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DOE OSTI2025

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗

DOE OSTI2026

Genomic-based biosurveillance for avian influenza: whole genome sequencing from wild mallards sampled during autumn migration in 2022–2023 reveals a high co-infection rate on migration stopover site in Georgia

The Caucasus region, including Georgia, is an important intersection for migratory waterbirds, offering potential for avian influenza virus (AIV) transmission between populations from different geographic areas. In 2022 and 2023, wild ducks were sampled during autumn migration events in Georgia to study the genetic relationships and molecular characteristics of influenza strains. Sequencing and phylogenetic analysis were used to compare the sampled strains to reference sequences from Africa, Asia, and Europe, allowing assessment of genetic relationships and virus transmission between migratory birds. Protein language modeling identified potential co-infections. Of 225 duck samples, 128 tested positive for the influenza M gene. 55 influenza-positive samples underwent whole-genome sequencing, revealing significant diversity. Analysis of the hemagglutinin (HA) segment showed notable differences among subtypes. Most samples were H6N1 and H6N6, but co-infections with combinations like H6H3, N8N1, N6H9, N2N6, and H9H6/N1N2 were also identified. These findings demonstrate the high variability of influenza viruses in migratory waterbirds in Georgia, including a notable rate of co-infections. Some samples exhibited uncommon genetic characteristics compared to other strains from the same year, suggesting Georgia’s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Deposition, Diagenesis, and Sequence Stratigraphy of the Pennsylvanian Morrowan and Atokan Intervals at Farnsworth Unit

Farnsworth Field Unit (FWU), a mature oilfield currently undergoing CO2-enhanced oil recovery (EOR) in the northeastern Texas panhandle, is the study area for an extensive project undertaken by the Southwest Regional Partnership on Carbon Sequestration (SWP). SWP is characterizing the field and monitoring and modeling injection and fluid flow processes with the intent of verifying storage of CO2 in a timeframe of 100–1000 years. Collection of a large set of data including logs, core, and 3D geophysical data has allowed us to build a detailed reservoir model that is well-grounded in observations from the field. This paper presents a geological description of the rocks comprising the reservoir that is a target for both oil production and CO2 storage, as well as the overlying units that make up the primary and secondary seals. Core descriptions and petrographic analyses were used to determine depositional setting, general lithofacies, and a diagenetic sequence for reservoir and caprock at FWU. The reservoir is in the Pennsylvanian-aged Morrow B sandstone, an incised valley fluvial deposit that is encased within marine shales. The Morrow B exhibits several lithofacies with distinct appearance as well as petrophysical characteristics. The lithofacies are typical of incised valley fluvial sequences and vary from a relatively coarse conglomerate base to an upper fine sandstone that grades into the overlying marine-dominated shales and mudstone/limestone cyclical sequences of the Thirteen Finger limestone. Observations ranging from field scale (seismic surveys, well logs) to microscopic (mercury porosimetry, petrographic microscopy, microprobe and isotope data) provide a rich set of data on which we have built our geological and reservoir models.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2023

DESI Survey Validation Data in the COSMOS/Hyper Suprime-Cam Field: Cool Gas Trace Main-sequence Star-forming Galaxies at the Cosmic Noon

We present the first result in exploring the gaseous halo and galaxy correlation using the Dark Energy Spectroscopic Instrument survey validation data in the Cosmic Evolution Survey (COSMOS) and Hyper Suprime-Cam field. We obtain multiphase gaseous halo properties in the circumgalactic medium by using 115 quasar spectra (signal-to-noise ratio > 3). We detect Mg ii absorption at redshift 0.6 < z < 2.5, C iv absorption at 1.6 < z < 3.6, and H i absorption associated with the Mg ii and C iv. By crossmatching the COSMOS2020 catalog, we identify the Mg ii and C iv host galaxies in 10 quasar fields at 0.9< z < 3.1. We find that within the impact parameter of 250 kpc, a tight correlation is seen between the strong Mg ii equivalent width and the host galaxy star formation rate. The covering fraction f c of the strong Mg ii selected galaxies, which is the ratio of the absorbing galaxy in a certain galaxy population, shows significant evolution in the main-sequence galaxies and marginal evolution in all the galaxy populations within 250 kpc at 0.9 < z < 2.2. The f c increase in the main-sequence galaxies likely suggests the coevolution of strong Mg ii absorbing gas and the main-sequence galaxies at the cosmic noon. Furthermore, Mg ii and C iv absorbing gas is detected out of the galaxy virial radius, tentatively indicating the feedback produced by the star formation and/or the environmental effects.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Saccharomycopsis sp. isolate UFMG-CM-Y6632 large subunit ribosomal RNA gene, partial sequence

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗

DOE OSTI2023

Saccharomycopsis sp. KB-2023a isolate UFMG-CM-Y6991, whole genome shotgun sequencing project

Amazonian Forest↗

DOE OSTI2021

Sequence Impedance Modeling of Grid-Forming Converters: Preprint

Grid-forming control of inverter-based resources (IBRs) has been identified as a critical technology for operating power systems with high levels of inverter-based resources. This paper presents sequence impedance modeling of grid-forming inverters to evaluate its small-signal stability properties. Droop based grid-forming control with full consideration of the multiloop structure is studied, and the impact of individual controller on the inverter impedance characteristics is discussed. The developed sequence impedance model is compared with that of the grid-following inverter. It is found from the developed sequence impedance models that grid-forming inverters are less prone to harmonic resonance problems during operation with weaker grids. The developed models are validated using PSCAD simulations.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2021

Athena: High-Performance Sparse Tensor Contraction Sequence on Heterogeneous Memory

Sparse tensor contraction sequence has been widely employed in many fields, such as chemistry and physics. However, how to efficiently implement the sequence faces multiple challenges, such as redundant computations and memory operations, massive memory consumption, and inefficient utilization of hardware. To address the above challenges, we introduce Athena, a high-performance framework for SpTC sequences. Athena introduces new data structures, leverages emerging Optane-based heterogeneous memory (HM) architecture, and stage parallelism. In particular, Athena introduces shared hash table-represented sparse accumulator to eliminate unnecessary input processing and data migration; Athena uses a novel data-semantic guided dynamic migration solution to make the best use of the Optane-based HM for high performance; Athena also co-runs execution phases with different characteristics to enable high hardware utilization. Evaluating with 12 datasets, we show that Athena brings 327-7362× speedup over the state-of-the-art SpTC algorithm. With the dynamic data placement guided by data semantics, Athena brings performance improvement on Optane-based HM over a state-of-the-art software-based data management solution, a hardware-based data management solution, and PMM-only by 1.58×, 1.82×, and 2.34× respectively.

Liu, Jiawen↗

DOE OSTI2021

Sequence Impedance Modeling of Grid-Forming Inverters

Grid-forming control of inverter-based resources has been identified as a critical technology for operating power systems with high levels of inverter-based resources. This paper presents the sequence impedance modeling of a grid-forming inverter to evaluate its small-signal stability properties. Droop control structure is implemented to control the inverter in grid-forming mode, and the impact of individual controller on the inverter impedance characteristics is discussed. The developed sequence impedance model is compared with that of the grid-following inverter. It is found from the developed sequence impedance models that grid-forming inverters are less prone to harmonic resonance problems during operation with weaker grids. The developed models are validated using PSCAD simulations.

grid-following inverter↗

DOE OSTI2022

Programmable pseudo-random sequence generator for use with universal lidar and its associated method of operation

A pseudo-random sequence generator for use within a universal lidar system and its corresponding method of operation. The pseudo-random sequence generator uses synchronized shift registers that are in series Binary adders are provided. The signal output of each of the shift registers is tapped and directed to the binary adders. High-speed switches are provided between the shift registers and the binary adders. The switches are programmed to connect only two of the shift registers to the binary adders for each of the pseudo-random patterns being generated. The binary adders generate an output signal that is received by the first shift register. The signal propagates through all the shift registers to the last shift register. The last shift register outputs a pseudo-random sequence.

Datta, Shubhashish↗

DOE OSTI2022

Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Here, our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Sequences of seismic and aseismic slip on bimaterial faults show dominant rupture asymmetry and potential for elevated seismic hazard

Here we perform numerical simulations of sequences of earthquake and aseismic slip on planar rate and state faults separating dissimilar material within the 2-D plane strain approximation. We resolve all stages of the earthquake cycle from aseismic slip to fast ruptures while incorporating full inertia effects during seismic event propagation. We show that bimaterial coupling results in favorable nucleation site and subsequent asymmetric rupture propagation. We demonstrate that increasing the material contrast enhances this asymmetry leading to higher slip rates and normal stress drops in the preferred rupture propagation direction. The normal stress drop, induced by the bimaterial effect, leads to strong dynamic weakening of the fault and may destabilize the creeping region on a heterogeneous rate and state fault, resulting in extended rupture propagation. Such rupture penetration into creeping patches may lead to more frequent opening of earthquake gates, causing increased seismic hazard. Furthermore, bimaterial coupling may lead to irregular seismicity pattern in terms of event length, peak slip rates, and hypocenter location, depending on the properties of the creeping patches bordering the seismogenically active part of the fault. Our results highlight robust characteristics of bimaterial interfaces that persist over long sequence of events and suggest the need for further exploration of the role of material contrast in earthquake physics and models of seismic hazard.

58 GEOSCIENCES↗

DOE OSTI2025

Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development

Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsis thaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence of these elements on expression patterns is already exerted during embryogenesis and functional in the context of the early embryo. Finally, we reveal the existence of a BOX-mediated autoregulatory feedback loop that, in large part, explains CNS influence on expression patterns. We thus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.

PLETHORA↗

DOE OSTI2024

One-Pot Self-Assembly of Sequence-Controlled Mesoporous Heterostructures via Structure-Directing Agents

Multimaterial heterostructures have led to characteristics surpassing the individual components. Nature controls the architecture and placement of multiple materials through biomineralization of nanoparticles (NPs); however, synthetic heterostructure formation remains limited and generally departs from the elegance of self-assembly. Here, in this study, a class of block polymer structure-directing agents (SDAs) are developed containing repeat units capable of persistent (covalent) NP interactions that enable the direct fabrication of nanoscale porous heterostructures, where a single material is localized at the pore surface as a continuous layer. This SDA binding motif (design rule 1) enables sequence-controlled heterostructures, where the composition profile and interfaces correspond to the synthetic addition order. This approach is generalized with 5 material sequences using an SDA with only persistent SDA-NP interactions (“P-NP 1 –NP 2 ”; NP i = TiO 2 , Nb 2 O 5 , ZrO 2 ). Expanding these polymer SDA design guidelines, it is shown that the combination of both persistent and dynamic (noncovalent) SDA-NP interactions (“PD-NP 1 –NP 2 ”) improves the production of uniform interconnected porosity (design rule 2). The resulting competitive binding between two segments of the SDA (P- vs D-) requires additional time for the first NP type (NP 1 ) to reach and covalently attach to the SDA (design rule 3). The combination of these three design rules enables the direct self-assembly of heterostructures that localize a single material at the pore surface while preserving continuous porosity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme

We present a coupled finite element spectral boundary integral framework for modeling sequences of earthquakes and aseismic slip on a 2-D planar rate-and-state fault with off-fault visco-plastic response in the plane strain approximation. The model resolves both slow aseismic deformation and inertia effects during rapid slip. As an application, we perform two sets of simulations with different choices of cohesion to explore the co-evolution of fault slip, bulk plasticity and local stress fields. The first set implements a relatively large value of the cohesion parameter, which results in limiting inelastic strain accumulation to dynamic rupture phases. The second set implements a smaller cohesion, allowing for plastic strain to accumulate in both seismic and aseismic phases. For the first model, our results indicate that the extent and distribution of plastic strain depend on the angle of maximum compressive principal stress. At larger angles, inelastic strain accumulates on the extensional side of a dynamically propagating rupture. At smaller angles, the extent of plasticity is limited to the compressional side of the domain. At smaller cohesion values, off-fault plasticity may occur during aseismic slip, which alters the nucleation characteristics and earthquake sequence pattern. Furthermore, our results at lower cohesion values indicate that plastic strain accumulation may occur in both the extensional and compressional sides of the off-fault bulk even at higher angles of maximum compression. In conclusion, this produces damage patterns that deviate from the traditional off-fault fan-like distribution observed in dynamic rupture simulations and emphasizes the significance of long-term deformation in interpreting observations.

58 GEOSCIENCES↗

DOE OSTI2025

Emerging protein sequencing technologies: proteomics without mass spectrometry?

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry. Areas Covered: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. Expert Opinion: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Time Sequence Machine Learning-Based Data Intrusion Detection for Smart Voltage Source Converter-Enabled Power Grid

Smart inverters of distributed energy resources can enable cloud computing, condition monitoring, result visualization, remote control, and peer-to-peer energy trading in advanced power systems. However, the advent of data injection attacks in the communication architecture can alter measurement characteristics of power grids and have devastating consequences. In this article, we propose a time sequence machine learning-based anomaly detection methodology for detecting cyber intrusion into control signal setpoints and dc voltage signal measurement bias of the voltage source converter (VSC) in wind generators. We first investigated the effects of four types of denial of service, tampering signal, and stealthy-type data intrusion attacks on smart VSCs and overall wind farms. We then proposed a novel time sequence machine learning-based intrusion detection framework that can be implemented to detect different cyberattacks in the VSCs. The performance of the proposed framework has been compared with that of autoencoder and clustering-based intrusion detection framework. The proposed framework was validated by using the IEEE 39 bus power system in the presence of four wind farms in different locations. Using several metrics for intrusion detection performance, we validated the effectiveness of the proposed framework.

42 ENGINEERING↗