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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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6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid

Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.

Agrobacterium-mediated transformation↗
DOE OSTI2024

Binary vector copy number engineering improves Agrobacterium -mediated transformation

The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60–100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Scaling Uintah on the Aurora Exascale System up to 122,880 Intel Ponte Vecchio Xe Stacks

The challenge of being able to scale application codes based on the Asynchronous Many-Task (AMT) Uintah framework on the Department of Energy (DOE) Aurora exascale system is addressed in this work by considering a challenging Reverse Monte Carlo Ray Tracing radiation benchmark calculation. This benchmark involves potentially global all-to-all communication and uses adaptive mesh refinement and ray tracing to achieve scalability. This benchmark has been used as part of previous scalability studies on a number of pre-exascale systems and on the DOE Frontier exascale system. This paper describes steps taken to enable this benchmark to run successfully on up to 10,240 nodes and 122,880 Intel® Ponte Vecchio Xe stacks on the DOE Aurora exascale system. This scalability was achieved through a limited number of experiments on Aurora, given machine loads and its uniqueness. These experiments constitute valuable lessons learned to achieve scalability at this level. The resulting scalability runs, while few in number, demonstrate relatively good strong-scaling characteristics. A detailed analysis of these results provides important indications about the path to scalability on Aurora for future work. Overall, these results continue the remarkable ability of this AMT approach to produce scalable solutions for challenging problems at extreme scale on heterogeneous architectures.

Garcia, Marta [Argonne National Laboratory (ANL)]↗
DOE OSTI2024

Comparative Analyses of Bioequivalence Assessment Methods for In Vitro Permeation Test Data

ABSTRACT For topical, dermatological drug products, an in vitro option to determine bioequivalence (BE) between test and reference products is recommended. In particular, in vitro permeation test (IVPT) data analysis uses a reference‐scaled approach for two primary endpoints, cumulative penetration amount (AMT) and maximum flux ( J max ), which takes the within donor variability into consideration. In 2022, the Food and Drug Administration (FDA) published a draft IVPT guidance that includes statistical analysis methods for both balanced and unbalanced cases of IVPT study data. This work presents a comprehensive evaluation of various methodologies used to estimate critical parameters essential in assessing BE. Specifically, we investigate the performance of the FDA draft IVPT guidance approach alongside alternative empirical and model‐based methods utilizing mixed‐effects models. Our analyses include both simulated scenarios and real‐world studies. In simulated scenarios, empirical formulas consistently demonstrate robustness in approximating the true model, particularly in effectively addressing treatment–donor interactions. Conversely, the effectiveness of model‐based approaches heavily relies on precise model selection, which significantly influences their results. The research emphasizes the importance of accurate model selection in model‐based BE assessment methodologies. It sheds light on the advantages of empirical formulas, highlighting their reliability compared to model‐based approaches and offers valuable implications for BE assessments. Our findings underscore the significance of robust methodologies and provide essential insights to advance their understanding and application in the assessment of BE, employed in IVPT data analysis.

Leon, Sami↗
DOE OSTI2025

Lessons Learned and Scalability Achieved When Porting Uintah to DOE Exascale Systems

A key challenge faced when preparing codes for Department of Energy (DOE) exascale systems was designing scalable applications for systems featuring hardware and software not yet available at leadership-class scale. With such systems now available, it is important to evaluate scalability of the resulting software solutions on these target systems. One such code designed with the exascale DOE Aurora and DOE Frontier systems in mind is the Uintah Computational Framework, an open-source asynchronous many-task (AMT) runtime system. To prepare for exascale, Uintah adopted a portable MPI+X hybrid parallelism approach using the Kokkos performance portability library (i.e., MPI+Kokkos). This paper complements recent work with additional details and an evaluation of the resulting approach on Aurora and Frontier. Results are shown for a challenging benchmark demonstrating interoperability of 3 portable codes essential to Uintah-related combustion research. These results demonstrate single-source portability across Aurora and Frontier with scaling characteristics shown to 3,072 Aurora nodes and 9,216 Frontier nodes. In addition to showing results run to new scales on new systems, this paper also discusses lessons learned through efforts preparing Uintah for exascale systems.

Holmen, John [ORNL] (ORCID:0000000259342641)↗
DOE OSTI2025

Profiles of Radiative Fluxes at ENA

Profiles of radiative fluxes observed at the Atmospheric Radiation Measurement (ARM)’s Eastern North Atlantic (ENA) observatory along with the ancillary measurements are reported. The below-cloud drizzle properties were derived by combining the data from the ceilometer and Ka-band ARM Zenith Radar (KAZR) following the technique explained by Ghate et al. (2021 JAMC). The cloud and drizzle water path values were derived from the brightness temperatures reported by the microwave radiometer following the technique of Cadeddu et al. (2020 AMT). The cloud water path was then scaled to the KAZR-reported radar reflectivity to calculate profiles of liquid water content (LWC). Following the analysis from Ghate et al. (2023 JGR), cloud droplet effective radius was calculated using the number concentration value of 100 cm-3. The cloud properties, along with the thermodynamic properties, served as an input to the Rapid Radiative Transfer Model (RRTM) to yield profiles of radiative fluxes at a 1-minute temporal and 50-m vertical resolution. The fluxes were then averaged to hourly temporal resolution for analysis. In Mitra et al. (2025 JClim), the calculated profiles were compared against those derived from the satellite measurements (SYN1deg). Flux profiles from the SYN1deg and the thermodynamic and cloud properties used for deriving them are also reported here. Both all-sky and clear-sky radiative flux profiles were calculated. Due to the large data volume, the surface and top-of-atmosphere (TOA) radiative fluxes for the six-year period, and the hourly profiles of the radiative fluxes for January 2018, are submitted here. Full profiles of radiative fluxes calculated from the thermodynamic and cloud properties measured at the ENA site at 1-minute temporal and 50-m vertical resolution for a six-year period are available from the authors. Six files here correspond to the following data: 1_ENARAD_CERES_with_cld_amount_timeseries.nc: Time-series of hourly values of RRTM-simulated values of upwelling and downwelling fluxes at the surface and TOA, observed boundary-layer cloud fractions, and upwelling and downwelling fluxes from the SYN1deg from July 2015 to January 2022. 2_CERES_2018_at_CERES_levels.nc: SYN1deg radiative fluxes at six levels for the year 2018. 3_ENARad_2018_at_CERES_levels.nc: RRTM calculated fluxes at the SYN1deg vertical levels for the year 2018. 4_ENARad_rrtminputs_hourly_201801.nc: Thermodynamic and cloud properties used as an input to the RRTM for January 2018. 5_CERES_inputs_hourly_201801.nc: Thermodynamic and cloud properties utilized by SYN1deg algorithm for January 2018. 6_ENARAD_hourly_201801.nc: Full profiles of hourly averaged radiative fluxes from the RRTM simulations for January 2018.

Atmosphere↗