose a novel multiblock based IBM that preserves the simplicity and effectiveness of the IBM on structured Cartesian meshes and enables handling of complex, anatomical geometries at a reduced memory overhead by minimizing the grid nodes in the exterior of the fluid domain. As pathological and medical device hemodynamics often involve complex, unsteady transitional or turbulent flow fields, a scale resolving turbulence model such as large eddy simulation (LES) is used in the present work. The proposed solver (here after referred as WenoHemo ), is developed by enhancing an existing in-house high-order incompressible flow solver that was previously validated for its numerics and several LES models by Shetty et al. (2010) [33]. In the present work, WenoHemoWenoHemo is systematically validated for additional numerics introduced, such as IBM and the multiblock approach, by simulating laminar flow over a sphere and laminar flow over a backward facing step respectively. Then, we validate the entire solver methodology by simulating laminar and transitional flow in abdominal aortic aneurysm (AAA). Finally, we perform blood flow simulations in the challenging clinically relevant thoracic aortic aneurysm (TAA), to gain insights into the type of fluid flow patterns that exist in pathological blood vessels. Results obtained from the TAA simulations reveal complex vortical and unsteady flow fields that need to be considered in designing and implanting medical devices such as stent graft

Diffuse Deformation and Surface Faulting Distribution from Submetric Image Correlation along the 2019 Ridgecrest, California, Ruptures

International audienceABSTRACT The 2019 Mw 6.4 and 7.1 Ridgecrest, California, earthquake sequence (July 2019) ruptured consecutively a system of high-angle strike-slip cross faults (northeast- and northwest-trending) within 34 hr. The complex rupture mechanism was illuminated by seismological and geodetic data, bringing forward the issue of the interdependency of the two fault systems both at depth and at the surface, and of its effect on the final surface displacement pattern. Here, we use high-resolution (WorldView and Pleiades) optical satellite image correlation to measure the near-fault horizontal and vertical surface displacement fields at 0.5 m ground resolution for the two earthquakes. We point out significant differences with previous geodetic- and geologic-based measurements, and document the essential role of distributed faulting and diffuse deformation in producing the observed surface displacement patterns. We derive strain fields from the horizontal displacement maps, and highlight the predominant role of rotation and shear strain in the surface rupture process. We discuss the segmentation of the rupture based on the fault geometry and along-strike slip variations. We also image several northeast-trending faults with similar orientation to the deeply embedded shear fabric identified in aftershock studies, and show that these cross faults are present all along the rupture, including at a scale <100 m. Finally, we compare our results to kinematic slip inversions, and show that the surface diffuse deformation is primarily associated with areas of shallow slip deficit; however, this diffuse deformation cannot be explained using elastic modeling. We conclude that inelastic processes play an important role in contributing to the total surface deformation associated with the 2019 Ridgecrest sequence

Measurement of ground displacement from optical satellite image correlation using the free open-source software MicMac

International audienceImage correlation is one of the most efficient techniques to determine horizontal ground displacements due to earthquakes, landslides, ice flows or sand dune migrations. Analyzing these deformations allows a better understanding of the causes and mechanisms of the events. By using sub-pixel correlation on before- and after-event ortho-images obtained from high resolution satellite images it is possible to compute the displacement field with high planimetric resolution. In this paper, we focus on measuring the ground displacements due to seismotectonic events. The three sub-pixel correlators used are: COSI-Corr - developed by Caltech, a free, closed-source correlator, dependent on commercial software (ENVI) and widely used by the geoscience community for measuring ground displacement; Medicis - developed by CNES, also a closed-source correlator capable of measuring this type of deformation; and MicMac - developed by IGN, the free open-source correlator we study and tune for measuring fine ground displacements. We measured horizontal ground deformation using these three correlators on SPOT images in three study cases: the 2001 Kokoxili earthquake, the 2005 dyke intrusion in the Afar depression and the 2008 Yutian earthquake

A simple and efficient incompressible Navier-Stokes solver for unsteady complex geometry flows on truncated domains

Incompressible Navier-Stokes solvers based on the projection method often require an expensive numerical solution of a Poisson equation for a pressure-like variable. This often involves linear system solvers based on iterative and multigrid methods which may limit the ability to scale to large numbers of processors. The artificial compressibility method (ACM) [6] introduces a time derivative of the pressure into the incompressible form of the continuity equation creating a coupled closed hyperbolic system that does not require a Poisson equation solution and allows for explicit time-marching and localized stencil numerical methods. Such a scheme should theoretically scale well on large numbers of CPUs, GPU'\u80\u99s, or hybrid CPU-GPU architectures. The original ACM was only valid for steady flows and dual-time stepping was often used for time-accurate simulations. Recently, Clausen [7] has proposed the entropically damped artificial compressibility (EDAC) method which is applicable to both steady and unsteady flows without the need for dual-time stepping. The EDAC scheme was successfully tested with both a finite-difference MacCormack'\u80\u99s method for the two-dimensional lid driven cavity and periodic double shear layer problem and a finite-element method for flow over a square cylinder, with scaling studies on the latter to large numbers of processors. In this study, we discretize the EDAC formulation with a new optimized high-order centered finite-difference scheme and an explicit fourth-order Runge-\u80\u93Kutta method. This is combined with an immersed boundary method to efficiently treat complex geometries and a new robust outflow boundary condition to enable higher Reynolds number simulations on truncated domains. Validation studies for the Taylor-\u80\u93Green Vortex problem and the lid driven cavity problem in both 2D and 3D are presented. An eddy viscosity subgrid-scale model is used to enable large eddy simulations for the 3D cases. Finally, an application to flow over a sphere is presented to highlight the boundary condition and performance comparisons to a traditional incompressible Navier-\u80\u93Stokes solver is shown for the 3D lid driven cavity. Overall, the combined EDAC formulation and discretization is shown to be both effective and affordable.Funding agencies: Rosenblatt Chair within the faculty of Mechanical Engineering; Zeff Fellowship Trust</p

Evolution of the off-fault deformation of strike-slip faults in a sand-box experiment

International audienceSurface deformation associated with strike-slip faults can be distributed in space, with deformation located either along the primary fault strand or around it and referred to as off-fault deformation (OFD). Fault displacement hazard evaluation require to identify and estimate surface slip rates along active fault strands. We calculate the horizontal and vertical displacement of the analogue models surfaces with optical image correlation and photogrammetry, to investigate the OFD's development with increasing cumulative deformation. The criterion uses the gradient of the horizontal displacement norm perpendicular to the basal fault. Below 0.005 (noise level), there is no deformation, up to 0.03, it is off-fault-deformation, above 0.03, it is on-fault. We confirm previous observations made on analogue models that the surface deformation starts with a broad diffuse deformation, then produces fault strands alternating with relay zones that may be abandoned and reactivated. OFD is located first between Riedels, then between synthetic shears, and finally takes place in the relay zones. We also show that the OFD initially accommodates 100% of the applied slip (no faults), then decreases abruptly during the Riedels stage down to 20 to 30% to finally remain stable for the rest of the experiment. The abandonment and reactivation of the relay zones has the consequence of maintaining the OFD ratio on a stable value. Our experiments show that, like the OFD ratio, the width of the fault zone decreases with cumulative displacement to reach a stable value. Consequently, the OFD is correlated with this fault zone width and its geometric complexities. The ratios of OFD observed in this study are also consistent with measurements of OFD made on seven natural faults that exhibit different cumulative displacements. Hence our models suggest that strike-slip faults will never reach a continuous, linear geometry, and will always maintain a minimum amount of OFD

A Simple Biogeochemical Process Removing Arsenic from a Mine Drainage Water

International audienceArsenic is a toxic element commonly found in mining environments. The present study aimed to determine the influence of the indigenous bacterial population on the biogeochemical evolution of arsenic concentration in a mine drainage water. Biological As(III)-oxidizing activity was detected in diverse micro-environments along the water stream, from the source to the discharge point. Laboratory experiments showed that the bacterial population promoted As(III) and Fe(II) oxidation in conditions close to those of the site, i.e., temperature, water composition and oxygen availability. Immobilization of bacteria on pozzolana in a column bioreactor increased oxidation rates compared to on-site natural conditions: As concentration in the bioreactor outlet was less than 50 μg L −1 , whereas on-site total As concentration at the discharge point is close to 100 μg L −1 . The highest As(III) removal rate in the inoculated column reached 1900 μg L −1 h −1 and As(III) removal rate in the non-inoculated blank column was 42 μg L −1 h −1 . Two strains of As(III)-oxidizing bacteria, related to Variovorax paradoxus and Leptothrix cholodnii, were respectively isolated from a laboratory reactor and directly from site sludge. A diverse population of bacteria affiliated to nine phylogenetic groups belonging to the Proteobacteria and to the Bacteroidetes was identified in a laboratory reactor by molecular analyses of 16S rRNA genes. Amongst these, microorganisms already known to be potentially responsible for As(III) or Fe(II) oxidation, as well as for As(V) reduction co-existed: they included members of the genera Gallionella, Pseudomonas, Ralstonia, Sphingomonas, Methylobacterium and Methylophilus. On-site experiments confirmed the laboratory results, i.e. the removal of As from the contaminated effluent, and a passive on site treatment is currently developed for improving the quality of the discharged water