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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular and structural characterization of a Bacillus cereus strain producing an anthrax-like capsule

Bacillus cereus is a ubiquitous Gram-positive, spore-forming, rod-shaped saprophytic bacterium, occasionally reported to cause food-borne illnesses. However, instances of B. cereus strains harboring anthrax toxin and capsule genes have elevated certain strains as formidable pathogens and biothreats. This study focuses on the genomic analysis and the structural characterization of capsular material produced by the virulent B. cereus PATH2418 strain, isolated from the wound of a traumatic open fracture patient. The genome was sequenced using Nanopore MinION sequencing, revealing a chromosome of 5,270,283 bp and three plasmids. One plasmid, pATH1, was found to encode an operon for the biosynthesis of a bacterial capsule. This operon had sequence homology to the Bacillus anthracis capBCADE operon, which encodes the poly-γ-D-glutamate (PDGA) capsule. The capsule production in B. cereus PATH2418 was influenced by temperature and CO 2 levels. Structural analysis of the capsular material using a combined approach of nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC) techniques confirmed the presence of a high-molecular-weight poly-γ-glutamate capsule, with an enantiomeric composition of approximately 67% D-glutamic acid and 33% L-glutamic acid, matching that of B. anthracis.

Bacillus cereus↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2022

MIONet: Learning Multiple-Input Operators via Tensor Product

As an emerging paradigm in scientific machine learning, neural operators aim to learn operators, via neural networks, that map between infinite-dimensional function spaces. Several neural operators have been recently developed. However, all the existing neural operators are only designed to learn operators defined on a single Banach space; i.e., the input of the operator is a single function. Here, for the first time, we study the operator regression via neural networks for multiple-input operators defined on the product of Banach spaces. We first prove a universal approximation theorem of continuous multiple-input operators. We also provide a detailed theoretical analysis including the approximation error, which provides guidance for the design of the network architecture. Based on our theory and a low-rank approximation, we propose a novel neural operator, MIONet, to learn multiple-input operators. MIONet consists of several branch nets for encoding the input functions and a trunk net for encoding the domain of the output function. Here, we demonstrate that MIONet can learn solution operators involving systems governed by ordinary and partial differential equations. In our computational examples, we also show that we can endow MIONet with prior knowledge of the underlying system, such as linearity and periodicity, to further improve accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Charging and ion ejection dynamics of large helium nanodroplets exposed to intense femtosecond soft xray pulses

Ion ejection from charged helium nanodroplets exposed to intense femtosecond soft X-ray pulses is studied by single-pulse ion time-of-flight (TOF) spectroscopy in coincidence with small-angle X-ray scattering. Scattering images encode the droplet size and absolute photon flux incident on each droplet, while ion TOF spectra are used to determine the maximum ion kinetic energy, Ekin, of He+ j fragments (j = 1-4). Measurements span HeN droplet sizes between N similar to 10(7) and similar to 10(10) (radii R-0 = 78-578 nm), and droplet charges between similar to 9x10(-5) and similar to 3x10(-3) e/atom. Conditions encompass a wide range of ionization and expansion regimes, from departure of all photoelectrons from the droplet, leading to pure Coulomb explosion, to substantial electron trapping by the electrostatic potential of the charged droplet, indicating the onset of hydrodynamic expansion. The unique combination of absolute Xray intensities, droplet sizes, and ion Ekin on an event-by-event basis reveals a detailed picture of the correlations between the ionization conditions and the ejection dynamics of the ionic fragments. The maximum E-kin of He+ is found to be governed by Coulomb repulsion from unscreened cations across all expansion regimes. The impact of ion-atom interactions resulting from the relatively low charge densities is increasingly relevant with less electron trapping. The findings are consistent with the emergence of a charged spherical shell around a quasineutral plasma core as the degree of ionization increases. The results demonstrate a complex relationship between measured ion E-kin and droplet ionization conditions that can only be disentangled through the use of coincident single-pulse TOF and scattering data.

Helium↗
DOE OSTI2022

Misanthropic entropy and renormalization as a communication channel

A central physical question is the extent to which infrared (IR) observations are sufficient to reconstruct a candidate ultraviolet (UV) completion. We recast this question as a problem of communication, with messages encoded in field configurations of the UV being transmitted to the IR degrees of freedom via a noisy channel specified by renormalization group (RG) flow, with noise generated by coarse graining/decimation. We present an explicit formulation of these considerations in terms of lattice field theory, where we show that the “misanthropic entropy” — the mutual information obtained from decimating neighbors — encodes the extent to which information is lost in marginalizing over/tracing out UV degrees of freedom. Our considerations apply both to statistical field theories as well as density matrix renormalization of quantum systems, where in the quantum case, the statistical field theory analysis amounts to a leading-order approximation. As a concrete example, we focus on the case of the 2D Ising model, where we show that the misanthropic entropy detects the onset of the phase transition at the Ising model critical point.

Physics↗
DOE OSTI2023

Qompress: Efficient Compilation for Ququarts Exploiting Partial and Mixed Radix Operations for Communication Reduction

Quantum computing is in an era of limited resources. Current hardware lacks high fidelity gates, long coherence times, and the number of computational units required to perform meaningful computation. Contemporary quantum devices typically use a binary system, where each qubit exists in a superposition of the 0 and 1 states. Furthermore, it is often possible to access the 2 or even 3 states in the same physical unit by manipulating the system in different ways. In this work, we consider automatically encoding two qubits into one four-state ququart via a compression scheme. We use quantum optimal control to design efficient proof-of-concept gates that fully replicate standard qubit computation on these encoded qubits.

compilation↗
DOE OSTI2023

Parameter Estimation for Decoding Sensor Signals

This paper introduces a parameter estimation approach for decoding digital sensor signals in a cyber-physical system. For unknown or not fully characterized digital sensor data, it can be difficult to decipher a desired signal from background or noise. In a cyber-physical system with networked sensors, we can leverage knowledge of the physical system to inform the decoding of the digital signals. This work in progress is a case study on deciphering commercial vehicle on-board sensor networks that communicate through the Controller Area Network (CAN). By understanding the stock vehicle sensor network, a vehicle can be extended into a scalable research platform with minimal instrumentation. Our challenge was to localize desired sensor signals encoded in network traffic that included other sensor data, control messages, as well as encoding and security overhead. Due to the vehicle’s unknown sensor network, our approach developed methods to efficiently analyze and identify key signals despite the large state-space for potential signal embeddings.

Nice, Matthew↗
DOE OSTI2023

On-Sensor Data Filtering using Neuromorphic Computing for High Energy Physics Experiments

This work describes the investigation of neuromorphic computing-based spiking neural network (SNN) models used to filter data from sensor electronics in high energy physics experiments conducted at the High Luminosity Large Hadron Collider. We present our approach for developing a compact neuromorphic model that filters out the sensor data based on the particle's transverse momentum with the goal of reducing the amount of data being sent to the downstream electronics. The incoming charge waveforms are converted to streams of binary-valued events, which are then processed by the SNN. We present our insights on the various system design choices - from data encoding to optimal hyperparameters of the training algorithm - for an accurate and compact SNN optimized for hardware deployment. Our results show that an SNN trained with an evolutionary algorithm and an optimized set of hyperparameters obtains a signal efficiency of about 91% with nearly half as many parameters as a deep neural network.

R. Kulkarni, Shruti↗
DOE OSTI2025

HP-MDR: High-performance and Portable Data Refactoring and Progressive Retrieval with Advanced GPUs

Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data retrieval with significantly reduced data movement cost. However, most existing progressive methods are designed for CPUs, leaving a gap for them to unleash the power of today’s heterogeneous computing systems with GPUs.In this work, we propose HP-MDR, a high-performance and portable data refactoring and progressive retrieval framework for GPUs. Our contributions are four-fold: (1) We carefully optimize the bitplane encoding and lossless encoding, two key stages in progressive methods, to achieve high performance on GPUs; (2) We propose pipeline optimization and incorporate it with data refactoring and progressive retrieval workflows to further enhance the performance for large data process; (3) We leverage our framework to enable high-performance data retrieval with guaranteed error control for common Quantities of Interest; (4) We evaluate HP-MDR and compare it with state of the arts using five real-world datasets. Experimental results demonstrate that HP-MDR delivers an average 13.68 × and 6.31 × throughput in data refactoring and progressive retrieval tasks, respectively. It also leads to 11.22 × throughput for recomposing required data representations under Quantity-of-Interest error control and 6.04 × performance for the corresponding end-to-end data retrieval, when compared with state-of-the-art solutions.

Li, Yanliang [University of Oregon]↗
DOE OSTI2026

QProR: An Efficient Framework for Quantity-of-Interest Based Progressive Retrieval with Guaranteed Error Control

Scientific applications generate an unprecedented volume of data, overwhelming the network and file systems’ bandwidth and posing challenges for efficient and scalable data retrieval and analysis. Progressive data compression offers a promising solution by enabling on-demand retrieval at reduced size. However, existing progressive methods either fail to bound the errors in essential quantities of interest (QoIs) derived from raw data or suffer from suboptimal retrieval efficiency. In this work, we propose QProR, an efficient QoI-based progressive framework that optimizes progressive retrieval for target QoIs. Our key contributions include: (1) a systematic framework that integrates error-controlled lossy compressors with bitplane encoding while decoupling the two processes for high flexibility and adaptability; (2) a novel weighted bitplane encoding method which incorperates QoI knowledge into data refactoring to enhance retrieval efficiency; (3) an optimized retrieval strategy that accounts for the varying impacts of different variables on multivariate QoIs; (4) comprehensive evaluations using six real-world datasets from multiple scientific applications and thorough comparisons against state of the arts. Experimental results demonstrate that QProR achieves up to 80.38% reduction in the retrieval size under the same requested QoI error tolerance, when compared with the best-performing existing methods. When transferring 384 GB of scientific data to remote sites, QProR delivers up to 1.68 × speedup in the end-to-end data transfer performance.

Li, Wenbo [University of Kentucky]↗
DOE OSTI2026

Emerging Flexible Designs for Geospatial Multimodal Foundation Models

Foundation models are rapidly transforming Earth observation by enabling scalable pretraining across diverse unlabeled geospatial modalities. However, their architectural diversity—ranging from encoder-only to encoder-decoder and masked autoencoding paradigms—makes it challenging to assess performance trade-offs in a consistent manner. In this work, we present an apples-to-apples comparison of leading FM architectures designed for geospatial multimodal reasoning, with a particular focus on flexibility across varied spectral band configurations. We standardize pretraining using identical self-supervised learning objectives and training datasets, and evaluate all models under consistent parameterization on the GEOBench benchmark across classification and segmentation tasks. Our results offer new insights into the design trade-offs between model flexibility, modality alignment, and downstream task performance. By highlighting architectural strengths and limitations under controlled conditions, this study provides practical guidance for building next-generation geospatial foundation models capable of robust multimodal reasoning.

Ambrozio Dias, Philipe [ORNL] (ORCID:0000000194277↗
DOE OSTI2023

GRAPH CONVOLUTIONAL NEURAL NETWORK (GCNN)FOR POLYMER PROPERTY PREDICTION

SF-22-121 Graph convolutional neural networks (GCNN) are powerful machine learning models that apply a message-passing algorithm on adjacent nodes in a graph. Due to the natural representation of molecules via discrete graphs (where nodes encode atoms and edges encode bonds), GCNNs are an intuitive machine learning model chemical space informatics, including the prediction of polymer properties. Here, molecules are represented in feature and adjacency matrices where they are directly used as inputs to a GCNN.

FEINSTEIN, JEREMY↗
DOE OSTI2022

U-Net Decoder CRF v0.1.0

We introduce a new encoder-decoder system that overcomes adaptability and scalability issues. We adapt multiple CNNs as encoders, allowing for the definition of multiple function parameter arguments to structure the models according to the targeted datasets and scientific problem. We leverage the flexibility of the U-Net architecture to act as a scalable decoder. The CRF-RNN layer is integrated into the decoder as an optional final layer, keeping the entire system fully compatible with back-propagation.

Avaylon, Matthew↗
DOE OSTI2024

Deep Learning-based Non-Stationary Bias Correction (NSBC)

This work develops the NSBC (non-stationary bias correction) methodology to correct temperature projection bias from E3SM. The NSBC deep learning framework consists of a three-part architecture: an auto-encoder for compressing the spatial information, an LSTM for predicting annual temperature mean, and a U-Net for capturing the residual bias in temperature. The non-stationary bias correction (NSBC) framework can correct the non-stationarity of the biases of the climate models, which significantly improves the accuracy of future temperature prediction and improves the overestimation of extreme high temperatures that many existing bias correction methods suffer from. Getting started 1. Obtain the historical climate simulation and observation data. The E3SM simulation data are available through https://aims2.llnl.gov/search/cmip6/. The pseudo observations, the Geophysical Fluid Dynamics Laboratory (GFDL)-ESM4 model (Krasting et al., 2018) are available through https://aims2.llnl.gov/search/cmip6/. The spatial resolution of E3SM and pseudo observation datasets are both regridded to a common 1° resolution grid using conservative interpolation. The regridded E3SM and pseudo observation with 1° resolution can be found throught ./data/. 2. Train the Auto-encoder model. Python 0-autoencoder.py 3. Train the LSTM Python 1-LSTM.py 4. Generate the annual mean temperature based on trained LSTM Python 2-generate_annual_mean_LSTM.py 5. Train the U-Net. Python 3-unet.py 6. Evaluation and compared with the baseline Python 4_evaluation.py Is there a deadline approaching that requires the release of yo

Lucas, Donald↗
DOE OSTI2025

Implementation of ISO 15118-202 messages within Everest EV Charging Open Source Framework [SWR-25-56]

This software implements the messages defined in the ISO 15118-202 standard within the Everest EV Charging open source framework. The protocol and messages defined in the ISO 15118-202 standard enable the exchange of additional information which is not available for exchange within the currently deployed EV/EVSE communications protocols. This information includes co-identification parameters, error message exchange and more. This fork of the everest-core repository adds a prototype of the Extensible Supply Equipment Communication Controller (SECC) Discovery Protocol (ESDP) implemented based on a draft of the ISO 15118-202 standard. This is achieved through additions and modifications to the EvseV2G module. The implementation provides a demonstration of the ESDP messages, encoding and decoding but does not include a full integration within the Everest framework. Much of the information being sent over ESDP in this implementation is set statically for the sake of demonstrating the protocol itself. This fork of the ext-switchev-iso15118 repository adds a prototype of the Extensible Supply Equipment Communication Controller (SECC) Discovery Protocol (ESDP) implemented based on a draft of the ISO 15118-202 standard. The implementation provides a demonstration of the ESDP messages, encoding and decoding but does not include a full integration within the Everest framework. Much of the information being sent over ESDP in this implementation is set statically for the sake of demonstrating the protocol itself. This fork adds the ESDP features for only the EVCC controller because that is the only portion that is utilized in the everest Software-in-the-Loop.

Watt, Ed [National Renewable Energy Laboratory (NR↗
DOE OSTI2025

genomeocean: a pretrained microbial genome foundational model (genomeoceanLLM) v1.0

We present Genomeocean, a foundational genome language model that represents the microbial genome sequences from complex environmental samples. By training on a large, diverse metagenomic dataset, Genomeocean learns species-specific sequence composition and can generate long, realistic open reading frames (ORFs). Our model employs a Byte-pair-encoding (BPE) tokenization strategy, allowing it to efficiently process large genomic datasets and generate long sequences up to 50kb. We demonstrate that fine-tuning Genomeocean can generate novel gene clusters encoding biosynthetic pathways, showcasing its ability to model both fundamental and complex biological processes. Our work establishes Genomeocean as a powerful tool for understanding microbial genome biology and paves the way for its application in a range of fields, from synthetic biology to microbiome research.

Wang, Zhong [Lawrence Berkeley National Laboratory↗
DOE OSTI2023

Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Multiple myeloma (MM) is a highly refractory hematologic cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single-cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which were previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA sequencing reiterated top candidates, further affirming the ability of single-cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

59 BASIC BIOLOGICAL SCIENCES↗