Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence development”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Dissipation Enables Strongly Detuning-Dependent Interference in Pulsed Dynamical Decoupling

One of the defining features of pulsed dynamical decoupling is its suppression of a driven qubit's sensitivity to static detuning errors between the drive field and qubit resonance. In this paper, we show that dissipation, in the form of excited-state decay, can change this behavior entirely, producing an interference signal with a strong detuning dependence. This signal arises from decay during driven evolution and relies on coherence retained by the qubit after such a decay event. We develop analytical and numerical models that capture the underlying mechanism and observe this same dissipation-induced detuning dependence experimentally in both a free-space strontium atom interferometer and a superconducting transmon qubit system. We also use this dissipation-induced detuning dependence as the basis for a new spectroscopic technique called Dissipative Carr-Purcell Spectroscopy (DCPS) and compare it with a traditional Ramsey sequence. Our results establish a regime of pulsed dynamical decoupling in which dissipation reshapes, rather than merely degrades, coherent control, and we expect these dynamics to be relevant to a wide range of quantum systems.

DeRose, Kenneth [Northwestern U.; Fermilab] (ORCID↗
DOE OSTI2026

Single-cell and spatial omics in plants: from cellular atlases to regulatory mechanisms

Single-cell RNA sequencing (scRNA-seq) has transformed transcriptomic studies by enabling gene expression profiling at the resolution of individual cells within and across a broad range of tissue types, revealing cellular heterogeneity that is obscured in bulk tissue transcriptomes. Over the past decade, improvements in microfluidics and library preparation have drastically increased throughput, allowing tens of thousands of cells to be assayed in a single experiment. Although initially developed in animal systems, scRNA-seq has rapidly emerged as a powerful and widely adopted approach in plant biology. Beyond transcriptomics, the integration of single-cell data with chromatin accessibility, proteomics, metabolomics, and spatial omics is enabling a system-level understanding of plant gene regulation and cellular organization. Network-based analytical frameworks further support the reconstruction of gene regulatory networks and the interpretation of complex single-cell data. In this review, we summarize the current technological landscape of plant single-cell studies, discuss key experimental and analytical challenges, and review emerging strategies for validating single-cell discoveries. We also discuss future directions in applying single-cell technologies to woody perennials plants and bioenergy-relevant crops, emphasizing their potential to accelerate the discovery of cell type-specific regulatory mechanisms underlying growth, stress resilience, and biomass production.

Li, Miaomiao [ORNL] (ORCID:0000000321326168)↗
DOE OSTI2025

Superspin renormalization and slow relaxation in random spin systems

We develop an excited-state real-space renormalization group (RSRG-X) formalism to describe the dynamics of conserved densities in randomly interacting spin-12 systems. Our formalism is suitable for systems with U(1) and Z2 symmetries, and we apply it to chains of randomly positioned spins with dipolar XX+YY interactions, as arise in Rydberg quantum simulators and other platforms. The formalism generates a sequence of effective Hamiltonians that provide approximate descriptions for dynamics on successively smaller energy scales. These effective Hamiltonians involve “superspins”: two-level collective degrees of freedom constructed from (anti)aligned microscopic spins. Conserved densities can then be understood as relaxing via coherent collective spin flips. For the well-studied simpler case of randomly interacting nearest-neighbor XX+YY chains, the superspins reduce to single spins. Our formalism also leads to a numerical method capable of simulating the dynamics up to an otherwise inaccessible combination of large system size and late time. Focusing on disorder-averaged infinite-temperature autocorrelation functions, in particular the spin survival probability Sp¯(t), we demonstrate quantitative agreement between our algorithm and exact diagonalization (ED) at low but nonzero frequencies. Such agreement holds for chains with nearest-neighbor, next-nearest-neighbor, and long-range dipolar interactions. Our results indicate decay of Sp¯(t) slower than any power law and feature no significant deviation from the ∼1/ln2(t) asymptote expected from the infinite-randomness fixed-point of the nearest-neighbor model. We also apply the RSRG-X formalism to two-dimensional long-range systems of moderate size and find slow late-time decay of Sp¯(t).

Zhao, Yi J↗
DOE OSTI2026

A Prodrug Strategy to Conditionally Trap Therapeutic Payloads for Improved Tumor Retention

Altered extracellular proteolysis has been exploited to selectively activate therapeutics in diseases such as cancer; however, once activated, extracellular drugs can diffuse away, limiting efficacy. We address this challenge by coupling proteolytic activation with membrane tethering to retain drugs within diseased tissue. To accomplish this, we developed “restricted interaction peptides” (RIPs), a delivery platform that leverages elevated proteolytic activity to activate membrane-interacting peptides, localizing cargos near the site of proteolysis. We demonstrate that RIPs can deliver diverse therapeutic cargos, including cytotoxins and radioisotopes. As proof of concept, we engineered “FRIP,” a RIP designed for cleavage by fibroblast activation protein (FAP), an endoprotease upregulated in solid tumors and fibrosis. Efficient P4–P4’ substrate sequences were identified and incorporated into FRIPs. Cell-based studies showed that, upon activation, the peptide adhered to membranes rapidly internalized and successfully delivered therapeutic cargos. Consistent with this, FRIPs delivering MMAE inhibited proliferation in an FAP-dependent manner. Imaging studies confirmed tumor targeting with minimal uptake in normal tissues. Finally, FRIPs delivering MMAE or Cu-67 exhibited potent antitumor effects. These findings establish membrane tethering as a strategy to enhance drug retention.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

Abstract Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN)cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. We evaluate enhancer activity for 59 elements using an in vivo transgenic assay and validate 44 (75%), demonstrating that single cell accessibility can be a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieve significant reduction in our variant search space and nominate candidate variants predicted to regulate known CCDD disease genesMAFB, PHOX2A, CHN1, andEBF3– as well as candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work delivers non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.

Science & Technology - Other Topics↗
DOE OSTI2025

Breeding of microbiomes conferring salt tolerance to plants

Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Quantum simulations of hadron dynamics in the Schwinger model using 112 qubits

Hadron wave packets are prepared and time evolved in the Schwinger model using 112 qubits of IBM’s 133-qubit Heron quantum computer ibm_torino. The initialization of the hadron wave packet is performed in two steps. First, the vacuum is prepared across the whole lattice using the recently developed SC-ADAPT-VQE algorithm and workflow. SC-ADAPT-VQE is then extended to the preparation of localized states, and used to establish a hadron wave packet on top of the vacuum. This is done by adaptively constructing low-depth circuits that maximize the overlap with an adiabatically prepared hadron wave packet. Due to the localized nature of the wavepacket, these circuits can be determined on a sequence of small lattices using classical computers, and then robustly scaled to prepare wave packets on large lattices for simulations using quantum computers. Time evolution is implemented with a second-order Trotterization. To reduce both the required qubit connectivity and circuit depth, an approximate quasilocal interaction is introduced. This approximation is made possible by the emergence of confinement at long distances, and converges exponentially with increasing distance of the interactions. Using multiple error-mitigation strategies, up to 14 Trotter steps of time evolution are performed, employing 13,858 two-qubit gates (with a CNOT depth of 370). The propagation of hadrons is clearly identified, with results that compare favorably with Matrix Product State simulations. Finally, prospects for a near-term quantum advantage in simulations of hadron scattering are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A Sensitivity-driven Wide Area Protection (SWAP) Coordination Tool for High Penetration of Inverter-based Resources (IBR)

Traditionally, power system generation sources have been composed of synchronous generators, of which the fault current behavior is understood with minimal differences between generation size and types due to the physics of their construction. Present protection schemes and modeling methods are based upon these understood characteristics. Most renewable generation is composed of inverter-based resources (IBR), in which fault current is determined by switching control software and hardware limitations, each of which can vary between manufacturers and even between models of the same manufacturer. The resulting fault current is low in magnitude, low in negative-sequence current, unpredictable phase angles, and is a challenge to model. These characteristics also result in a challenge to traditional protection schemes and fault simulation software. To address several of these concerns, the project has the following goals: 1. Improve IBR models: Improve IBR models used in short circuit (SC) programs to accurately capture the response of IBRs at the bulk power system (BPS) level for fault and protection studies. 2. Develop automation tool: Develop an automation tool that allows engineers to identify protection coordination and sensitivity issues by performing SC and protection coordination studies in a high IBR-penetrated grid by applying variations to the IBR models, faults, contingencies, etc. 3. Develop schemes: Develop new protection mitigation solution schemes that complement the existing protection systems to ensure safe operation of the BPS with higher IBR penetration levels. The project team did not achieve this final goal, as the Department of Energy (DOE) stopped the project early due to changes in DOE funding priorities. The termination notice came at the beginning of the final project phase, while the team was identifying and beginning to investigate protection issues. It should be noted that the team discussed a 100% penetration scenario. However, this scenario would require the use of grid-forming IBR models that are not presently available. Since developing these models requires additional effort, the 100% penetration scenario was not pursued during this project. In the future, developing the methodology and models for the 100% scenario could benefit the industry.

14 SOLAR ENERGY↗
DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗
DOE OSTI2025

Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic Caldicellulosiruptorales

ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The orderCaldicellulosiruptoraleshas drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction ofAnaerocellum (f. Caldicellulosiruptor) besciiidentified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair withinA. besciiis conserved in all sequenced species ofCaldicellulosiruptorales, suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes forA. bescii. These results show that two separate regulatory schemes (dual repression) are coordinated byA. besciito effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned.Anaerocellum bescii, the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

Biotechnology & Applied Microbiology↗
DOE OSTI2024

Integration of equitable resilience metrics into climate-informed electric utility planning processes: phase one

Working together, Sandia National Laboratories, Southern California Edison (SCE) - an Investor-Owned Utility (IOU) - and the California Public Utilities Commission (CPUC) are studying how electric utilities can use equity and resilience metrics to help inform the prioritization and sequencing of resilience-driven infrastructure investments. To this end, this project evaluated “Social Burden,” an equitable resilience metric which measures the potential impact of disruptions in access to non-electric critical services on people and estimates community resilience to these disruptions. The Social Burden was expanded to incorporate SCE’s existing equity metric and applied to evaluate the potential impacts from a range of climate-informed hypothetical outage scenarios developed under SCE’s 2022 Climate Adaptation Vulnerability Assessment. One baseline (“blue-sky”) state and eight different outage scenarios were evaluated to measure the potential impacts of the outages on non-electric infrastructure, critical services, and people. Key findings include: 1) the Social Burden framework is flexible enough to adapt to and build upon existing utility equity and/or resilience metrics, 2) Social Burden results highlight the high degree of non-electric service redundancy within the SCE service area with most (6/8) hypothetical outage scenarios predicted to increase people’s Social Burden by less than 10%; however, 3) access to critical services and people’s ability to obtain them is unequal and spatially clustered, meaning that there are some hypothetical outage scenarios (2/8) that will exert a higher toll on communities directly experiencing the outage as well as some nearby communities with pre-existing vulnerabilities. The report concludes with recommendations for potential use cases of the expanded Social Burden metric and identifies priority follow-on work. Potential use cases may include incorporating equity into IOU’s prioritization of climate resilience investments. Additionally, Social Burden analysis may provide additional data and insights to augment grid planning, potentially by identifying additional needs and/or prioritizing previously identified needs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Functional characterization of glycosyltransferases in duckweed to enable predictive biology

Glycosyltransferases (GTs) catalyze the formation of glycosidic linkages to produce almost all complex carbohydrates. This project used a multi-disciplinary, high-throughput (HTP) biochemical and computational biology approach focused on duckweed as a model energy crop, to study carbohydrate metabolic processes. To achieve this, developed and carried out out high-throughput (HTP) functional characterization of plant glycosyltransferases (GTs) role of enzymatic microenvironments be assessed through a combined proteomic and computational biology approach, and the combined data was used to populate deep-learning frameworks to predict plant GT function. Functional validation achieved through this research is being used to assign gene function and study plant processes at the systems level to efficiently link the genome sequence with gene function. Together, the combined approaches used within this study provide a foundation for how computational prediction, in combination with high-throughput functional validation, can be used to study plant processes at the systems level and translate knowledge gained to efficiently link genome sequence with gene function in a species agnostic manner.

09 BIOMASS FUELS↗
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
DOE OSTI2024

Assessing Inverter-Based Resources Modeling Gaps in Commonly Used Short-Circuit Programs

Future bulk power systems are expected to operate with a high penetration of inverter-based resources (IBR). This is anticipated to fundamentally change the system’s short-circuit behaviors and demand a change in existing transmission line protection settings or schemes. Phasor-domain short circuit programs (e.g., ASPEN, CAPE, and CYME) remain the mainstream tools for developing protection settings. However, the system protection community has shared concerns about the accuracy of IBR models in short-circuit programs. This report compares the performance of existing generic IBR models in short-circuit programs with detailed electro-magnetic transient (EMT) models provided by several different IBR manufacturers in PSCAD, to quantify the short-circuit program’s IBR model accuracy, assess their ability to replicate individual IBR controls such as negative sequence current injections, and identify specific gaps in the existing generic phasor-domain IBR models that are currently available.

42 ENGINEERING↗
DOE OSTI2024

Unusual plastic strain-induced phase transformation phenomena in silicon

Pressure-induced phase transformations (PTs) in Si, the most important electronic material, have been broadly studied, whereas strain-induced PTs have never been studied in situ. Here, we reveal in situ various important plastic strain-induced PT phenomena. A correlation between the direct and inverse Hall-Petch effect of particle size on yield strength and pressure for strain-induced PT is predicted theoretically and confirmed experimentally for Si-I→Si-II PT. For 100 nm particles, the strain-induced PT Si-I→Si-II initiates at 0.3 GPa under both compression and shear while it starts at 16.2 GPa under hydrostatic conditions. The Si-I→Si-III PT starts at 0.6 GPa but does not occur under hydrostatic pressure. Pressure in small Si-II and Si-III regions of micron and 100 nm particles is ~5–7 GPa higher than in Si-I. For 100 nm Si, a sequence of Si-I → I + II → I + II + III PT is observed, and the coexistence of four phases, Si-I, II, III, and XI, is found under torsion. Retaining Si-II and single-phase Si-III at ambient pressure and obtaining reverse Si-II→Si-I PT demonstrates the possibilities of manipulating different synthetic paths. The obtained results corroborate the elaborated dislocation pileup-based mechanism and have numerous applications for developing economic defect-induced synthesis of nanostructured materials, surface treatment (polishing, turning, etc.), and friction.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Preparing angular momentum eigenstates using engineered quantum walks

Coupled angular-momentum eigenstates are widely used in atomic and nuclear physics calculations and are building blocks for spin networks and the Schur transform. To combine two angular momenta J 1 and J 2 , forming eigenstates of their total angular momentum J=J 1 +J 2 , we develop a quantum-walk scheme that does not require inputting O(j 3 ) nonzero Clebsch–Gordan (CG) coefficients classically. In fact, our scheme may be regarded as a unitary method for computing CG coefficients on quantum computers with a typical complexity of O⁡(j) and a worst-case complexity of O⁡(j 3 ). Equivalently, our scheme provides decompositions of the dense CG unitary into sparser unitary operations. Our scheme prepares angular-momentum eigenstates using a sequence of Hamiltonians to move an initial state deterministically to desired final states, which are usually highly entangled states in the computational basis. In contrast with usual quantum walks, whose Hamiltonians are prescribed, we engineer the Hamiltonians in su⁡(2)×su⁡(2), which are inspired by, but different from, Hamiltonians that govern magnetic resonances and dipole interactions. To achieve a deterministic preparation of both ket and bra states, we use projection and destructive interference to double pinch the quantum walks, such that each step is a unit-probability population transfer within a two-level system. We test our state preparation scheme on classical computers, reproducing tables of CG coefficients. Finally, we also implement small test problems on current quantum hardware.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Basics of Electrorefining in the Fuel Cycle Facility

The basic electrochemical concepts that are relevant to the Fuel Cycle Facility electrorefiner (FCF ER) are discussed. Key points are developed in the report that equip the reader to examine the literature for the ER process, and these points are clearly identified. Basic electrochemical concepts are presented and definitions are given prior to a discussion of the energetics and rates of electrorefining. A brief explanation of power supply operation for the electrorefining operation is then given, followed by an elementary discussion of chemical equilibrium. With this background information, FCF ER operations are described in terms of typical operations, their sequence, and the attending chemical reactions.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗