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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Versatile Simulated Data Transport Layer for in Situ Workflows Performance Evaluation

In situ processing does not only allow scientific applications to face the explosion in data volume and velocity but also to address the time constraints of many simulation-analysis workflows by providing scientists with early insights about their applications at runtime. Multiple frameworks implement the concept of a data transport layer (DTL) to enable such in situ workflows. These tools are very versatile, directly or indirectly access the data generated on the same node, another node of the same compute cluster, or a completely distinct node, and allow data publishers and subscribers to run on the same computing resources or not. This versatility puts on researchers the onus of taking key decisions related to resource allocation and how to transport data to ensure the most efficient execution of their in situ workflows. However, domain scientists and workflow practitioners lack the appropriate tools to assess the respective performance of particular design and deployment options. In this paper we introduce a versatile simulated DTL designed to provide researchers with insights on the respective performance of different execution scenarios of in situ workflows. This open-source, standalone library builds on the SimGrid toolkit and can be linked to any SimGrid-based simulator. It facilitates the evaluation of the performance behavior, at scale, of different data transport configurations and the study of the effects of resource allocation strategies. We demonstrate the scalability, versatility, and accuracy of this simulated DTL by reproducing the execution of two synthetic benchmarks and of a real-world in situ workflow composed of an MPI application and a parallel data analysis. Results of simulations run on a single core show that the proposed library can simulate the interactions of tens of thousands of simulated processes deployed on two interconnected commodity clusters in a few seconds, and the execution by a thousand simulated processes of an in situ workflow in less than three minutes.

Suter, Fred [ORNL] (ORCID:0000000319021955)↗
DOE OSTI2020

GPU-acceleration of the ELPA2 distributed eigensolver for dense symmetric and hermitian eigenproblems

The solution of eigenproblems is often a key computational bottleneck that limits the tractable system size of numerical algorithms, among them electronic structure theory in chemistry and in condensed matter physics. Large eigenproblems can easily exceed the capacity of a single compute node, thus must be solved on distributed-memory parallel computers. We here present GPU-oriented optimizations of the ELPA two-stage tridiagonalization eigensolver (ELPA2). On top of cuBLAS-based GPU offloading, we add a CUDA kernel to speed up the back-transformation of eigenvectors, which can be the computationally most expensive part of the two-stage tridiagonalization algorithm. Furthermore, we benchmark the performance of this GPU-accelerated eigensolver on two hybrid CPU–GPU architectures, namely a compute cluster based on Intel Xeon Gold CPUs and NVIDIA Volta GPUs, and the Summit supercomputer based on IBM POWER9 CPUs and NVIDIA Volta GPUs. Consistent with previous benchmarks on CPU-only architectures, the GPU-accelerated two-stage solver exhibits a parallel performance superior to the one-stage counterpart. Finally, we demonstrate the performance of the GPU-accelerated eigensolver developed in this work for routine semi-local KS-DFT calculations comprising thousands of atoms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A New Configuration of Paralleled Modular ANPC Multilevel Converter Controlled by an Improved Modulation Method for 1 MHz, 1 MW EV Charger

In this work, a new configuration of the modular multilevel converter (MLC) based on the parallel connection of three-level active-neutral-point-clamped (3L-ANPC) cells as well as its improved modulation method is proposed for 1 MHz, 1 MW electric vehicle (EV) megacharger. In the proposed paralleled modular ANPC-MLC, only six high-frequency silicon carbide (SiC) power switches operating at 333 kHz are required to generate 1 MHz switching frequency spectrum. Moreover, the operating voltage of all power devices is halved, the magnitude of the first switching frequency harmonic cluster is decreased by the factor of five, and the load current is equally distributed between the 3L-ANPC legs by employing the proposed improved modulation method. Hence, the modularity, efficiency, and power density of the proposed converter are notably increased, whereas the value of passive components and the overall switching loss are remarkably decreased. In addition, an optimized design of the one 3L-ANPC cell of the proposed paralleled modular ANPC-MLC for 1 MHz, 1MW EV megacharger using Ansys SIwave, Icepak, and Q3D finite element method platforms is presented and analyzed in detail. The provided experimental results of the down-scaled setup verify the feasibility and viability of the proposed configuration as well as its improved switching pattern.

42 ENGINEERING↗
DOE OSTI2024

Impact of Iron Species Dispersion on Fe/ZSM–5 Catalyst Performance for Methane Dehydroaromatization (MDA)

Methane dehydroaromatization (MDA) is one of the most promising technologies for directly transforming methane into aromatics. Unlike the extensively investigated Mo/ZSM-5 catalysts, the structure and, consequently, the catalytic activity of Fe/ZSM-5 are markedly influenced by the method of preparation, as shown here. In this study, we prepared 2 % and 4 % Fe/ZSM-5 catalysts via wet impregnation (WI) and incipient wetness impregnation (IWI). Characterizations (XRD, STEM, UV-Vis, NH 3 -TPD and H 2 -TPR) reveal that 2 %Fe-WI mainly possesses isolated or low-polymerized Fe species within zeolite channels, leading to a rapid activation and a higher benzene yield due to the faster reduction to iron suboxides under MDA conditions. In contrast, 2 %Fe-IWI contains bulk iron oxide aggregates, resulting in a slower activation as these aggregates transform into iron carbide through successive reduction and carbonization. Here, a deactivation kinetic study applied to the 2 % catalysts further demonstrates the quantitative relation between Fe site isolation and catalytic activity. Although both 4 % catalysts inevitably form sizable iron oxide clusters and particles due to the high Fe/Al ratio, similar trends are noted, with the WI catalysts exhibiting a shorter induction/activation period and a higher yield of benzene, paralleling observations made with 2 % catalysts.

03 NATURAL GAS↗
DOE OSTI2023

A Robust Parallel Distributed State Estimation for Large Scale Distribution Systems

The growing need and interest in real-time monitoring of large distribution networks motivated by the rapid population of renewable sources, EVs and etc. demand a computationally efficient state estimation framework. Furthermore, this paper presents an improved computational framework for implementing a robust state estimator using a multi-core processor. The main contribution of the paper is the proposed computational framework along with two partitioning strategies which enable fast and robust state estimation for large scale radial and/or meshed distribution systems. Formulation of the proposed method and its implementation are described in detail. Performance of the estimator is tested by simulations first using a small 84-bus radial distribution system. Then the method’s scalability is demonstrated by simulations on two very large scale distribution networks one configured radially and the other meshed each containing over 12,500 buses.

42 ENGINEERING↗
DOE OSTI2021

Fracture Description of the HFTS-2 Slant Core, Delaware Basin, West Texas

Previous work in the Midland Basin Hydraulic Fracture Test Site project (HFTS1) has shown the value of core recovered from a stimulated volume in providing information on the geometry and extent of hydraulic fractures. This project (HFTS2) is in the Wolfcamp Formation of the Delaware Basin. A slant core through the stimulated volume was acquired above and below a stimulated well and the results of the fracture description are presented here. Here, nine, 3-inch-diameter whole cores from the slant well were examined for fractures prior to slabbing, together with a CT scan of the core. We used criteria developed during the HFTS1 project to identify hydraulic, natural, drilling-induced and core-handling fractures. Material collected from a few fracture faces was cleaned, sieved, and examined under a microscope to look for proppant. A total of 1261 fractures, including 500 hydraulic fractures, were described in 948 feet of core. Hydraulic fractures are not evenly distributed through the cores; they tend to occur in clusters. Many are remarkably planar, smooth, and featureless, while others have twist hackles, steps, plumose, and kinks. Natural, subvertical fractures, mostly less than 1 mm in width, sealed with blocky calcite, are oriented NE-SW (Set 1) and WNW-ESE (Set 2). Two Set 1 fractures have drusy cement on parted faces and were possibly open prior to drilling. A few subvertical sealed fractures with different orientations are also present. Bed-parallel natural fractures, most having fibrous cement (beef), and some showing top-to-north bed-parallel shear are present. Faults with normal/oblique movement were found in one part of the core. Drilling induced and core-handling breaks were identified in all cores, and were also noted to have reactivated some natural fractures. The results from this work will allow hydraulic fracture distribution relative to the stimulated well to be assessed. The number of fractures is generally greater than the number of perforations, but these can be compared for different stages and perforation clusters. Surface features provide information about the direction of hydraulic fracture propagation and about segmentation and bifurcation that might increase the number of fracture strands. Reactivation of natural fractures, including bedding-parallel fractures, occurs although the mechanism of parting is mostly unknown. The wider HFTS2 project will make use of this fracture description to improve hydraulic fracture modeling (geomechanics and engineering), to help explain pressure depletion and fiber optics observations (reservoir depletion and frac geometry), to help verify indirect fracture diagnostic techniques such as microseismic monitoring (geophysics), and to help calibrate horizontal well image logs.

58 GEOSCIENCES↗
DOE OSTI2022

GronOR: Scalable and Accelerated Nonorthogonal Configuration Interaction for Molecular Fragment Wave Functions

GronOR is a program package for nonorthogonal configuration interaction calculations. Electronic wave functions are constructed in terms of antisymmetrized products of multiconfiguration molecular fragment wave functions. The computational complexity of the nonorthogonal methodologies implemented in GronOR applied to large molecular assemblies requires a design that takes full advantage of massively parallel supercomputer architectures and accelerator technologies. This work describes the implementation strategy and resulting performance characteristics. In addition to parallelization and acceleration, the software development strategy includes aspects of fault resiliency and heterogeneous computing. The program was designed for large-scale supercomputers but also runs effectively on small clusters and workstations for small molecular systems. GronOR is available as open source to the scientific community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Optimizing High Performance Markov Clustering for Pre-Exascale Architectures

HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations and heavily makes use of the sparse matrix-sparse matrix multiplication kernel (SpGEMM). The existing parallel algorithms in HipMCL are not scalable to Exascale architectures, both due to their communication costs dominating the runtime at large concurrencies and also due to their inability to take advantage of accelerators that are increasingly popular. In this work, we systematically remove scalability and performance bottlenecks of HipMCL. We enable GPUs by performing the expensive expansion phase of the MCL algorithm on GPU. Additionally, we propose a CPU-GPU joint distributed SpGEMM algorithm called pipelined Sparse SUMMA and integrate a probabilistic memory requirement estimator that is fast and accurate. Furthermore, we develop a new merging algorithm for the incremental processing of partial results produced by the GPUs, which improves the overlap efficiency and the peak memory usage. We also integrate a recent and faster algorithm for performing SpGEMM on CPUs. We validate our new algorithms and optimizations with extensive evaluations. With the enabling of the GPUs and integration of new algorithms, HipMCL is up to 12.4x faster, being able to cluster a network with 70 million proteins and 68 billion connections just under 15 minutes using 1024 nodes of ORNL's Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Quantum Electrodynamics Coupled-Cluster at Scale: High-Performance Implementation for Complex Systems

Coupled-cluster theory (CC) is a highly accurate and versatile method for simulating complex interactions within quantum systems. The extension of CC theory to model mixed electron-photon processes with quantum electrodynamics (QED) has improved our capability to predict cavity-modified chemistry, a field where photons are used as cost-effective and eco-friendly alternatives to catalyze/inhibit chemical reactions. However, calculations with CC methods, even without incorporating QED effects, are often prohibitively expensive. Simulations of larger systems require scalable infrastructures that exist for traditional CC methods but not for QED-CC methods. As such, we present a GPU-enabled, high-performance, open-source implementation of the quantum electrodynamics coupled-cluster method with single and double excitations (QED-CCSD) within the ExaChem quantum chemistry software package. ExaChem relies on the Tensor Algebra for Many-body Methods (TAMM) infrastructure: a parallel heterogeneous tensor library designed to achieve scalable performance on modern heterogeneous supercomputing platforms. Furthermore, we discuss theoretical foundations, algorithmic details, and numerical benchmarks to showcase the larger systems that ExaChem can simulate and how the integration of photonic degrees-of-freedom alters their ground-state properties.

Basis sets↗
DOE OSTI2019

A Scalable Online Monitoring System Based on Elasticsearch for Distributed Data Acquisition in Cms

The part of the CMS Data Acquisition (DAQ) system responsible for data readout and event building is a complex network of interdependent distributed applications. To ensure successful data taking, these programs have to be constantly monitored in order to facilitate the timeliness of necessary corrections in case of any deviation from specified behaviour. A large number of diverse monitoring data samples are periodically collected from multiple sources across the network. Monitoring data are kept in memory for online operations and optionally stored on disk for post-mortem analysis. We present a generic, reusable solution based on an open source NoSQL database, Elasticsearch, which is fully compatible and non-intrusive with respect to the existing system. The motivation is to benefit from an off the-shelf software to facilitate the development, maintenance and support efforts. Elasticsearch provides failover and data redundancy capabilities as well as a programming language independent JSON-over-HTTP interface. The possibility of horizontal scaling matches the requirements of a DAQ monitoring system. The data load from all sources is balanced by redistribution over an Elasticsearch cluster that can be hosted on a computer cloud. In order to achieve the necessary robustness and to validate the scalability of the approach the above monitoring solution currently runs in parallel with an existing in-house developed DAQ monitoring system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Prediction of DIII-D Pedestal Structure From Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. Here, an experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (n e ) and electron temperature (T e ) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (I p ), toroidal magnetic field (B Φ ), neutral beam heating power (P NBI ) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Attribute-Aware RBFs: Interactive Visualization of Time Series Particle Volumes Using RT Core Range Queries

Smoothed-particle hydrodynamics (SPH) is a mesh-free method used to simulate volumetric media in fluids, astrophysics, and solid mechanics. Visualizing these simulations is problematic because these datasets often contain millions, if not billions of particles carrying physical attributes and moving over time. Radial basis functions (RBFs) are used to model particles, and overlapping particles are interpolated to reconstruct a high-quality volumetric field; however, this interpolation process is expensive and makes interactive visualization difficult. Existing RBF interpolation schemes do not account for color-mapped attributes and are instead constrained to visualizing just the density field. To address these challenges, we exploit ray tracing cores in modern GPU architectures to accelerate scalar field reconstruction. We use a novel RBF interpolation scheme to integrate per-particle colors and densities, and leverage GPU-parallel tree construction and refitting to quickly update the tree as the simulation animates over time or when the user manipulates particle radii. We also propose a Hilbert reordering scheme to cluster particles together at the leaves of the tree to reduce tree memory consumption. Finally, we reduce the noise of volumetric shadows by adopting a spatially temporal blue noise sampling scheme. Our method can provide a more detailed and interactive view of these large, volumetric, time-series particle datasets than traditional methods, leading to new insights into these physics simulations.

Particle Volumes↗
DOE OSTI2022

Prediction of DIII-D Pedestal Structure from Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. An experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (ne) and electron temperature (Te) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (Ip), toroidal magnetic field (Bφ), neutral beam heating power (PNBI) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Exploring Anomalous Photoelectron Angular Distributions in the Photoelectron Spectra of Gd 3 O 3 – : Study of Gd 3 O 2 – and Gd 3 O 3 – Using Photoelectron Spectroscopy and Density Functional Theory Calculations

Anion photoelectron (PE) spectra of lanthanide oxide clusters obtained previously have exhibited anomalous photoelectron angular distributions which were attributed to strong PE–valence electron (PEVE) interactions. Here, to further explore this effect, we have obtained the PE spectra of Gd 3 O 2 – and Gd 3 O 3 – , two clusters that have similarly complex electronic structures but contrasting symmetries. The spectra exhibit manifolds of detachment transitions at similar binding energies in a 0.5 eV window of energy. The electron affinity of Gd 3 O 2 is measured to be 1.29 ± 0.05 eV, and that of Gd 3 O 3 is 1.31 ± 0.05 eV. As seen in previous studies on lanthanide oxide cluster anions in lower than conventional oxidation states, transitions in spectra obtained lower photon energies are more congested than those obtained with higher photon energy, a signature of strong PEVE interactions. While the detachment transitions have predominantly parallel photoelectron angular distributions (PAD), the PAD varies across the manifold of transitions in the PE spectrum of Gd 3 O 3 – in a way that suggests four different subgroups of transitions. Results of calculations on Gd 3 O 2 – suggest kite or V-shape structures with antiferromagnetic coupling between one of the 4f 7 subshells with the two others. Calculations on Gd 3 O 3 – more definitively point to ring structures with a nearly isoenergetic ferromagnetically coupled high spin (24-tet) state and a dectet state in which one of the 4f 7 subshells is antiferromagnetically coupled with the other two. Taking these results as qualitative, we propose that strong mixing between the unperturbed states predicted computationally leads to overlapping transitions with different PADs.

anions↗
DOE OSTI2026

A biosynthetic gene cluster for three post-chorismate pathways in Arabidopsis

Chorismate is a branch-point metabolite in the biosynthesis of aromatic amino acids, vitamins, antibiotics and various other aromatic products in bacteria, fungi and plants. Although 13 chorismate-utilizing enzymes have been identified in bacteria, only 6 have been described in plants, where an estimated 30% of all photosynthetically fixed carbon passes through chorismate. Here, in this study, we describe a biosynthetic gene cluster (BGC) consisting of five core genes, including two reductases, two methyltransferases and one glucosyltransferase. Genetic and biochemical evidence shows that these five enzymes collectively give rise to three biosynthetic pathways, each originating from chorismate: two parallel pathways produce a class of non-aromatic, isomeric compounds abundant in the roots of Arabidopsis thaliana, whereas the third pathway produces methylated and glucosylated chorismate derivatives that subsequently react non-enzymatically with glutathione. Genome analysis revealed that variants of this BGC are present in some but not all species in the Brassicaceae family. Taken together, our study uncovered a BGC, containing three chorismate-utilizing enzymes, that controls three distinct post-chorismate pathways in A. thaliana. This work not only advances our understanding of carbon flow in this model plant but also highlights that the biochemical complexity encoded by plant BGCs is greater than previously appreciated.

Peng, Meng [Ghent Univ. (Belgium); Flemish Institu↗
DOE OSTI2024

Studying CPU and memory utilization of applications on Fujitsu A64FX and Nvidia Grace Superchip

ARM-based manycore CPU architectures are well-positioned to provide the rising memory throughput requirements of modern data intensive scientific applications in High Performance Computing (HPC). The Fujitsu A64FX CPU platform is based on the ARM v8.2A architecture, and is the processor of the flagship Japanese supercomputer - "Fugaku", which was previously ranked as the #1 supercomputer in the world according to the Top500 list. The Nvidia Grace superchip features 144 Neoverse V2 cores based on the ARMv9 architecture with 4x128b SVE2, providing exceptional computational power. The chip supports up to 480GB of memory, making it ideal for AI, machine learning, and scientific computing workloads. In this paper, we conduct a thorough performance exploration of a variety of parallel bandwidth-sensitive benchmarks and applications compiled with the native Fujitsu compiler on a Fugaku A64FX compute node and ARM (LLVM) Compiler on an NVIDIA Grace superchip compute node, engaging all the computational cores per cluster using OpenMP multithreading (assuming the cores can drive the available bandwidth). Our ultimate goals are to study the resource utilization of scientific applications and benchmarks on A64FX and Grace superchip, considering graph application scenarios ( GAP Benchmark suite) and eleven appli- cation proxies from the Rodinia heterogeneous benchmark suite (considering domains such as Data Mining, Bioinformatics, Fluid Dynamics, Pattern Recognition, etc.). Through exhaustive performance monitoring, we quantify the resource utilization of diverse OpenMP-based HPC applications on both the Fujitsu A64FX and the Nvidia Grace Superchip platforms.

benchmarking, Performance Analysis, High performan↗
DOE OSTI2025

A Melanoma Brain Metastasis CTC Signature and CTC:B-cell Clusters Associate with Secondary Liver Metastasis: A Melanoma Brain–Liver Metastasis Axis

Melanoma brain metastasis is linked to dismal prognosis and low overall survival and is detected in up to 80% of patients at autopsy. Circulating tumor cells (CTC) are the smallest functional units of cancer and precursors of fatal metastasis. We previously used an unbiased multilevel approach to discover a unique ribosomal protein large/small subunit (RPL/RPS) CTC gene signature associated with melanoma brain metastasis. In this study, we hypothesized that CTC-driven melanoma brain metastasis secondary metastasis (“metastasis of metastasis” per clinical scenarios) has targeted organ specificity for the liver. We injected parallel cohorts of immunodeficient and newly developed humanized NBSGW (huNBSGW) mice with cells from CTC-derived melanoma brain metastasis to identify secondary metastatic patterns. We found the presence of a melanoma brain–liver metastasis axis in huNBSGW mice. Furthermore, RNA sequencing analysis of tissues showed a significant upregulation of the RPL/RPS CTC gene signature linked to metastatic spread to the liver. Additional RNA sequencing of CTCs from huNBSGW blood revealed extensive CTC clustering with human B cells in these mice. CTC:B-cell clusters were also upregulated in the blood of patients with primary melanoma and maintained either in CTC-driven melanoma brain metastasis or melanoma brain metastasis CTC–derived cells promoting liver metastasis. CTC-generated tumor tissues were interrogated at single-cell gene and protein expression levels (10x Genomics Xenium and HALO spatial biology platforms, respectively). Collectively, our findings suggest that heterotypic CTC:B-cell interactions can be critical at multiple stages of metastasis.

60 APPLIED LIFE SCIENCES↗