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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

On the possibility of footprint compression with one lens in nonlinear accelerator lattice

Electromagnetic interaction of colliding beams along with other nonlinear fields often limits the beams' lifetimes and luminosities. Nonlinearities result in the spread of betatron frequencies (footprint) and, thus, may enhance dynamic diffusion of particles due to high order resonances. One of the possible ways to eliminate nonlinearities and overcome the corresponding difficulties is compensation of nonlinear forces, but, in practice, it is hardly possible to obtain exact linearity of the system. The compensation with a single nonlinear lens cannot cope with distributed nonlinearities, nonlinearities due to parasitic crossings, etc. Here, we present a method to compute parameters of nonlinear element (lens) that eliminates both the footprint and resonance strength without achieving full compensation.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Reconsidering tympanal-acoustic interactions leads to an improved model of auditory acuity in a parasitoid fly

Although most binaural organisms locate sound sources using neurological structures to amplify the sounds they hear, some animals use mechanically coupled hearing organs instead. One of these animals, the parasitoid fly Ormia ochracea (O. ochracea), has astoundingly accurate sound localization abilities. It can locate objects in the azimuthal plane with a precision of 2°, equal to that of humans, despite an intertympanal distance of only 0.5 mm, which is less than 1/100th of the wavelength of the sound emitted by the crickets that it parasitizes. O. ochracea accomplishes this feat via mechanically coupled tympana that interact with incoming acoustic pressure waves to amplify differences in the signals received at the two ears. In 1995, Miles et al developed a model of hearing mechanics in O. ochracea that represents the tympana as flat, front-facing prosternal membranes, though they lie on a convex surface at an angle from the flies' frontal and transverse planes. The model works well for incoming sound angles less than ±30° but suffers from reduced accuracy (up to 60% error) at higher angles compared to response data acquired from O. ochracea specimens. Despite this limitation, it has been the basis for bio-inspired microphone designs for decades. Here, we present critical improvements to this classic hearing model based on information from three-dimensional reconstructions of O. ochracea's tympanal organ. We identified the orientation of the tympana with respect to a frontal plane and the azimuthal angle segment between the tympana as morphological features essential to the flies' auditory acuity, and hypothesized a differentiated mechanical response to incoming sound on the ipsi- and contralateral sides that depend on these features. We incorporated spatially-varying model coefficients representing this asymmetric response, making a new quasi-two-dimensional (q2D) model. The q2D model has high accuracy (average errors of under 10%) for all incoming sound angles. This improved biomechanical model may inform the design of new microscale directional microphones and other small-scale acoustic sensor systems.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Insights on the cycling behavior of a highly-prelithiated silicon–graphite electrode in lithium-ion cells

Nanosized silicon materials are being developed for use in the anodes of high-energy lithium-ion batteries. However, the high surface areas of these materials increase the rate of parasitic reactions in the electrode, which consume cyclable Li + and degrade battery performance. Prelithiation offers a realistic strategy to compensate for this reactivity, by injecting additional charge into the cell to counterbalance the Li + loss. Interestingly, the benefits offered by prelithiation extend beyond its more obvious purpose. Here, by using a reference electrode in NMC532//Si–Gr cells, we show how prelithiation alters the cycling potentials experienced by the Si-containing anode and how that translates into gains in cycle life. The rate of consumption of the prelithiated charge is lower than that expected from the behavior of non-prelithiated cells. Curiously, the Si particles become partially unresponsive during the C/3 cycling apparently because of kinetic constraints. Electrochemical studies on harvested electrodes in half-cells show that capacities are intact after the long-term cycling and that most of the lithium reservoir is still present in the anode. We conclude that the high capacity retention displayed by the prelithiated cells mainly results from a higher participation of graphite particles during the extended electrochemical cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The first sequenced Sphaerotilus natans bacteriophage– characterization and potential to control its filamentous bacterium host

ABSTRACT Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.

Ferreira, Rute↗
DOE OSTI2022

Expression and structure of the Chlamydia trachomatis DksA ortholog

Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksA Ct ) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksA Ct in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksA Ct is similar to the DksA ortholog of Escherichia coli (DksA Ec ), DksA Ct did not functionally complement DksA Ec . Transcription of dksA Ct is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksA Ct and the correlation between dksA Ct and nrdR expression is consistent with a role for DksA Ct in the C. trachomatis developmental cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Artemether-Lumefantrine Treatment Selects Plasmodium falciparum Multidrug Resistance 1 ( pfmdr1 ) Increased Copy Number Among African Malaria Infections

Abstract Background Decreased efficacy of artemether-lumefantrine, the globally most used antimalarial, has recently emerged in Africa. Methods An efficacy trial was carried out based on directly observed artemether-lumefantrine therapy at Bengo, Northern Angola. One-hundred Plasmodium falciparum uncomplicated malaria patients (2–10 years old) were enrolled, hospitalized for the treatment period, and followed up for 42 days. Polymerase chain reaction (PCR) correction was performed with pfmsp1/2 plus glurp, with analysis considering 2 or 3 coincident markers. Infections were tested by quantitative PCR (qPCR) for pfmdr1 copy number (pfmdr1×N), a potential P. falciparum marker of lumefantrine resistance previously identified in the region. In vitro clone mixtures were built and used to determine the relation between qPCR copy number scores and actual intrainfection quantitative fractions of pfmdr1×N. Results We observed a significant posttreatment selection of gene amplification, suggesting a role in the parasite in vivo response to this drug. pfmdr1×2 qPCR scores of 1.3, 1.4, and 1.5 were determined to correspond to 15%, 25%, and 35% intrainfection rates. Patients carrying infections with a score ≥1.4 at baseline were linked to decreased artemether-lumefantrine day 42 efficacy (79% vs 97% single-copy pfmdr1). All infections were pfmdr1 N86 carriers and no pfk13 mutations were found. Conclusions Our study suggests pfmdr1×N as a marker of P. falciparum in vivo response to lumefantrine in Africa, while indicating patients carrying infections with a pretreatment pfmdr1×N score ≥1.4 before treatment are a group experiencing decreased artemether-lumefantrine performance.

Fançony, Claudia (ORCID:0000000344211769)↗
DOE OSTI2021

Characterization of growth and development of sorghum genotypes with differential susceptibility to Striga hermonthica

Two sorghum varieties, Shanqui Red (SQR) and SRN39, have distinct levels of susceptibility to the parasitic weed Striga hermonthica, which have been attributed to different strigolactone composition within their root exudates. Root exudates of the Striga-susceptible variety Shanqui Red (SQR) contain primarily 5-deoxystrigol, which has a high efficiency for inducing Striga germination. SRN39 roots primarily exude orobanchol, leading to reduced Striga germination and making this variety resistant to Striga. The structural diversity in exuded strigolactones is determined by a polymorphism in the LOW GERMINATION STIMULANT 1 (LGS1) locus. Yet, the genetic diversity between SQR and SRN39 is broad and has not been addressed in terms of growth and development. Here, we demonstrate additional differences between SQR and SRN39 by phenotypic and molecular characterization. A suite of genes related to metabolism was differentially expressed between SQR and SRN39. Increased levels of gibberellin precursors in SRN39 were accompanied by slower growth rate and developmental delay and we observed an overall increased SRN39 biomass. The slow-down in growth and differences in transcriptome profiles of SRN39 were strongly associated with plant age. Additionally, enhanced lateral root growth was observed in SRN39 and three additional genotypes exuding primarily orobanchol. In summary, we demonstrate that the differences between SQR and SRN39 reach further than the changes in strigolactone profile in the root exudate and translate into alterations in growth and development.

09 BIOMASS FUELS↗
DOE OSTI2023

Occurrence and molecular characterization of Enterocytozoon bieneusi in wild and domestic animal species in Portugal

Abstract The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.

Figueiredo, Ana M. (ORCID:0000000226236340)↗
DOE OSTI2020

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗
DOE OSTI2024

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

Abstract Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Tapping into the physiological responses to mistletoe infection during heat and drought stress

Mistletoes are important co-contributors to tree mortality globally, particularly during droughts. In Australia, mistletoe distributions are expanding in temperate woodlands, while their hosts have experienced unprecedented heat and drought stress in recent years. We investigated whether the excessive water use of mistletoes increased the probability of xylem emboli in a mature woodland during the recent record drought that was compounded by multiple heatwaves. Additionally, we continuously recorded transpiration ($T_{SLA}$) of infected and uninfected branches from two eucalypt species over two summers, monitored stem and leaf water potentials ($\Psi $) and used hydraulic vulnerability curves to estimate percent loss in conductivity (PLC) for each species. Variations in weather (vapor pressure deficit, photosynthetically active radiation, soil water content), host species and % mistletoe foliage explained 78% of hourly $T_{SLA}$. While mistletoe acted as an uncontrollable sink for water in the host even during typical summer days, daily $T_{SLA}$ increased up to 4-fold in infected branches on hot days, highlighting the previously overlooked importance of temperature stress in amplifying water loss in mistletoes. The increased water use of mistletoes resulted in significantly decreased host $\Psi _{\rm{leaf}}$ and $\Psi _{\rm{trunk}}$. It further translated to an estimated increase of up to 11% PLC for infected hosts, confirming greater hydraulic dysfunction of infected trees that place them at higher risk of hydraulic failure. However, uninfected branches of Eucalyptus fibrosa F.Muell. had much tighter controls on water loss than uninfected branches of Eucalyptus moluccana Roxb., which shifted the risk of hydraulic failure towards an increased risk of carbon starvation for E. fibrosa. The contrasting mechanistic responses to heat and drought stress between both co-occurring species demonstrates the complexity of host–parasite interactions and highlights the challenge in predicting species-specific responses to biotic agents in a warmer and drier climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

High-precision phase control of an optical lattice with up to 50 dB noise suppression

An optical lattice is a periodic light crystal constructed from the standing-wave interference patterns of laser beams. It can be used to store and manipulate quantum degenerate atoms and is an ideal platform for the quantum simulation of many-body physics. A principal feature is that optical lattices are flexible and possess a variety of multidimensional geometries with modifiable band structure. An even richer landscape emerges when control functions can be applied to the lattice by modulation of the position or amplitude with Floquet driving. However, the desire of realizing high-modulation bandwidths while preserving extreme lattice stability has been difficult to achieve. In this paper, we demonstrate an effective solution that consists of overlapping two counterpropagating lattice beams and controlling the phase and intensity of each with independent acousto-optic modulators. Our phase controller mixes sampled light from both lattice beams with a common optical reference. This dual heterodyne locking method allows exquisite determination of the lattice position, while also removing parasitic phase noise accrued as the beams travel along separate paths. Here, we report up to 50 dB suppression in lattice phase noise in the 0.1–1 Hz band, along with significant suppression spanning more than 4 decades of frequency. The absolute phase diffusion of the lattice position is only 10 Å when integrated over 10 s. This method permits precise, high-bandwidth modulation (greater than 50 kHz) of the optical lattice intensity and phase. We demonstrate the efficacy of this approach by executing intricate time-varying phase profiles for atom interferometry.

Atom interferometry↗
DOE OSTI2023

Realizing symmetry-protected topological phases in a spin-1/2 chain with next-nearest-neighbor hopping on superconducting qubits

Quantum simulation on near-term quantum hardware is a topic of intense interest. The preparation of novel quantum states of matter provides a quantitative assessment of the capabilities of near-term digital quantum computers to implement circuits with structure of relevance to quantum simulation. Here, we conduct a benchmark study by realizing symmetry-protected topological (SPT) phases of a spin-1/2 Hamiltonian with next-nearest-neighbor hopping on up to 11 qubits on a programmable superconducting quantum processor using adiabatic state preparation. Using recompilation techniques to reduce the gate count to around 50 two-qubit gates, we observe clear signatures of the two distinct SPT phases, such as excitations localized to specific edges and finite string-order parameters. Finally, we identify a parasitic phase associated with the two-qubit gate as the dominant imperfection that limits the depth of the circuits, indicating a research topic of interest for future hardware development.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Implementation of a Binary Neural Network on a Passive Array of Magnetic Tunnel Junctions

The increasing scale of neural networks and their growing application space have produced demand for more energy- and memory-efficient artificial-intelligence-specific hardware. Avenues to mitigate the main issue, the von Neumann bottleneck, include in-memory and near-memory architectures, as well as algorithmic approaches. In this report we leverage the low-power and the inherently binary operation of magnetic tunnel junctions (MTJs) to demonstrate neural network hardware inference based on passive arrays of MTJs. In general, transferring a trained network model to hardware for inference is confronted by degradation in performance due to device-to-device variations, write errors, parasitic resistance, and nonidealities in the substrate. To quantify the effect of these hardware realities, we benchmark 300 unique weight matrix solutions of a two-layer perceptron to classify the Wine dataset for both classification accuracy and write fidelity. Despite device imperfections, we achieve software-equivalent accuracy of up to 95.3% with proper tuning of network parameters in 15 x 15 MTJ arrays having a range of device sizes. The success of this tuning process shows that new metrics are needed to characterize the performance and quality of networks reproduced in mixed signal hardware.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Intrinsic and Extrinsic Factors Influencing the Dynamics of VO 2 Mott Oscillators

Oscillatory devices have gained significant interest recently as key components of computing systems based on biomimetic neuronal spiking. An understanding of the time scales underlying the spiking is essential for engineering fast, controllable, low energy devices. However, we find that the intrinsic dynamics of these devices are difficult to properly characterize, as they can be heavily influenced by the external circuitry used to measure them. Here we demonstrate these challenges using a VO 2 Mott oscillator with a sub-100 nm effective size, achieved using a nanogap cut in a metallic carbon nanotube electrode. Given the nanoscale thermal volume of this device, it would be expected to exhibit rapid oscillations. However, due to external parasitics present within commonly used current sources, we see orders of magnitude slower dynamics. Here, we outline methods for determining when measurements are dominated by extrinsic factors and discuss the operating conditions under which intrinsic oscillation frequencies may be observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Ramsey envelope modulation in NV diamond magnetometry

Nitrogen-vacancy (NV) spin ensembles in diamond provide an advanced magnetic sensing platform, with applications in both the physical and life sciences. The development of isotopically engineered 15 NV diamond offers advantages over naturally occurring 14 NV for magnetometry, due to its simpler hyperfine structure. However, for sensing modalities requiring a bias magnetic field not aligned with the sensing NV axis, the absence of a quadrupole moment in the 15 N nuclear spin leads to pronounced envelope modulation effects in time-dependent measurements of 15 NV spin evolution. While such behavior in spin echo experiments are well studied, analogous effects in Ramsey measurements and the implications for magnetometry remain underexplored. Here, we derive the modulated 15 NV Ramsey response to a misaligned bias field, using a simple vector description of the effective magnetic field on the nuclear spin. The predicted modulation properties are then compared to experimental results, revealing significant magnetic sensitivity loss if unaddressed. We demonstrate that double-quantum coherences of the NV S=1 electronic spin states dramatically suppress these envelope modulations, while additionally proving resilient to other parasitic effects such as strain heterogeneity and temperature shifts.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Three-Wave Mixing Kinetic Inductance Traveling-Wave Amplifier with Near-Quantum-Limited Noise Performance

We present a theoretical model and experimental characterization of a microwave kinetic inductance traveling-wave (KIT) amplifier, whose noise performance, measured by a shot-noise tunnel junction (SNTJ), approaches the quantum limit. Biased with a dc current, this amplifier operates in a three-wave mixing fashion, thereby reducing by several orders of magnitude the power of the microwave pump tone and associated parasitic heating compared to conventional four-wave mixing KIT amplifier devices. It consists of a 50 Ω artificial transmission line whose dispersion allows for a controlled amplification bandwidth. We measure $16.5^{+1}_{–1.3}$ dB of gain across a 2 GHz bandwidth with an input 1 dB compression power of –63 dBm, in qualitative agreement with theory. Using a theoretical framework that accounts for the SNTJ-generated noise entering both the signal and idler ports of the KIT amplifier, we measure the system-added noise of an amplification chain that integrates the KIT amplifier as the first amplifier. This system-added noise, 3.1 ± 0.6 quanta (equivalent to 0.66 ± 0.15 K) between 3.5 and 5.5 GHz, is the one that a device replacing the SNTJ in that chain would see. This KIT amplifier is therefore suitable to read large arrays of microwave kinetic inductance detectors and promising for multiplexed superconducting qubit readout.

42 ENGINEERING↗
DOE OSTI2026

Cumulative fidelity of large-momentum-transfer clock atom interferometers in the presence of laser noise

Clock atom interferometry is an emerging technique in precision measurements that is particularly well suited for sensitivity enhancement through large momentum transfer (LMT). While current systems have demonstrated momentum separations of several hundreds of photon momenta, next-generation quantum sensors are targeting an LMT enhancement factor beyond 10 4 . However, the viability of LMT clock interferometers has recently come into question due to the potential impact of laser frequency noise. Here, in this work, we resolve this concern by analyzing the cumulative fidelity of sequential state inversions in an LMT atom interferometer. We show that the population error from 𝑛 pulses applied from alternating directions scales linearly with 𝑛. This is a significant advantage over the 𝑛 2 scaling that occurs when probing a two-level system 𝑛 times from the same direction. We further show that contributions to the interferometer signal from parasitic paths generated by imperfect pulses are negligible, for any loss mechanism. These results establish that laser frequency noise is not a practical limitation for the development of high-fidelity LMT clock atom interferometers.

Mach-Zehnder atom interferometry↗