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At least 775 records · Page 43

All sources NASA NTRS DOE OSTI

DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Self-Security for Grid-Interactive Smart Inverters Using Steady-State Reference Model

Smart inverters exchange information with other devices through a shared communication link, making the inverters more prone to receive harmful commands from external parties. This erroneous data can be received due to an anomaly in the system, such as a device fault, unintentional utility operator action, or a cyber-attack. In this paper, a device-level self-security strategy is implemented using reference models for a grid-interactive inverter to examine the incoming power setpoints, detect the anomalies, and protect the system accordingly. The PQ setpoints received from the utility supervisory controller are autonomously examined using the inverter’s normal and stable operating regions before engaging the setpoints to the inverter’s local controller. Grid parameters are estimated in real-time during the examination process. The efficacy of the self-security algorithm is tested using a three-phase 3-kVA SiC-MOSFET inverter and a 12-kW NHR 9410 regenerative grid emulator. The results verify that the proposed method can detect harmful PQ setpoints that can cause abnormal or unstable inverter operation.

Gursoy, Mehmetcan↗

DOE OSTI2025

S-QGPU: Shared quantum gate processing unit for distributed quantum computing

We propose a distributed quantum computing (DQC) architecture in which individual small-sized quantum computers are connected to a shared quantum gate processing unit (S-QGPU). The S-QGPU comprises a collection of hybrid two-qubit gate modules for remote gate operations. In contrast to conventional DQC systems, where each quantum computer is equipped with dedicated communication qubits, S-QGPU effectively pools the resources (e.g., the communication qubits) together for remote gate operations, and, thus, significantly reduces the cost of not only the local quantum computers but also the overall distributed system. Our preliminary analysis and simulation show that S-QGPU's shared resources for remote gate operations enable efficient resource utilization. When not all computing qubits (also called data qubits) in the system require simultaneous remote gate operations, S-QGPU-based DQC architecture demands fewer communication qubits, further decreasing the overall cost. Alternatively, with the same number of communication qubits, it can support a larger number of simultaneous remote gate operations more efficiently, especially when these operations occur in a burst mode.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

The genome of jojoba ( Simmondsia chinensis ): A taxonomically isolated species that directs wax ester accumulation in its seeds

Seeds of the desert shrub, jojoba ( Simmondsia chinensis ), are an abundant, renewable source of liquid wax esters, which are valued additives in cosmetic products and industrial lubricants. Jojoba is relegated to its own taxonomic family, and there is little genetic information available to elucidate its phylogeny. Here, we report the high-quality, 887-Mb genome of jojoba assembled into 26 chromosomes with 23,490 protein-coding genes. The jojoba genome has only the whole-genome triplication (γ) shared among eudicots and no recent duplications. These genomic resources coupled with extensive transcriptome, proteome, and lipidome data helped to define heterogeneous pathways and machinery for lipid synthesis and storage, provided missing evolutionary history information for this taxonomically segregated dioecious plant species, and will support efforts to improve the agronomic properties of jojoba.

Sturtevant, Drew↗

DOE OSTI2023

Monte Carlo Analyses of the FOEHN Experiment

The FOEHN critical experiment, which has been carried out at Cadarache (France) in the reactor EOLE in the early 70s, was designed to verify RHF design analyses. This study focuses on the impact of the FOEHN experiment uncertainties on the calculation of the energy deposition. The latter has been obtained by the Monte Carlo codes Serpent and MCNP. In the calculation of the energy deposition, the first code relies on KERMA factors whereas the latter code relies on Q-values. The two Monte Carlo codes share the same geometry and material specifications. In addition to the design and experiment parameters uncertainties, nuclear data also impacts the calculation of the energy deposition. In this study, the MCNP simulations use three different nuclear data library sets: ENDF/B versions VII.0, VII.1, and VIII.0. Finally, the ksens card of MCNP, using perturbation theory, has been used to identify the cross sections and isotopes with largest impact on the effective multiplication factor. By showing that the use of different software and computational methodologies and design parameters uncertainties do not significantly impact the core power distribution, this work demonstrate the appropriateness of the tools and methods employed for the conversion of involute-plate reactors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Portuguese Wood Pellets Market: Organization, Production and Consumption Analysis

Wood pellets are a form of energy that can be seen as an alternative to fossil fuels, thus contributing to the reduction of greenhouse gas emissions. In other words, wood pellets can be considered a solution contributing to the mitigation of climate change. The use of wood pellets has grown significantly in recent years, with different markets emerging, such as Portugal, both from production and consumption perspectives. The wood pellet industry in Portugal began its development about 15 years ago, with the companies installed in the country initially almost exclusively dedicated to the production of wood pellets for export to central and northern European markets. However, over the years, the domestic market, initially considered insignificant, began to develop; it recently reached a considerable consuming share of the national production. This study presents an analysis of the Portuguese wood pellet market using data collected on the sector, and specifically on producers and consumers. The information was gathered using surveys presented directly to consumers and producers and through interviews with other stakeholders in the sector. From the analysis of the information, it was possible to understand the market’s dynamics, its current evolution and its prospects for the upcoming years, since it can already be considered mature and consolidated.

Nunes, Leonel J. R. (ORCID:0000000154048163)↗

DOE OSTI2020

Rotationally Driven Ultraviolet Emission of Red Giant Stars

Main-sequence stars exhibit a clear rotation-activity relationship, in which rapidly rotating stars drive strong chromospheric/coronal ultraviolet and X-ray emission. While the vast majority of red giant stars are inactive, a few percent exhibit strong ultraviolet emission. Here we use a sample of 133 red giant stars observed by Sloan Digital Sky Survey APOGEE and Galaxy Evolution Explorer to demonstrate an empirical relationship between near-UV (NUV) excess and rotational velocity (v sin i). Beyond this simple relationship, we find that NUV excess also correlates with rotation period and with Rossby number in a manner that shares broadly similar trends to those found in M dwarfs, including activity saturation among rapid rotators. Our data also suggest that the most extremely rapidly rotating giants may exhibit so-called supersaturation, which could be caused by centrifugal stripping of these stars rotating at a high fraction of breakup speed. As an example application of our empirical rotation-activity relation, we demonstrate that the NUV emission observed from a recently reported system comprising a red giant with a black hole companion is fully consistent with arising from the rapidly rotating red giant in that system. Most fundamentally, our findings suggest a common origin of chromospheric activity in rotation and convection for cool stars from main sequence to red giant stages of evolution.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A data driven approach for cross-slip modelling in continuum dislocation dynamics

Cross-slip is a thermally activated process by which screw dislocation changes its glide plane to another slip plane sharing the same Burgers vector. The rate at which this process happens is determined by a Boltzmann type expression that is a function of the screw segment length and the stress acting on the dislocation. In continuum dislocation dynamics (CDD), the information regarding the length of the screw dislocation segment and local stress state on dislocations are lost due to the coarse-grained representation of the density. Here, in this work, a data driven approach to characterize the lost information by analyzing the discrete dislocation configurations is proposed to enable cross-slip modeling in the CDD framework in terms of the coarse-grained dislocation density and stress fields. The analysis showed that the screw segment length follows an exponential distribution, and the stress fluctuations, defined as the difference between the stress on the dislocations and the mean field stress in CDD, follows a Lorentzian distribution. A novel approach for cross slip implementation in CDD employing the screw segment length and stress fluctuation statistics was proposed and rigorously tested by comparing the CDD cross-slip rates with discrete dislocation dynamics (DDD) rates. This approach has been applied in conjunction with three cross-slip models used in DDD simulations differing mainly in the functional form of cross slip activation energy. It was found that different cross-slip activation energy formulations yielded different cross-slip rates, yet the effect on mechanical stress-strain response and dislocation density evolution was minimal for the [001] type loading.

42 ENGINEERING↗

DOE OSTI2025

SLAB: simultaneous labeling and binding affinity prediction for protein–ligand structures

Machine learning models are often used as scoring functions to predict the binding affinity of a protein–ligand complex. These models are trained with limited amounts of data with experimentally measured binding affinity values. A large number of compounds are labeled inactive through single-concentration screens without measuring binding affinities. These inactive compounds, along with the active ones, can be used to train binary classification models, while regression models are trained using compounds with binding affinities only. However, the classification and regression tasks are often handled separately, without sharing the learned feature representations. In this paper, we propose a novel model architecture that jointly performs regression and classification objectives, aiming to maximize data utilization and improve predictive performance by leveraging two complementary tasks. In our setup, the regression yields the binding affinity, whereas the classification task yields the label as active or inactive. We demonstrate our method using PDBbind, the standard 3D structure database, as well as a dataset of flavivirus protease compounds with binding affinity data. Our experiments show that the new joint training strategy improves the accuracy of the model, increasing applicability in various practical drug screening scenarios.

Biological and medical sciences↗

DOE OSTI2024

Optimizing High-Throughput Inference on Graph Neural Networks at Shared Computing Facilities with the NVIDIA Triton Inference Server

Abstract With machine learning applications now spanning a variety of computational tasks, multi-user shared computing facilities are devoting a rapidly increasing proportion of their resources to such algorithms. Graph neural networks (GNNs), for example, have provided astounding improvements in extracting complex signatures from data and are now widely used in a variety of applications, such as particle jet classification in high energy physics (HEP). However, GNNs also come with an enormous computational penalty that requires the use of GPUs to maintain reasonable throughput. At shared computing facilities, such as those used by physicists at Fermi National Accelerator Laboratory (Fermilab), methodical resource allocation and high throughput at the many-user scale are key to ensuring that resources are being used as efficiently as possible. These facilities, however, primarily provide CPU-only nodes, which proves detrimental to time-to-insight and computational throughput for workflows that include machine learning inference. In this work, we describe how a shared computing facility can use the NVIDIA Triton Inference Server to optimize its resource allocation and computing structure, recovering high throughput while scaling out to multiple users by massively parallelizing their machine learning inference. To demonstrate the effectiveness of this system in a realistic multi-user environment, we use the Fermilab Elastic Analysis Facility augmented with the Triton Inference Server to provide scalable and high-throughput access to a HEP-specific GNN and report on the outcome.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

The chemical nature of the young 120-Myr-old nearby Pisces–Eridanus stellar stream flowing through the Galactic disc

Recently, a new cylindrical-shaped stream of stars up to 700 pc long was discovered hiding in the Galactic disc using kinematic data enabled by the Gaia mission. This stream of stars, dubbed Pisces–Eridanus (Psc–Eri), was initially thought to be as old as 1 Gyr, yet its stars shared a rotation period distribution consistent with a population that was 120 Myr old. Here, we explore the detailed chemical nature of this stellar stream. We carried out high-resolution spectroscopic follow-up of 42 Psc–Eri stars using McDonald Observatory and combined these data with information for 40 members observed with the low-resolution LAMOST spectroscopic survey. Together, these data enabled us to measure the abundance distribution of light/odd-Z (Li, Na, Al, Sc, V), α (Mg, Si, Ca, Ti), Fe-peak (Cr, Mn, Fe, Co, Ni, Zn), and neutron capture (Sr, Y, Zr, Ba, La, Nd, Eu) elements along the Psc–Eri stream. We find that the stream is (1) near-solar metallicity with [Fe/H] = –0.03 dex and (2) has a metallicity spread of 0.07 dex (or 0.04 dex when outliers are excluded). We also find that (3) the abundance of Li indicates that Psc–Eri is ~120 Myr old, consistent with its gyrochronology age. Additionally, Psc–Eri has (4) [X/Fe] abundance spreads that are just larger than the typical uncertainty in most elements, (5) it is a cylindrical-like system whose outer edges rotate about the centre, and (6) no significant abundance gradients along its major axis except a potentially weak gradient in [Si/Fe]. These results show that Psc–Eri is a uniquely close young chemically interesting laboratory for testing our understanding of star and planet formation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

2022 Bull E-Bike Pilot Program Study

In 2022, the City of Durham conducted an e-bike pilot program study to learn more about how electric bikes (e-bikes) could improve the transportation experience in the "Bull City" (a.k.a., Durham, North Carolina). The study used pedal-assist e-bikes, which feature an electric motor and battery to help power the bike. The motor amplifies the power behind each pedal stroke, augmenting the energy you put into the bike. #### Data Collection Agency The City of Durham's Transportation Department conducted the study. #### Survey Methodology Program participants used electric-assist e-bikes for at least 4 weeks between August and November 2022 in exchange for sharing information about their experiences, including tracking their travel via a smartphone app. In addition to the e-bike, participants received maintenance support along with a helmet, bike lock, and other accessories. Data collection was enabled by the [NLR OpenPATH platform](https://www.nlr.gov/transportation/openpath.html). #### Survey Records and Data Survey records include a total of 76 participants. The dataset contains 3 months of partially automated travel diaries, combining sensed and surveyed travel behavior data—patterns of multimodal, end-to-end, individual human mobility—as well as demographic and socioeconomic information from participants. The number of total trips was 6,488, the number of e-bike trips was 2,183, and the number of e-bike miles traveled was 5,450.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

UPC++ v1.0 Programmer’s Guide, Revision 2020.10.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

$\overline{TKE}$ Parameterization and $\bar{v}$ Uncertainty Analysis for CGMF

Previous work was performed on tuning CGMF parameters for 235 U, 238 U, and Plutonium isotopes. Now work is being done to tune minor uranium isotopes. However, uranium isotopes like 232 U and 236 U have almost no experimental data. We are applying cross-isotope models to extrapolate and tune CGMF on isotopes that lack experimental data. There exist several internal CGMF physics quantities that affect the output of CGMF—multi-chance fission probability, excitation energy sharing, spin-cutoff factor, spin scaling, and fragment total kinetic energy to name a few. The mean fragment total kinetic energy, $\overline{TKE}$, is particularly interesting because of its strong anti-correlation with $\bar{v}$. We are most interested in the mean fragment total kinetic energy before neutron emissions. $\overline{TKE}$ is assumed to be pre-neutron emission unless otherwise stated. Currently in CGMF, the $\overline{TKE}$ model for 233,234,235,238 U are tuned independently to reproduce ν for the associated isotopes. In this report, we will tune a cross-isotope $\overline{TKE}$ model to experimental $\overline{TKE}$ data for 232,233,234,235,236,238 U. Because of the unreliable and sparse nature of $\overline{TKE}$ experimental data, future work will use more reliable experimental $\bar{v}$ data to infer the $\overline{TKE}$ model (and likely other internal CGMF parameters) for uranium isotopes. Such work has been performed previously using a sensitivity analysis and Kalman filter methods.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2023

Genomes_SET2_178 - Shared

The dataset consists of 178 bacterial genomes in total. Of these, 145 genomes were drawn from published literature linked to Biolog Gen III growth data, while 33 genomes came from soil isolates collected at the Cedar Creek Ecosystem Science Research Reserve (CCESR) in Minnesota. The isolates were sequenced on an Illumina HiSeq platform (~50× coverage), assembled with Megahit, and annotated using RAST at PATRIC, with strict quality filtering (<90% completeness or >5% contamination).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

Abstract Summary Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences. Availability and implementation https://edge-covid19.edgebioinformatics.org, and https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗