Hypersonic Shock Wave-Boundary Layer Interaction on a Cone-Slice-Wedge Model in a Shock Tunnel
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Wagner, Justin Lawrence [Sandia National Laborator↗
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Results for “slicing”
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Multiple-slice simulations of coherent electron cooling performance with low beam current
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43 PARTICLE ACCELERATORS↗
Hypersonic Shock Wave-Boundary Layer Interaction Experiments on a Cone-Slice-Ramp over a Range of Enthalpies
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Wagner, Justin Lawrence [Sandia National Laborator↗
Organotypic platform for studying cancer cell metastasis
Highlights: • Liver and brain slices can be stable, realistic in vitro 3D models. • Cell stiffness and adhesion to the tissue play determinant roles in cellular invasion in 3D. • MEK inhibitors can lead to increased cell stiffness and adhesion forces, and consequently reduced cancer cell invasion. • MDA-MB-231 breast cancer cells migrate faster and deeper into brain tissue compared to liver tissue. Metastasis is the leading cause of mortality in cancer patients. To migrate to distant sites, cancer cells would need to adapt their behaviour in response to different tissue environments. Thus, it is essential to study this process in models that can closely replicate the tumour microenvironment. Here, we evaluate the use of organotypic liver and brain slices to study cancer metastasis. Morphological and viability parameters of the slices were monitored daily over 3 days in culture to assess their stability as a realistic 3D tissue platform for in vitro metastatic assays. Using these slices, we evaluated the invasion of MDA-MB-231 breast cancer cells and of a subpopulation that was selected for increased motility. We show that the more aggressive invasion of the selected cells likely resulted not only from their lower stiffness, but also from their lower adhesion to the surrounding tissue. Different invasion patterns in the brain and liver slices were observed for both subpopulations. Cells migrated faster in the brain slices (with an amoeboid-like mode) compared to in the liver slices (where they migrated with mesenchymal or collective migration-like modes). Inhibition of the Ras/MAPK/ERK pathway increased cell stiffness and adhesion forces, which resulted in reduced invasiveness. These results illustrate the potential for organotypic tissue slices to more closely mimic in vivo conditions during cancer cell metastasis than most in vitro models.
60 APPLIED LIFE SCIENCES↗
2.5D Super-Resolution Approaches for X-Ray Computed Tomography-Based Inspection of Additively Manufactured Parts
X-ray computed tomography (XCT) is a key tool in non-destructive evaluation of additively manufactured (AM) parts, allowing for internal inspection and defect detection. Despite its widespread use, obtaining high-resolution CT scans can be extremely time consuming. This issue can be mitigated by performing scans at lower resolutions; however, reducing the resolution compromises spatial detail, limiting the accuracy of defect detection. Super-resolution algorithms offer a promising solution for overcoming resolution limitations in XCT reconstructions of AM parts, enabling more accurate detection of defects. While 2D super-resolution methods have demonstrated state-of-the-art performance on natural images, they tend to under-perform when directly applied to XCT slices. On the other hand, 3D super-resolution methods are computationally expensive, making them infeasible for large-scale applications. To address these challenges, we propose a 2.5D super-resolution approach tailored for XCT of AM parts. Our method enhances the resolution of individual slices by leveraging multi-slice information from neighboring 2D slices without the significant computational overhead of full 3D methods. Specifically, we use neighboring low-resolution slices to super-resolve the center slice, exploiting inter-slice spatial context while maintaining computational efficiency. This approach bridges the gap between 2D and 3D methods, offering a practical solution for high-throughput defect detection in AM parts.
Sullivan, Haley↗
Few-view computed tomography reconstruction using deep neural network inference
A system for generating 2D slices of a 3D image of a target volume is provided. The system receives a target sinogram collected during a computed tomography scan of the target volume. The system inputs the target sinogram to a convolutional neural network (CNN) to generate predicted 2D slices of the 3D image. The CNN is trained using training 2D slices of training 3D images. The system initializes 2D slices to the predicted 2D slices. The system reconstructs 2D slices of the 3D image from the target sinogram and the initialized 2D slices.
Kim, Hyojin↗
Improving ICARUS Track Reconstruction Algorithms
The ICARUS experiment is part of the Short-Baseline Neutrino (SBN) program at Fermilab. The main goal of the experiment is to investigate the possibility of sterile neutrinos in the O(1 eV) mass region and provide clarification of the anomaly detected from the Liquid Scintillator Neutrino Detector (LSND) and MiniBooNE experiments. The ICARUS-T600 detector is a Liquid Argon Time Projection Chamber (LAr-TPC), that can provide excellent 3D imaging and calorimetric reconstruction of any ionizing particles. This detection technique allows a detailed study of neutrino interactions, spanning a wide energy spectrum (from a few keV to several hundreds of GeV). The detector consists of two identical adjacent modules, filled with a total of 760 tons of ultra-pure liquid argon. Each module houses two LAr-TPCs separated by a common cathode with a maximum drift distance of 1.5 m, equivalent to about 1 ms drift time for the nominal $500$ V/m electric drift field. The anode is made of three parallel wire planes positioned 3 mm apart, where the stainless-steel wires are oriented on each plane at a different angle with respect to the horizontal direction ($+60^\degree$,$-60^\degree$,$0^\degree$). The first two planes (Induction 1 and Induction 2) provide a non-destructive charge measurement, whereas the ionization charge is fully collected by the last collection plane. In total, 53248 wires with a 3 mm pitch and length up to 9 m are installed in the detector. In the first stage of the reconstruction, segments of waveforms corresponding to physical signals (hits) are searched for in the deconvolved wire waveform with a threshold-based hit-finding algorithm. Each hit is then fitted with a Gaussian, whose area is proportional to the number of drift electrons generating the signal. In the second stage of the reconstruction, hits are passed as input to Pandora, a framework software composed of different pattern recognition algorithms, that performs a 3D reconstruction of the full image recorded in the collected event, including the identification of interaction vertices and tracks and showers inside the TPC. These are organized into a hierarchical structure (called slice) of particles generated starting from a primary interaction vertex. In some cases, related to the inefficiencies in the hit detection or excessive deflection of the particle trajectory, Pandora breaks the particle's track into two or more smaller pieces and considers each piece as an independent track. We studied this phenomenon focusing on primary muons from ν_μ CC interactions contained in a single module with a track at least 20 cm long, to exclude delta rays. The study determined that about $7-8\%$ of the muon tracks are broken. Approximately $80\%$ of the times, Pandora assigns all segments of the track to the same slice (intra-slice track split), while in the remaining $20\%$ of the cases, one of the segments is associated with another slice (extra-slice track split). To mitigate this phenomenon, we designed an algorithm that detects and stitches the tracks broken by Pandora for the intra-slice split. In Monte Carlo simulations, the algorithm showed an efficiency exceeding $80\%$ and a purity exceeding $93\%$.
Ricci, Alessandro Maria [Pisa U.; INFN, Pisa] (ORC↗
Subduction, Underplating, and Return Flow Recorded in the Cycladic Blueschist Unit Exposed on Syros, Greece
Exhumed high-pressure/low-temperature (HP/LT) metamorphic rocks provide insights into deep (~20–70 km) subduction interface dynamics. On Syros Island (Cyclades, Greece), the Cycladic Blueschist Unit preserves blueschist-to-eclogite facies oceanic- and continental-affinity rocks that record the structural and thermal evolution linked to Eocene subduction. Despite decades of research, the metamorphic and deformation history (P-T-D) and timing of subduction and exhumation are matters of ongoing discussion. We suggest that Syros comprises three coherent tectonic slices and that each slice underwent subduction, underplating, and syn-subduction return flow along similar P-T trajectories, but at progressively younger times. Subduction and exhumation are distinguished by lineations and ductile fold axis orientations, and are kinematically consistent with previous studies that document top-to-the-S-SW shear (prograde-to-peak subduction), top-to-the-NE shear (blueschist facies exhumation), and then E-W coaxial stretching (greenschist facies exhumation). Amphibole zonations record cooling during decompression, indicating return flow above a cold slab. Multi-mineral Rb-Sr isochrons and compiled metamorphic geochronology show that the three slices record distinct stages of peak subduction (53–52, ~50, and 45 Ma) that young with structural depth. Retrograde blueschist and greenschist facies fabrics span ~50–40 and ~43–20 Ma, respectively, and also young with structural depth. Synthesized data sets support a revised tectonic framework for Syros, involving subduction of structurally distinct coherent slices and simultaneous return flow of previously accreted tectonic slices in the subduction channel shear zone. Distributed, ductile, dominantly coaxial return flow in an Eocene-Oligocene subduction channel proceeded at rates of ~1.5–5 mm/yr and accommodated ~80% of the total exhumation of this HP/LT complex.
58 GEOSCIENCES↗
A novel approach for adaptive skeleton toolpath generation
Industry 4.0 is revolutionizing manufacturing through the integration of automation and real-time data sharing in cyber-physical systems. At the forefront of this revolution is large-format additive manufacturing. In large-format printing, parts are often designed to be an even number of beads wide to produce a completely dense part. However, voids can still arise. This is often due to the part not being an even number of bead widths wide in some areas, or in geometry containing acute angles, as the process of generating closed contours cannot completely fill the space. Voids can be tolerated in smaller models, but in large-format additive manufacturing they may cause mechanical defects. To fill these voids, open loop paths called skeletons are often used, but they are typically limited by the physical constraints defined in the slicing software. To address this, researchers at Oak Ridge National Laboratory have extended skeleton toolpaths via an adaptive methodology. These adaptive skeletons were found to better fill void spaces through manipulation of physical parameters of the build process and were calculated as part of the slicing process.
42 ENGINEERING↗
Schrödinger evolution of two-dimensional black holes
This paper systematically treats the evolving quantum state for two-dimensional black holes, with particular focus on the CGHS model, but also elucidating features generalizing to higher dimensions. This is done in Schrödinger picture(s), to exhibit the dynamic evolution of the state at intermediate times. After a review of classical solutions, also connecting to descriptions of higher-dimensional black holes, it overviews the canonical quantum treatment of the full evolution, including gravitational dynamics. Derived in an approximation to this, following conversion to “perturbation picture”, is the evolution of the quantum matter on the background geometry. Features of the evolving matter state are described, based on choice of a time slicing to put the evolution into ADM form. The choices of slicing as well as coordinates on the slices result in different quantum “pictures” for treating the evolution. If such a description is based on smooth trans-horizon slices, that avoids explicit reference to ultra-planckian modes familiar from traditional treatments, and exhibits the Hawking excitations as emerging from a “quantum atmosphere” with thickness comparable to the inverse temperature. Detailed study of the state exhibits the entanglement structure between Hawking quanta and the partner excitations inside the black hole, and the corresponding “missing information”. This explicit description also allows direct study of the evolution and features, e.g. as seen by infalling observers, of these partner excitations, helping to address various puzzles with them. Explicit treatment of the evolving state, and its extension to higher dimensions, provides further connections to information theory and a starting point for study of corrections that can unitarize evolution, arising from new quantum gravity effects — whether wormholes or something entirely different.
2D Gravity↗
The g-code file
The slicing process for additive manufacturing (AM) involves many steps, including slicing the object to be printed and fitting toolpaths to each resulting layer. The toolpaths define the trajectories that the machine must follow during printing to construct the object. Once the slicing is complete and all toolpaths have been found and properly planned, this data must be transferred to the 3D printer in a way the printer can use to construct the object. This is achieved by exporting a file, usually a g-code file, from the slicing software. The g-code file is a text-based file that contains instructions for the machine, controlling the system and defining the motions for each toolpath. The file, which often contains thousands of lines of code, is mostly composed of numbers that command positions for axis motions. This chapter will outline the contents of a g-code file, discuss various commands and their implementation, then provide example codes and files for object construction.
Roschli, Alex↗
Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types
Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.
Soil microbial biomass↗
Equilibrium core modeling of a pebble bed reactor similar to the Xe-100 with SCALE
As the nuclear industry moves towards licensing and constructing advanced reactors, new attention has been focused on the advanced reactor designs that have past operational experience, such as pebble-bed high-temperature gas-cooled reactors (PB-HTGRs). Pebble-bed reactor designs have many advantages, such as their higher operating temperatures and online refueling capabilities. However, high-fidelity computational modeling of pebble-bed reactor designs, from reactor startup to operation at equilibrium, is more challenging compared to conventionally fueled reactors due to the continuous movement of the fuel pebbles through the reactor during operation. In previous work at Oak Ridge National Laboratory (ORNL), the SCALE Leap-In method for Cores at Equilibrium (SLICE) was developed around tools within the SCALE code system. This iterative method can effectively generate pebble-bed reactor zone-wise fuel inventories at equilibrium core operation within a reasonable computational time. The objective of this work was to further verify the ORNL SLICE method and to investigate the impact of considering temperature profiles during the application of the method. The SLICE method was applied to a modular high-temperature gas-cooled reactor design based upon publicly available design specifications of the Xe-100 pebble-bed reactor. Upon comparing the results from the SLICE method to published literature, the differences in the eigenvalue k effective were on the order of several hundred pcm (percent millirho). To investigate one possible cause of these differences, a study looking at the sensitivity of the full-core equilibrium k effective and discharge nuclide inventory to temperature was performed by developing equilibrium cores of two additional temperature profiles. From this temperature study, differences on the order of hundreds of pcm for the full-core equilibrium k effective , and up to 15% difference for the discharge inventories were found. In conclusion, these results indicated the strong dependence on temperature that needs to be considered for future work in equilibrium modeling of PB-HTGRs.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Response of hypoxia to future climate change is sensitive to methodological assumptions
Climate-induced changes in hypoxia are among the most serious threats facing estuaries, which are among the most productive ecosystems on Earth. Future projections of estuarine hypoxia typically involve long-term multi-decadal continuous simulations or more computationally efficient time slice and delta methods that are restricted to short historical and future periods. We make a first comparison of these three methods by applying a linked terrestrial–estuarine model to the Chesapeake Bay, a large coastal-plain estuary in the eastern United States. Results show that the time slice approach accurately captures the behavior of the continuous approach, indicating a minimal impact of model memory. However, increases in mean annual hypoxic volume by the mid-twenty-first century simulated by the delta approach (+ 19%) are approximately twice as large as the time slice and continuous experiments (+ 9% and + 11%, respectively), indicating an important impact of changes in climate variability. Our findings suggest that system memory and projected changes in climate variability, as well as simulation length and natural variability of system hypoxia, should be considered when deciding to apply the more computationally efficient delta and time slice methods.
54 ENVIRONMENTAL SCIENCES↗
Emittance preservation for the electron arm in a single PWFA-LC stage using quasi-adiabatic plasma density ramp matching sections
Plasma-based acceleration (PBA) is being considered for a next generation linear collider (LC). In some PBA-LC designs for the electron arm, the extreme beam parameters are expected to trigger background ion motion within the witness beam, which can lead to longitudinally varying nonlinear focusing forces and result in an unacceptable emittance growth of the beam. To mitigate this, we propose to use quasi-adiabatic plasma density ramps as matching sections at the entrance and exit of each stage. We match the witness electron beam to the low density plasma entrance, where the beam initially has a large matched spot size so the ion motion effects are relatively small. As the beam propagates in the plasma density upramp, it is quasi-adiabatically focused, and its distribution maintains a non-Gaussian equilibrium distribution in each longitudinal slice throughout the process, even when severe ion collapse has occurred. This only causes small amounts of slice emittance growth. The phase mixing between slices with different betatron frequencies leads to additional projected emittance growth within the acceleration stage. A density downramp at the exit of an acceleration section can eliminate much of the slice and projected emittance growth as the beam and ion motion adiabatically defocuses and decreases, respectively. Simulation results from QuickPIC with Azimuthal Decomposition show that within a single acceleration stage with a 25 GeV energy gain, this concept can limit the projected emittance growth to only ∼2% for a 25 GeV, 100 nm emittance witness beam and ∼20% for a 100 GeV, 100 nm normalized emittance witness beam. The trade-off between the adiabaticity of the plasma density ramp and the initial ion motion at the entrance for a given length of the plasma density ramp is also discussed.
Physics↗
Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the statistical support for transmission occurring in different possible time slices. We compared our time-slice model results to previously described methods: a tree-based logical transmission interval, a simple parsimony-like rules-based method, and a more complex coalescent model. Across simulations with multiple transmitted lineages, different transmission times relative to the source’s infection, and different sampling times relative to transmission, we found that overall our time-slice model provided accurate and narrower estimates of the time of transmission. We also identified situations when transmission time or direction was difficult to estimate by any method, particularly when transmission occurred long after the source was infected and when sampling occurred long after transmission. Applying our model to real HIV transmission pairs showed some agreement with facts known from the case investigations. We also found, however, that uncertainty on the inferred transmission time was driven more by uncertainty from time calibration of the phylogeny than from the model inference itself. Encouragingly, comparable performance of the Markov time-slice model and the coalescent model—which make use of different information within a tree—suggests that a new method remains to be described that will make full use of the topology and node times for improved transmission time inference.
59 BASIC BIOLOGICAL SCIENCES↗
Seismic response to paleo-sand dunes in the Nugget Sandstone Formation, southwestern Wyoming
We have analyzed a 3D seismic survey acquired for a carbon sequestration project on top of the Moxa Arch in southwestern Wyoming. We observed a zone of discontinuous reflectors on vertical slices of seismic amplitude volume, whereas, the northwest–southeast lineations were observed on the time slices. We performed a seismic to well tie that suggested that the lineations occur within the Nugget Sandstone. The Nugget Sandstone is an eolian sandstone deposit of Early Jurassic age, deposited as a subtropical dune field, and equivalent to the Navajo Sandstone of southwestern Utah. Petrophysical analysis indicates that the Nugget Sandstone is dominated by clean sandstone (70%–80%), whereas evaporites, including halite and anhydrite, are present in certain zones. Previous outcrop studies on the Navajo Sandstone indicate the wind direction to be predominantly northeast–southwest. Seismic attributes, including coherence and curvature, displayed on stratal slices within the Nugget Sandstone interval indicate the presence of lineations in the northwest–southeast direction with irregular spacing. These lineations are approximately perpendicular to the inferred dominant wind direction. We computed the dominant wind direction from the average azimuth of the lineations as seen on the curvature attribute in the Nugget Sandstone interval. Geological feature: Eolian sand dunes with interdunal evaporites Seismic appearance: Parallel lineations with irregular spacing on seismic attribute horizon slices Alternative interpretations: Canyons at continental slopes; slope failures Features with a similar appearance: Marine bars; contourites Formation: The Nugget Sandstone — equivalent to the Navajo Sandstone Age: Early Jurassic Location: Moxa Arch, Wyoming Seismic data: Obtained by the University of Wyoming with U.S. DOE funding Contributors: Dhruv Agrawal, Brady Lujan, Sumit Verma, Shuvajit Bhattacharya, and Subhashis Mallick Analysis tools: Coherence and curvature attributes; seismic inversion; petrophysical inversion
Geochemistry & Geophysics↗
Modeling and Simulation of Xe-100-type Pebble Bed Gas-Cooled Reactor with SCALE
The US Department of Energy (DOE) announced the Advanced Reactor Demonstration Program (ARDP) to accelerate the deployment of advanced reactor concepts. Awardees of ARDP funds are expected to demonstrate the operation of an advanced reactor within 7 years of receiving the award. X-Energy’s advanced reactor concept, the Xe-100, was selected as one of two advanced reactor concepts to receive funding to demonstrate the operation of its high-temperature gas-cooled pebble-bed reactor before the end of this decade. As a result of this push to bring advanced reactors to maturation and commercialization, transition and deployment scenario studies are being performed under the Systems Analysis and Integration (SA&I) campaign within the DOE Office of Nuclear Energy (DOE-NE) to evaluate the transition of the current US commercial fleet of light-water reactors (LWRs) to a future fleet of advanced reactors consisting of a mix of ARDP type reactor concepts and advanced LWRs. To accurately evaluate the front- and back-end resource requirements, it is important to perform reactor physics calculations to determine the discharge burnup and isotopic content, fuel residence time, as well as other parameters. For this purpose, a summer project funded by the SA&I campaign allowed for the setup of SCALE models for full-core Xe-100 type high-temperature gas-cooled pebble-bed reactor and a Xe-100 type slice using publicly available information. The core-averaged equilibrium compositions and zone-wise equilibrium compositions for the slice and 3D models, respectively, were obtained following an iterative depletion method developed by Bostelmann et al. using SCALE’s reactor physics sequence TRITON. The slice model was used with TRITON to generate burnup-dependent cross section libraries at different temperatures which can be used with SCALE’s ORIGAMI code to rapidly determine fuel inventory and therefore to perform quick sensitivity studies on parameters such as the pebble location in the core. The SCALE/TRITON transport and depletion calculation for the Xe-100 type slice model indicates that the isotopic concentrations are in good agreement at 1,300 effective full power days (EFPD) for 235 U. An analysis of 236 U results match 239 Pu results would seem to indicate a typographical error in Mulder and Boyes wherein the reported results of 236 U and 239 Pu are reversed. In addition to SCALE/TRITON calculations, a new capability within SCALE/ORIGAMI for the simulation of pebble-bed reactors was used to study the burnup sensitivity with respect to the pebble pathway through the core. The SCALE/ORIGAMI results show that pebbles that travel closer to the reflector for the entire depletion history have a higher burnup than pebbles that travel through the middle of the core because of the higher thermal to fast flux ratio near the reflector. Consequently, a pebble’s burnup is strongly affected by the pebble’s pathway for each pass. Additional phenomena such as temperature distributions in the core and different travel times of the pebbles in the individual radial zones further affect the burnup distribution. The sensitivity of the discharge vector to the pebble pathways taken during each pass can be evaluated in the future using SCALE/ORIGAMI now that the SCALE inputs have been established.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗