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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Nucleic Acid-Based Detection Protease Activity

Proteases include clinically relevant markers for clotting disorders, certain cancers as well as toxins. Assays for protease activity often use designed peptides mimicking natural substrates and detection with colorometric and fluorescence-based detection that is difficult to multiplex without expensive and resource demanding instruments. This work demonstrates detection of proteolytic activity using PCR and sequencing-readable reporter molecules. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. Thrombin, an essential component of the clotting cascade, was used as a model system for testing peptide substrate recognition and release of a designed oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing.

Wunschel, David S [Pacific Northwest National Labo↗
DOE OSTI2026

Native Chemical Ligation of Peptoid Oligomers

Bioorganic chemists are inspired by natural biopolymers to design peptidomimetic oligomers that can exhibit sequence-structure-function relationships. Biomimetic polymers can be synthesized to incorporate a specific sequence of nonbiological monomer units using a variety of iterative solution-phase or solid-phase reaction schemes. These protocols generally provide access to a vast diversity of oligomeric compounds but are limited with respect to their ability to attain protein-like chain lengths. This constraint can preclude access to sequence-defined synthetic macromolecules with sufficient sizes required to exhibit tertiary structure and other protein-mimetic attributes. In contrast, peptide chemists have overcome this limitation by developing convergent synthetic methods, such as native chemical ligation, to join individual, smaller peptide chains together to make larger peptides or full proteins. A similar convergent approach is needed to establish efficient synthetic routes to non-natural sequence-defined macromolecules. Herein, we adapt the peptide native chemical ligation method to peptoid oligomers, demonstrating how short chains can be conjoined to create sequence-defined peptoid macromolecules. Nanosheet-forming peptoid polymers with distinct surface loop display domains were generated by sequential ligation of several discrete fragments. This method provides a reliable convergent ligation route for sequence-defined polypeptoids that results in a native amide bond joining the fragments. We envision that this strategy will be useful in synthesizing peptoid-based proteomimetics that incorporate diverse chemical features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Alamos, Simon↗
DOE OSTI2024

Scaling the polymerization of polyaldehydes through continuous flow synthesis

Abstract A plug flow reactor was constructed to scale the synthesis of metastable, phthalaldehyde-based polymers to achieve production rates of 1–2 kg per day. The flow-induced mixing and in-line polymerization quench and precipitation sequences resulted in improved polymer purity and long-term stability compared to the same materials made from a conventional batch process. Cryogenic rheology was used to probe the complex fluid dynamics encountered during the polymerization of PPA homopolymers. It is envisioned that this continuous flow manufacturing approach could be extended to other low ceiling temperature or aldehyde monomer systems to help implement and support a plastic circular economy. Graphical abstract

Schwartz, Jared M.↗
DOE OSTI2025

Tracking Dendritic Growth in Hydrogen-Based Hematite Reduction via Computer Vision

The reduction of hematite to metallic iron using hydrogen (H2) as a reducing agent presents a promising pathway for decarbonizing steel production. In this study, we employ a combination of in situ confocal scanning laser microscopy (CSLM) and advanced computer vision techniques to quantitatively analyze dendritic growth of ferrite during H2-based reduction of iron oxide at high temperatures. A workflow integrating Watershed Image Segmentation (WIS) and Lucas-Kanade Optical Flow (LKOF) is developed to extract both global and local kinetic information from time-resolved micrograph sequences. H2 reduction experiments conducted at 1400 degrees C and 1500 degrees C demonstrate a clear correlation between temperature and reduction rate, as evidenced by accuracy of fitted Johnson-Mehl-Avrami-Kolmogorov (JMAK) parameters. Optical flow analysis further elucidates the anisotropic and branched nature of dendritic growth, providing spatially resolved velocity fields that correlate well with global transformation kinetics. The proposed methodology demonstrates strong agreement with experimental measurements and literature values, offering a robust framework for automated image-based analysis to study kinetics through microstructural evolution in the reduction of iron ore, and likely other reaction-diffusion phenomena.

08 HYDROGEN↗
DOE OSTI2025

Exploring the Effects of Varying Pre-Chamber Geometry in a Heavy-Duty Natural Gas Optical Engine under Dilution Conditions

Pre-chamber combustion is an advanced ignition strategy that has been shown to enhance spark ignition (SI) combustion stability in natural gas (NG) engines by providing distributed ignition sites from turbulent jets and enhancing main-chamber turbulence. Pre-chamber combustion has been proven especially advantageous compared to SI in ultra-lean and dilute operating conditions. This work involves experimental investigation of the effects of varying passive pre-chamber nozzle configuration on pre-chamber and main chamber combustion under simulated exhaust gas recirculation (EGR) dilution (0 and 20%) conditions in a heavy-duty, single-cylinder, optically accessible NG engine at stoichiometric fuel-air ratio. Pre-chamber nozzle configurations include four pre-chambers with constant nozzle area to pre-chamber volume ratio (A/V) with different nozzle sizes and orientations and one configuration with larger nozzles. The optical engine is operated in a skip-fire sequence consisting of 18 motored cycles followed by two consecutive fired cycles to elucidate the effect of combustion residuals (internal EGR) on combustion evolution. Pressure-based diagnostics are used to monitor pre-chamber and subsequent main chamber combustion, and optical diagnostics include high-speed OH* chemiluminescence to visualize the development of pre-chamber jets and the resulting ignition of the main chamber charge. Heat release analysis of the in-cylinder pressure data indicates that a faster pre-chamber pressure rise does not always translate into faster main-chamber combustion. The pre-chamber with the smallest nozzle diameter produced the highest pre-chamber pressure rise and fastest combustion under non-diluted conditions. However, dilution delays the main chamber ignition for smaller nozzles despite a comparable rise in pre-chamber pressure compared to configurations with larger nozzles. This effect is more pronounced for cycles with in-cylinder combustion residuals in addition to external dilution. Additionally, it was observed that pre-chambers with swirling nozzles have a faster pressure rise in the pre-chamber and main chamber under dilute conditions. Optical diagnostics suggest that the main reason for the delay between the pre-chamber pressure rise and main-chamber combustion lies in jet quenching and delayed re-ignition, which can even lead to misfire if jets emitted from small nozzles combined with dilution fail to re-ignite.

Dhotre, Akash [University Of Minnesota-Twin Cities↗
DOE OSTI2026

Data for Transposon Signatures of Allopolyploid Genome Evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

Genomics↗
DOE OSTI2026

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli

Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.

Kammerdiener, Elise K. [Oak Ridge National Laborat↗
DOE OSTI2024

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Abstract Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in bothSalinibacter ruber, an environmental halophilic organism, andEscherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Science & Technology - Other Topics↗
DOE OSTI2026

Data-Driven Modeling and Correction of Vehicle Dynamics

We develop a data-driven framework for learning and correcting nonautonomous vehicle dynamics. Physics-based vehicle models are often simplified for tractability and therefore exhibit inherent model-form uncertainty, motivating the need for data-driven correction. Moreover, nonautonomous dynamics are governed by time-dependent control inputs, which pose challenges in learning predictive models directly from temporal snapshot data. To address these, we reformulate the vehicle dynamics via a local parameterization of the time-dependent inputs, yielding a modified system composed ofa sequence of local parametric dynamical systems. Here, we approximate these parametric systems using two complementary approaches. First, we employ the dimension reduction and interpolation in parameter space (DRIPS) methodology to construct efficient linear surrogate models, equipped with lifted observable spaces and manifold-based operator interpolation. This enables data-efficient learning of vehicle models whose dynamics admit accurate linear representations in the lifted spaces. Second, for more strongly nonlinear systems, we employ flow map learning (FML), a deep neural network (DNN) approach that approximates the parametric evolution map without requiring special treatment of nonlinearities. We further extend FML with a transfer-learning-based model correction procedure, enabling the correction of misspecified prior models using only a sparse set of high-fidelity or experimental measurements, without assuming a prescribed form for the correction term. Through a suite of numerical experiments on unicycle, simplified bicycle, and slip-based bicycle models, we demonstrate that DRIPS offers robust and highly data-efficient learning of nonautonomous vehicle dynamics, while FML provides expressive nonlinear modeling and effective correction of model-form errors under severe data scarcity.

data-driven modeling↗
DOE OSTI2025

From subsidies to stressors: Positively skewed ecological gradients alter biological responses to nutrients in streams

Abstract Subsidy–stress gradients offer a useful framework for understanding ecological responses to perturbation and may help inform ecological metrics in highly modified systems. Historic, region‐wide shifts from bottomland hardwood forest to row crop agriculture can cause positively skewed impact gradients in alluvial plain ecoregions, resulting in tolerant organisms that typically exhibit a subsidy response (increased abundance in response to environmental stressors) shifting to a stress response (declining abundance at higher concentrations). As a result, observed biological tolerance in modified ecosystems may differ from less modified regions, creating significant challenges for detecting biological responses to restoration efforts. Using the agriculturally dominated Mississippi Alluvial Plain (MAP) ecoregion in Mississippi, USA, as a case study, we tested the hypothesis that macroinvertebrate taxa that typically display a subsidy response to nutrient enrichment in less modified ecoregions (i.e., nutrient‐tolerance) shift to a stress response to increasing nutrients in highly modified watersheds with elevated baseline nutrient conditions (i.e., nutrient intolerance). The abundance and diversity of MAP‐specific intolerant taxa identified with threshold indicator taxa analysis were either unresponsive or exhibited a subsidy response to increasing nutrients in less modified ecoregions in Mississippi with less land alteration and lower nutrient concentrations, but declined at higher concentrations, providing evidence for a stress response to elevated nutrients in the MAP. Additionally, MAP‐specific tolerant and intolerant taxa richness responded to increased nutrients predictably and consistently across space and time within the MAP. However, in MAP streams, elevated specific conductance was predicted to dampen the response of tolerant and intolerant taxa richness to increasing nutrient concentrations, highlighting the importance of considering multistressor interactions when interpreting biological data. Lastly, we demonstrate the efficacy of this approach with sediment bacterial communities characterized with amplicon sequencing, which lack sufficient life history characteristics necessary for the development of multimetric indices. Both macroinvertebrate and bacterial communities responded similarly to increasing nutrient concentrations, suggesting DNA‐based approaches may provide an efficient biological assessment tool for monitoring water quality improvements in highly modified watersheds.

DeVilbiss, Stephen E. [U.S. Geological Survey Lowe↗
DOE OSTI2026

Noise-canceling quantum feedback: Non-Hermitian dynamics with applications to state preparation and magic state distillation

Time-continuous quantum measurement allows for the tracking of a quantum system in real time via sequences of short, and individually weak, measurement intervals. Such measurements are necessarily invasive, imparting backaction to the system, and allowing the observer to update their state estimate based on stochastic measurement outcomes. Feedback control then involves real-time interventions by an observer, conditioned on the time-continuous measurement signal that they receive. Here, we consider here diffusive quantum trajectories and focus on the “noise-canceling” subset of feedback protocols that aim to minimize the degree of stochasticity in the dynamics. We derive such a class of feedback operations, showing that under the idealized assumptions of pure states, unit measurement efficiency, and zero time delay in implementing feedback operations, perfectly noise-canceling feedback always exists. We consider the resulting noise-canceled dynamics generated by an effective non-Hermitian Hamiltonian; while non-Hermitian Hamiltonians from continuous monitoring generally describe rare dynamics (accessible by costly postselection), the use of noise-canceling feedback here leads to non-Hermitian dynamics that occur deterministically. We demonstrate this via examples of entangled state preparation and stabilization. We then illustrate the potential for the application of noise cancellation to boost success rates in magic state distillation protocols. We show that adding feedback based on noise cancellation into a time-continuous five-to-one distillation protocol leads to higher probabilities of successful distillation across a range of input errors and increases the threshold on input errors for which the protocol is effective. Our results highlight the efficacy of noise-canceling feedback-aided protocols for quantum state preparation and stabilization tasks.

Karmakar, Tathagata [University of California, Ber↗
DOE OSTI2025

Emergence of pseudoresonance in high-intensity resonant inelastic x-ray scattering

We report resonant inelastic x-ray scattering (RIXS) spectra of neon atoms interacting with intense x-ray pulses generated using an x-ray free-electron laser (XFEL). We find that an unexpected peak emerges near the 𝐾⁢𝛼 line of Ne, which does not coincide with any physical resonances of neon ions. We perform theoretical calculations based on a quantum-state-resolved rate-equation approach with x-ray-induced processes including possible resonant excitations. Our dynamics simulations demonstrate that a sequence of multiple resonant photoabsorption events are involved and the interplay of those multiple resonances in combination with the relatively large spectral bandwidth of XFEL radiation leads to the emergent resonance-like structure at a position where no resonances exist. Our finding offers critical guidance for future applications of high-intensity RIXS at XFEL facilities.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae

CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in Saccharomyces cerevisiae . Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.

Aptazyme↗
DOE OSTI2024

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Single‐Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human‐Derived Microglia

Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

AGFormer: Adaptive Spatiotemporal graph informed transformer for multi-reservoir inflow forecasting

Accurate reservoir inflow forecasting is crucial for effective water resource management, yet most machine learning models focus on single-reservoir prediction and overlook spatial dependencies among hydrologically connected reservoirs. Here, we propose AGFormer (Adaptive Graph-Informed Transformer), an end-to-end framework that integrates adaptive graph learning with temporal sequence modeling for multi-reservoir inflow forecasting. A shared encoder and graph attention mechanism generate reservoir-specific embeddings, which are then processed by the Transformer-based encoder–decoder for multi-step inflow forecasting. We also introduce a pretraining paradigm to learn robust temporal embeddings from misaligned historical records. Evaluated on 30 reservoirs in the Upper Colorado River Basin, AGFormer achieves superior seven-day-ahead forecasts, with NSE > 0.75 for 20 reservoirs—outperforming Encoder–Decoder LSTM, GCN+LSTM, and Transformer baselines. Adaptive graph learning captures dynamic inter-reservoir dependencies, and feature attribution aligns with snowmelt-driven hydrology. Incorporating forecasted meteorological inputs further enhances accuracy, demonstrating AGFormer’s potential to support reservoir management under dynamic hydrological conditions.

Adaptive graph learning↗
DOE OSTI2025

Detecting Masquerade Attacks in Controller Area Networks Using Graph Machine Learning

Modern vehicles rely on a myriad of electronic control units (ECUs) interconnected via controller area networks (CANs) for critical operations. Despite their ubiquitous use and reliability, CANs are susceptible to sophisticated cyberattacks, particularly masquerade attacks, which inject false data that mimic legitimate messages at the expected frequency. These attacks pose severe risks such as unintended acceleration, brake deactivation, and rogue steering. Traditional intrusion detection systems (IDS) often struggle to detect these subtle intrusions due to their seamless integration into normal traffic. This paper introduces a novel framework for detecting masquerade attacks in the CAN bus using graph machine learning (ML). We hypothesize that the integration of shallow graph embeddings with time series features derived from CAN frames enhances the detection of masquerade attacks. We show that by representing CAN bus frames as message sequence graphs (MSGs) and enriching each node with contextual statistical attributes from time series, we can enhance detection capabilities across various attack patterns compared to using graph-based features only. Our method ensures a comprehensive and dynamic analysis of CAN frame interactions, improving robustness and efficiency. Extensive experiments on the ROAD dataset validate the effectiveness of our approach, demonstrating statistically significant improvements in the detection rates of masquerade attacks compared to a baseline that uses graph-based features only as confirmed by Mann-Whitney U and Kolmogorov-Smirnov tests (p < 0.05) .

Marfo, William [Univ. of Texas, El Paso, TX (Unite↗