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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A tunable autonomous RNA-fueled micro-engine

Autonomous molecular machines capable of converting chemical energy into mechanical motion are foundational components for synthetic nanoscale systems. Inspired by biological motors, we report the construction of a tunable, RNA-fueled DNA origami engine that drives the cyclic movement of a 500 nm-diameter particle at the microscale. The engine operates via sequential RNA–DNA hybridization and enzymatic cleavage by RNase H, enabling reversible switching between folded and unfolded conformations without external intervention. By modulating RNA and enzyme concentrations and controlling temperature, we achieve tunable switching kinetics, with transition periods as short as ~10 s. Kinetic modeling reveals that the folding pathway is governed by both productive RNA binding and the enzymatic clearance of misfolded intermediates, while unfolding is primarily controlled by RNase H activity. Since the RNA fuel binds specifically to the DNA strands, each engine is addressable simply by changing the sequences. This work demonstrates a programmable, self-resetting molecular actuator and offers a blueprint for building more complex nanomechanical systems with forces and energies comparable to molecular motors.

DNA nanomachines↗
DOE OSTI2025

Activation Domain Hunter (ADhunter) v2.0

ADhunter is a software program that enables accurate identification and quantification of transcriptional activation domains. Unlike previous software, ADhunter uses protein representations from a pre-trained protein language model, model ensembling, and a training dataset from a diverse sampling of protein sequence space for state-of-the-art performance. These advantages enable improved perception of transcriptional activation domains across sequence space that can be used for mapping natural genetic circuits and engineering synthetic genetic circuits. In particular, ADhunter enables fine-tuned control of gene expression through synthetic transcription factors that can be used for complex control of cellular programs.

Waldburger, Lucas [Lawrence Berkeley National Labo↗
DOE OSTI2024

High-performance silicon photonic single-sideband modulators for cold-atom interferometry

The laser system is the most complex component of a light-pulse atom interferometer (LPAI), controlling frequencies and intensities of multiple laser beams to configure quantum gravity and inertial sensors. Its main functions include cold-atom generation, state preparation, state-selective detection, and generating a coherent two-photon process for the light-pulse sequence. To achieve substantial miniaturization and ruggedization, we integrate key laser system functions onto a photonic integrated circuit. Our study focuses on a high-performance silicon photonic suppressed-carrier single-sideband (SC-SSB) modulator at 1560 nanometers, capable of dynamic frequency shifting within the LPAI. By independently controlling radio frequency (RF) channels, we achieve 30-decibel carrier suppression and unprecedented 47.8-decibel sideband suppression at peak conversion efficiency of –6.846 decibels (20.7%). We investigate imbalances in both amplitudes and phases between the RF signals. Using this modulator, we demonstrate cold-atom generation, state-selective detection, and atom interferometer fringes to estimate gravitational acceleration, g ≈ 9.77 ± 0.01 meters per second squared, in a rubidium ( 87 Rb) atom system.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Quantitative trait locus (QTL) mapping and transcriptome profiling identify QTLs and candidate genes associated with heat stress response during reproductive development in Camelina sativa

Camelina sativa (L.) Crantz is a low-input oilseed crop that has great potential in providing sustainable feedstock for biofuels and bioproducts. Climate change is threatening production of camelina with rising global temperatures. Elucidating the genetic response to high temperatures is essential for successful breeding of heat-tolerant camelina varieties. Here, we report a combinatorial approach to identifying candidate genes associated with heat stress by quantitative trait locus (QTL) mapping and comparative transcriptome profiling. A population of recombinant inbred lines (RILs) was grown in a controlled growth chamber under the high-temperature regimes for 14 days beginning at the onset of the reproductive stage. Several traits related to seed production were evaluated at maturity. The QTL analysis identified several regions with co-located traits on chromosomes 8, 10, and 12. Two RILs with contrasting phenotypic responses to heat stress were chosen for gene expression profiling via RNA sequencing. Multiple pathways and genes were found to be strongly affected by heat stress, and many genes expressed differently between the two RILs. Several genes identified within the QTL regions were considered strong candidates that may control heat tolerance during reproduction in camelina. These studies provide resources for future studies that may assist in improving the heat tolerance of camelina.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Directing Nanoparticle Organization in Response to Diverse Chemical Inputs

Signaling cascades are crucial for transducing stimuli in biological systems, enabling multiple stimuli to regulate a downstream target with precisely controlled timing and amplifying signals through a series of intermediary reactions. Developing a robust signaling system with such capabilities would be pivotal for programming complex behaviors in synthetic DNA-based molecular devices. However, although “software” such as nucleic acid circuits could potentially be harnessed to relay signals to DNA-based nanostructure hardware, such explorations have been limited. Here, in this study, we develop a platform for transducing a variety of stimuli via messenger-mediated reactions to regulate the release and reloading of gold nanoparticles (AuNPs) in a 3D DNA framework. In the first step, an in vitro transcription circuit is engineered to sense and amplify chemical stimuli, including arbitrary DNA sequences and proteins, producing RNA. In the second step, the RNA releases the DNA-coated AuNPs from the DNA framework via a strand displacement reaction. AuNP reloading is controlled by a separate step driven by degradation of the RNA. Our platform holds promise for applications requiring dynamic multiagent control over DNA-based devices, offering a versatile tool for advanced molecular device engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Controlled synthesis of hierarchically-structured hybrid materials through peptoid engineering

This disclosure concerns a method for making a hybrid organic/inorganic material having an architecture. The method includes combining a peptoid comprising a sequence of N-substituted glycine residues and an inorganic material or inorganic material precursor to form a hybrid organic/inorganic material comprising the peptoid and the inorganic material, the hybrid organic/inorganic material having an architecture based at least in part on the peptoid sequence. The hybrid organic/inorganic materials include a cluster of nanoparticles of an inorganic material and peptoids, the cluster formed by random attachment of nanoparticles to one another by peptoid-peptoid and peptoid-nanoparticle surface interactions, wherein the hybrid material has an architecture based at least in part on the peptoid sequence.

Chen, Chun-Long↗
DOE OSTI2022

Cyber-Resilient Frequency Control of Power Grids with Energy Storage Systems

The integration of synchronous generators and energy storage systems operated through communication networks introduces new challenges and vulnerabilities to the electric grid, where cyber attacks can corrupt sensor measurements or control inputs and interrupt functions such as frequency regulation. This paper proposes a defense methodology for the design of resilient operating constraints imposed on each generation and storage unit in order to prevent any attack sequence from driving the system's frequency to unsafe conditions. The resilient operating constraints are found by using ellipsoidal approximations of the reachable set of the power system, leading to a convex optimization problem with linear matrix inequalities. Numerical results in a single-area power system with synchronous generation and energy storage demonstrate how the resilient constraints provide security guarantees against any type of attack affecting frequency measurements or controller setpoints.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Controlled precision QUBO-based algorithm to compute eigenvectors of symmetric matrices

We describe an algorithm to compute the extremal eigenvalues and corresponding eigenvectors of a symmetric matrix which is based on solving a sequence of Quadratic Binary Optimization problems. This algorithm is robust across many different classes of symmetric matrices; It can compute the eigenvector/eigenvalue pair to essentially any arbitrary precision, and with minor modifications, can also solve the generalized eigenvalue problem. Performance is analyzed on small random matrices and selected larger matrices from practical applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Importance of appropriate genome information for the design of mating type primers in black and yellow morel populations

Abstract Morels are highly prized edible fungi where sexual reproduction is essential for fruiting-body production. As a result, a comprehensive understanding of their sexual reproduction is of great interest. Central to this is the identification of the reproductive strategies used by morels. Sexual reproduction in fungi is controlled by mating-type ( MAT ) genes and morels are thought to be mainly heterothallic with two idiomorphs, MAT1-1 and MAT1-2. Genomic sequencing of black (Elata clade) and yellow (Esculenta clade) morel species has led to the development of PCR primers designed to amplify genes from the two idiomorphs for rapid genotyping of isolates from these two clades. To evaluate the design and theoretical performance of these primers we performed a thorough bioinformatic investigation, including the detection of the MAT region in publicly available Morchella genomes and in-silico PCR analyses. All examined genomes, including those used for primer design, appeared to be heterothallic. This indicates an inherent fault in the original primer design which utilized a single Morchella genome, as the use of two genomes with complementary mating types would be required to design accurate primers for both idiomorphs. Furthermore, potential off-targets were identified for some of the previously published primer sets, but verification was challenging due to lack of adequate genomic information and detailed methodologies for primer design. Examinations of the black morel specific primer pairs (MAT11L/R and MAT22L/R) indicated the MAT22 primers would correctly target and amplify the MAT1-2 idiomorph, but the MAT11 primers appear to be capable of amplifying incorrect off-targets within the genome. The yellow morel primer pairs (EMAT1-1 L/R and EMAT1-2 L/R) appear to have reporting errors, as the published primer sequences are dissimilar with reported amplicon sequences and the EMAT1-2 primers appear to amplify the RNA polymerase II subunit ( RPB2 ) gene. The lack of the reference genome used in primer design and descriptive methodology made it challenging to fully assess the apparent issues with the primers for this clade. In conclusion, additional work is still required for the generation of reliable primers to investigate mating types in morels and to assess their performance on different clades and across multiple geographical regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Characterization of Humanized Mouse Model of Organophosphate Poisoning and Detection of Countermeasures via MALDI-MSI

Organophosphoate (OP) chemicals are known to inhibit the enzyme acetylcholinesterase (AChE). Studying OP poisoning is difficult because common small animal research models have serum carboxylesterase, which contributes to animals’ resistance to OP poisoning. Historically, guinea pigs have been used for this research; however, a novel genetically modified mouse strain (KIKO) was developed with nonfunctional serum carboxylase (Es1 KO) and an altered acetylcholinesterase (AChE) gene, which expresses the amino acid sequence of the human form of the same protein (AChE KI). KIKO mice were injected with 1xLD50 of an OP nerve agent or vehicle control with or without atropine. After one to three minutes, animals were injected with 35 mg/kg of the currently fielded Reactivator countermeasure for OP poisoning. Postmortem brains were imaged on a Bruker RapifleX ToF/ToF instrument. Data confirmed the presence of increased acetylcholine in OP-exposed animals, regardless of treatment or atropine status. More interestingly, we detected a small amount of Reactivator within the brain of both exposed and unexposed animals; it is currently debated if reactivators can cross the blood–brain barrier. Further, we were able to simultaneously image acetylcholine, the primary affected neurotransmitter, as well as determine the location of both Reactivator and acetylcholine in the brain. This study, which utilized sensitive MALDI-MSI methods, characterized KIKO mice as a functional model for OP countermeasure development.

2-PAM↗
DOE OSTI2023

Arabidopsis thaliana strain:Col-3 Raw sequence reads

We performed RNA sequencing (RNA-seq) analyses in Col-0 and tgnap1-2 at 24 h of treatment with Pst DC3000 in three biological replicates. Mock controls, which were treated with 10 mM MgCl2, were included.

Brandizzi, Federica↗
DOE OSTI2022

Arabidopsis thaliana strain:Col-0 Raw sequence reads

To investigate transcriptome changes in pir1-1 mutants, we performed RNA sequencing (RNA-seq) analyses in Col-0 and pir1-1at 24 h of adaptive endoplasmic reticulum stress in three biological replicates. Mock controls, which were treated with DMSO, are included.

Arabidopsis Proteins/genetics/metabolism↗
DOE OSTI2025

Feedforward equilibrium trajectory optimization with GSPulse

One of the common tasks required for designing new plasma scenarios or evaluating capabilities of a tokamak is to design the desired equilibria using a Grad-Shafranov (GS) equilibrium solver. However, most standard equilibrium solvers are time-independent and do not include dynamic effects such as plasma current flux consumption, induced vessel currents, or voltage constraints. Another class of tools, plasma equilibrium evolution simulators, do include time-dependent effects. These are generally structured to solve the forward problem of evolving the plasma equilibrium given feedback-controlled voltages. In this work, we introduce GSPulse, a novel algorithm for equilibrium trajectory optimization, that is more akin to a pulse planner than a pulse simulator. GSPulse includes time-dependent effects and solves the inverse problem: given a user-specified set of target equilibrium shapes, as well as limits on the coil currents and voltages, the optimizer returns trajectories of the voltages, currents, and achievable equilibria. This task is useful for scoping performance of a tokamak and exploring the space of achievable pulses. The computed equilibria satisfy both Grad-Shafranov force balance and axisymmetric circuit dynamics. The optimization is performed by restructuring the free-boundary equilibrium evolution equations into a form where it is computationally efficient to optimize the entire dynamic sequence. GSPulse can solve for hundreds of equilibria simultaneously within a few minutes. GSPulse has been validated against NSTX-U and MAST-U experiments and against SPARC feedback control simulations, and is being used to perform scenario design for SPARC. The computed trajectories can be used as feedforward inputs that are connected to the feedback controller to inform and improve feedback performance. The code for GSPulse is available open-source at github.com/jwai-cfs/GSPulse_public.

equilibrium↗
DOE OSTI2022

Aging of galaxies along the morphological sequence, marked by bulge growth and disk quenching

Aims: We revisit the color bimodality of galaxies using the extensive EFIGI morphological classification of nearby galaxies. Methods: The galaxy profiles from the Sloan Digital Sky Survey (SDSS) gri images were decomposed as a bulge and a disk by controlled profile modeling with the Euclid SourceXtractor++ software. The spectral energy distributions from our resulting gri SDSS photometry complemented with Galaxy Evolution Explorer (GALEX) NUV photometry were fitted with the ZPEG software and PEGASE.2 templates in order to estimate the stellar masses and specific star formation rates (sSFR) of whole galaxies as well as their bulge and disk components. Results: The absolute NUV-r color versus stellar mass diagram shows a continuous relationship between the present sSFR of galaxies and their stellar mass, which spans all morphological types of the Hubble sequence monotonously. Irregular galaxies to intermediate-type Sab spirals make up the “Blue Cloud” across 4 orders of magnitude in stellar mass but a narrow range of sSFR. This mass build-up of spiral galaxies requires major mergers, in agreement with their frequently perturbed isophotes. At high mass, the Blue Cloud leads to the “Green Plain”, dominated by S0a and Sa early-type spirals. It was formerly called the “Green Valley”, due to its low density, but we rename it because of its wide stretch and nearly flat density over ~2 mag in NUV-r color (hence sSFR), despite a limited range of stellar mass (1 order of magnitude). The Green Plain links up the “Red Sequence”, containing all lenticular and elliptical galaxies with a 2 order of magnitude mass interval, and systematically higher masses for the ellipticals. We confirm that the Green Plain cannot be studied using u - r optical colors because it is overlayed by the Red Sequence, hence NUV data are necessary. Galaxies across the Green Plain undergo a marked growth by a factor 2 to 3 in their bulge-to-total mass ratio and a systematic profile change from pseudo to classical bulges, as well as a significant reddening due to star formation fading in their disks. The Green Plain is also characterized by a maximum stellar mass of 10 11.7 M ⊙ beyond which only elliptical galaxies exist, hence supporting the scenario of ellipticals partly forming by major mergers of massive disk galaxies. Conclusions: The EFIGI attributes indicate that dynamical processes (spiral arms and isophote distortions) contribute to the scatter of the Main Sequence of star-forming galaxies (Blue Cloud), via the enhancement of star formation (flocculence, HII regions). The significant bulge growth across the Green Plain confirms that it is a transition region, and excludes a predominantly quick transit due to rapid quenching. The high frequency of bars for all spirals as well as the stronger spiral arms and flocculence in the knee of the Green Plain suggest that internal dynamics, likely triggered by flybys or (mainly minor) mergers, may be the key to the bulge growth of massive disk galaxies, which is a marker of the aging of galaxies from star forming to quiescence. The Hubble sequence can then be considered as an inverse sequence of galaxy physical evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Heterostructural interface engineering for ultrawide-gap nitrides from first principles: Ta C / Al N and Ta C / Ga N rocksalt-wurtzite interfaces

Epitaxial lattice matching is an important condition for the formation of coherent interfaces with low defect densities. However, lattice-matched substrates with the same crystal structure as the active layer are often not available, suggesting opportunities for utilizing heterostructural interfaces. For example, at high Al contents that are interesting for ultrawide-gap applications in power electronics, Al x ⁢Ga 1-x ⁢N semiconductor alloys in the (0001) orientation of the wurtzite (wz) structure become lattice-matched to (111)-oriented rocksalt (rs) Ta⁢C substrates. To predict the expected interface atomic structures under different synthesis conditions, we perform high-throughput density-functional-theory calculations, using an algorithm for systematic sampling of the possible stacking sequences of the atomic layers on the in-plane hexagonal lattice. The approach considers octahedral, tetrahedral, and prismatic coordination motifs, and is generally applicable for the modeling of commensurate rs/wz heterostructural interfaces. Our results provide guidance for synthesis control of substrate-film bonding and the polarity of ultrawide-gap Al x⁢ Ga 1-x⁢ N alloys on Ta⁢C substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A Digital Three Level Space Vector Modulator for High Frequency Vector Sequence Generation

This letter proposes a digital high-speed three-level space vector pulse width modulator (3L-SVPWM). A conventional 3L-SVPWM is typically computation-based, involving a sequential execution of sub-tasks on a digital signal processor (DSP) based controller. The resulting high computation time of 5.4 μs limits the implementation of additional control blocks for switching frequencies greater than 100 kHz. This is overcome by transforming sub-tasks into digital blocks with 1-0 decisions and simpler arithmetic operations. The sub-task blocks are executed concurrently on a programmable logic device (PLD). Hence, a fast 3L-SVPWM execution in 140 ns is achieved. The proposed digital 3L-SVPWM enables high switching frequency operation of wide bandgap (WBG) device-based 3 L inverters to generate high fundamental frequency waveforms. A finite state machine is an integral part of the proposed implementation with the ability to generate any vector sequence, maximizing the usage of redundant vector states in 3L-SVPWM. Here, the proposed digital 3L-SVPWM operation is demonstrated with a GaN-based 3 L active neutral point clamped (3L-ANPC) inverter. Experimental results are presented at 250 kHz switching frequency to generate vector sequences for center-aligned SVPWM (CA-SVPWM) and common mode voltage reduced SVPWM (CMVR-SVPWM). The results also showcase a high fundamental frequency generation capability of 10 kHz.

active neutral point clamped inverter↗