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DOE OSTI2025

A nonhydrostatic formulation for MPAS-Ocean

The Model for Prediction Across Scales-Ocean (MPAS-Ocean) is an open-source, global ocean model and is one component of a family of climate models within the MPAS framework, including atmosphere, sea-ice, and land-ice models. Here, in this work, a new formulation for the ocean model is presented that solves the nonhydrostatic, incompressible Boussinesq equations on an unstructured, staggered, z-level grid. The introduction of this nonhydrostatic capability is necessary for the resolution of internal wave dynamics and large eddy simulations. Compared to the standard, hydrostatic formulation, a nonhydrostatic pressure solver and a vertical momentum equation are added, where the PETSc (Portable Extensible Toolkit for Scientific Computation) library is used for the inversion of a large sparse system for the nonhydrostatic pressure. Numerical results on a stratified seiche, internal solitary wave, overflow and lock-exchange test cases are presented, and the parallel efficiency of the code is evaluated using up to 1024 processors.

3D Poisson equation↗

DOE OSTI2025

A nonhydrostatic formulation for MPAS-Ocean

3D Poisson equation↗

DOE OSTI2021

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. Furthermore, 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.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

EXSCLAIM!: Harnessing materials science literature for self-labeled microscopy datasets

This work introduces the EXSCLAIM! toolkit for the automatic extraction, separation, and caption-based natural language annotation of images from scientific literature. EXSCLAIM! is used to show how rule-based natural language processing and image recognition can be leveraged to construct an electron microscopy data set containing thousands of keyword-annotated nanostructure images. Moreover, it is demonstrated how a combination of statistical topic modeling and semantic word similarity comparisons can be used to increase the number and variety of keyword annotations on top of the standard annotations from EXSCLAIM! With large-scale imaging datasets constructed from scientific literature, users are well positioned to train neural networks for classification and recognition tasks specific to microscopy-tasks often otherwise inhibited by a lack of sufficient annotated training data.

36 MATERIALS SCIENCE↗

DOE OSTI2022

AI and extreme scale computing to learn and infer the physics of higher order gravitational wave modes of quasi-circular, spinning, non-precessing black hole mergers

We use artificial intelligence (AI) to learn and infer the physics of higher order gravitational wave modes of quasi-circular, spinning, non precessing binary black hole mergers. We trained AI models using 14 million waveforms, produced with the surrogate model NRHybSur3dq8, that include modes up to $\ell$ ≤ 4 and (5,5), except for (4,0) and (4,1), that describe binaries with mass-ratios $\textit{q}$ ≤ 8, individual spins $s^z_{\{1,2\}} \in$[–0.8,0.8], and inclination angle $θ \in$ [0,π]. Our probabilistic AI surrogates can accurately constrain the mass-ratio, individual spins, effective spin, and inclination angle of numerical relativity waveforms that describe such signal manifold. We compared the predictions of our AI models with Gaussian process regression, random forest, k-nearest neighbors, and linear regression, and with traditional Bayesian inference methods through the PyCBC Inference toolkit, finding that AI outperforms all these approaches in terms of accuracy, and are between three to four orders of magnitude faster than traditional Bayesian inference methods. Our AI surrogates were trained within 3.4 hours using distributed training on 1,536 NVIDIA V100 GPUs in the Summit supercomputer.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Measurement of the low-energy antitriton inelastic cross section

In this Letter, the first measurement of the inelastic cross section for antitriton–nucleus interactions is reported, covering the momentum range of 0.8 ≤ p < 2.4 GeV/c. The measurement is carried out using data recorded with the ALICE detector in pp and Pb–Pb collisions at a centre-of-mass energy per nucleon of 13 TeV and 5.02 TeV, respectively. The detector material serves as an absorber for antitriton nuclei. The raw yield of (anti)triton nuclei measured with the ALICE apparatus is compared to the results from detailed ALICE simulations based on the GEANT4 toolkit for the propagation of (anti)particles through matter, allowing one to quantify the inelastic interaction probability in the detector material. This analysis complements the measurement of the inelastic cross section of antinuclei up to A = 3 carried out by the ALICE Collaboration, and demonstrates the feasibility of the study of the isospin dependence of inelastic interaction cross section with the analysis techniques presented in this Letter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2013

Applying uncertainty quantification to multiphase flow computational fluid dynamics

Multiphase computational fluid dynamics plays a major role in design and optimization of fossil fuel based reactors. There is a growing interest in accounting for the influence of uncertainties associated with physical systems to increase the reliability of computational simulation based engineering analysis. The U.S. Department of Energy's National Energy Technology Laboratory (NETL) has recently undertaken an initiative to characterize uncertainties associated with computer simulation of reacting multiphase flows encountered in energy producing systems such as a coal gasifier. The current work presents the preliminary results in applying non-intrusive parametric uncertainty quantification and propagation techniques with NETL's open-source multiphase computational fluid dynamics software MFIX. For this purpose an open-source uncertainty quantification toolkit, PSUADE developed at the Lawrence Livermore National Laboratory (LLNL) has been interfaced with MFIX software. In this study, the sources of uncertainty associated with numerical approximation and model form have been neglected, and only the model input parametric uncertainty with forward propagation has been investigated by constructing a surrogate model based on data-fitted response surface for a multiphase flow demonstration problem. Monte Carlo simulation was employed for forward propagation of the aleatory type input uncertainties. Several insights gained based on the outcome of these simulations are presented such as how inadequate characterization of uncertainties can affect the reliability of the prediction results. Also a global sensitivity study using Sobol' indices was performed to better understand the contribution of input parameters to the variability observed in response variable.

42 ENGINEERING↗

DOE OSTI2021

X-ray computed tomography-based porosity analysis: Algorithms and application for porous woody biomass

The properties of lignocellulosic biomass, such as bulk physical, thermal, and mechanical properties, as well as the mobility of enzymes or catalysts, are largely affected by porosity, pore structures, and pore size distribution. While X-ray computed tomography (CT) has been introduced to effectively produce 3D volumetric images of material microstructure, a quantitative porosity analysis from the 3D images has never been done. This work introduces a first-of-its-kind X-ray CT-based quantitative porosity analysis method and applies the developed toolkit to characterize the internal porosity distribution of loblolly pine. A sample loblolly pine chip was scanned by a nano-resolution X-ray CT system and digitally reconstructed after a sequence of image processing operations. Here, a comprehensive porosity analysis was then performed to quantify the envelope porosity, the spatial distribution of local porosity, and the directional porosity. Solutions to the various challenges in image processing, porosity calculation, and large data handling are provided.

42 ENGINEERING↗

DOE OSTI2015

Simulation study of a 'fission electron-collection' neutron detector

In this work, a 'fission electron-collection' neutron detector was studied using the Monte Carlo method. The detector consists of two metal electrodes mounted in a vacuum, named coated and collection electrodes, respectively. The first electrode is coated with triuranium octoxide. The detector uses the 'fission electron-collection' technique, which does not need an intermediate material but directly collects electrons from the coating. Such a detector can realize a flat energy response and a fast time response, both of which are important in the fluence measurement of pulsed neutron sources. In this paper, the physical processes of detection are presented, as well as Monte Carlo simulation studies using the Geant4 toolkit. From the results, the sensitivity of the detector is approximately 1.5 x 10{sup -21} [C/(n/cm{sup 2})], and the FWHM of response function is 2.5 nanoseconds. Additionally, the characterization of escaping electrons is also presented, and the sensitivity of the detector is determined for various coating thicknesses. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

DRiFT current mode, trigger settings and flexible detector specifications applied to scintillator arrays

MCNP radiation transport output is post-processed by DRiFT, a Detector Response Function Toolkit to simulate detailed nuclear instrumentation response. DRiFT can be used to assess the performance and potential limitations of scintillator, gas, and semiconductor detectors under a variety of simulated conditions not easily achievable in a laboratory setting. This work describes new updates in DRiFT for scintillator simulations which focus on the capability to simulate scintillators in current mode, an expansion of trigger options, and the ability to customize individual detector properties in a simulation. These improvements are designed to facilitate the ability to model large arrays of scintillator detectors with higher fidelity than was previously possible and are demonstrated in three examples. The first shows the difference between operating DRiFT in current and pulse mode. In the second example, which is intended to demonstrate deviations in individual detector performance, each detector has properties (PMT gain, optical transport, scintillation yield, etc.) that vary between detectors and are specified in DRiFT. A final example examines how DRiFT could be used to optimize digitizer settings in high rate measurements with split signals using the new common trigger option.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2025

Groundwater flowpath characteristics drive variability in per- and polyfluoroalkyl substances (PFAS) loading across a stream-wetland system

Groundwater dependent ecosystems in areas with industrial and military land use are at risk of direct exposure to a wide range of contaminants, including PFAS chemicals. Glaciated terrain often has mixed high and low permeability sediments coupled with groundwater flow-through lake features. These hydrogeologic attributes create highly complex ‘source to seep’ dynamics that make spatiotemporal contaminant transport patterns difficult to predict. We investigated one such system in detail using a suite of heat-tracing and chemical methods. Numerous (n=57) preferential groundwater discharge zones (vertical flux rates ranging 0.2 to 3.2 m/d) were identified across the upper Quashnet River stream-wetland system in Mashpee, MA, USA, adjacent to an Air Force Base with several known PFAS source areas. Surface-water and groundwater samples were collected and analyzed (n=145) for precursors and terminal PFAS compounds between March and September 2022. Samples were collected at identified seeps along the Quashnet River (n=59), from wells upgradient from the stream-wetland system (n= 44), from contributing flow-through kettle lakes (n=8), and at multiple locations along the Quashnet River (n=34). Samples from seeps and wells had measured PFAS concentrations ranging from non-detect to approximate 3,500 ng/L (mean= 1,650 ng/L), and a range of deuterium excess values (3.2 to 15.9 per mil) indicative of varying degrees of groundwater-lake interaction prior to emergence at the discharge zones. Groundwater-lake interaction along flowpaths that sourced the sampled seeps was farther supported by significant correlations (p < 0.01) between deuterium excess and %PFAS precursors, and between %PFAS precursors and multiple terminal PFAS compounds (e.g., PFPeS, PFBS, PFHxS). However, some sampled seeps contributing groundwater to the stream-wetland system had much higher total PFAS concentrations (>1000 ng/L) than the upgradient kettle lakes, despite showing lake (evaporative) isotopic signatures, indicating the potential for groundwater flowpath convergence at wetland discharge zones and the influence of lakebed PFAS precursor reactions. PFAS compounds and water isotopic composition at sampled multilevel groundwater wells, rivers, lakes, and seeps suggest that a complex mixture of source groundwater and flowpath characteristics are responsible for diverse observed PFAS mixtures at preferential discharge zones across the stream-wetland system. Further, total PFAS loading patterns to the Quashnet River via groundwater discharge remained remarkably similar from winter to summer to fall conditions, despite a regional dry period in late summer 2022 with the upper river channel completely drying. This work addresses gaps in the existing PFAS literature by demonstrating the importance of subsurface fate and transport on PFAS compound concentrations in controlling contaminant mass loading in preferential groundwater discharge zones and presents a transferrable field toolkit for efficient characterization of spatially preferential PFAS transport dynamics.

Contaminant transport↗

DOE OSTI2017

JDFTx: Software for joint density-functional theory

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Recent advances, and unresolved issues, in the application of computational modelling to the prediction of the biological effects of nanomaterials

Nanomaterials research is one of the fastest growing contemporary research areas. The unprecedented properties of these materials have meant that they are being incorporated into products very quickly. Regulatory agencies are concerned they cannot assess the potential hazards of these materials adequately, as data on the biological properties of nanomaterials are still relatively limited and expensive to acquire. Computational modelling methods have much to offer in helping understand the mechanisms by which toxicity may occur, and in predicting the likelihood of adverse biological impacts of materials not yet tested experimentally. This paper reviews the progress these methods, particularly those QSAR-based, have made in understanding and predicting potentially adverse biological effects of nanomaterials, and also the limitations and pitfalls of these methods. - Highlights: • Nanomaterials regulators need good information to make good decisions. • Nanomaterials and their interactions with biology are very complex. • Computational methods use existing data to predict properties of new nanomaterials. • Statistical, data driven modelling methods have been successfully applied to this task. • Much more must be learnt before robust toolkits will be widely usable by regulators.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

Research toward renewable and sustainable energy has identified candidate terpenes capable of blending/replacing petroleum-derived jet, diesel and tactical fuels. Additionally, despite being naturally produced and stored by many plants, there are few examples of commercial recovery of terpenes from plants due to low yields. Plant terpene biosynthesis is regulated at multiple levels leading to wide variability in terpene content and chemistry. Advances in the plant molecular toolkit including annotated genomes, high-throughput omics profiling and genome-editing provides an ideal platform for high-resolution analysis and in-depth understanding of plant terpene metabolism. Concomitantly, such information is useful for bioengineering strategies of metabolic pathways for candidate terpenes. Within this paper, we review the status of terpenes as an advanced biofuel and discuss the potential of plants as a viable agronomic solution for future advanced terpene-derived biofuels.

09 BIOMASS FUELS↗

DOE OSTI2020

Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways

Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic part function, gene expression patterns, and biosynthetic pathway performance in vitro before implementing designs in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here in this paper, we report the development and optimization of a high-yielding (236 ± 24 μg/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map aerobic cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗

DOE OSTI2025

On the effectiveness of neural operators at zero-shot weather downscaling

Machine-learning (ML) methods have shown great potential for weather downscaling. These data-driven approaches provide a more efficient alternative for producing high-resolution weather datasets and forecasts compared to physics-based numerical simulations. Neural operators, which learn solution operators for a family of partial differential equations, have shown great success in scientific ML applications involving physics-driven datasets. Neural operators are grid-resolution-invariant and are often evaluated on higher grid resolutions than they are trained on, i.e., zero-shot super-resolution. Given their promising zero-shot super-resolution performance on dynamical systems emulation, we present a critical investigation of their zero-shot weather downscaling capabilities, which is when models are tasked with producing high-resolution outputs using higher upsampling factors than are seen during training. To this end, we create two realistic downscaling experiments with challenging upsampling factors (e.g., 8x and 15x) across data from different simulations: the European Centre for Medium-Range Weather Forecasts Reanalysis version 5 (ERA5) and the Wind Integration National Dataset Toolkit. While neural operator-based downscaling models perform better than interpolation and a simple convolutional baseline, we show the surprising performance of an approach that combines a powerful transformer-based model with parameter-free interpolation at zero-shot weather downscaling. We find that this Swin-Transformer-based approach mostly outperforms models with neural operator layers in terms of average error metrics, whereas an Enhanced Super-Resolution Generative Adversarial Network-based approach is better than most models in terms of capturing the physics of the ground truth data. We suggest their use in future work as strong baselines.

17 WIND ENERGY↗

DOE OSTI2021

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗