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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 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Quantitative Specifications to Avoid Degradation during E-Beam and Induced Current Microscopy of Halide Perovskite Devices

Degradation due to electron beam exposure has posed a challenge in the use of electron microscopy to probe halide perovskite materials and devices. Herein, the interaction between the electron beam and the perovskite across acceleration voltages and at low probe currents is investigated in a scanning electron microscope (SEM) by monitoring the electron-beaminduced current (EBIC) response in perovskite solar cells in a planview configuration. SEM probe conditions are identified where dozens of repeated scans over a single region of the perovskite solar cell induce minimal electronic degradation. Overall, the induced current response of the perovskite device is found to strongly depend upon the beam condition: rapid decay occurs at high beam powers, the current activates at the lowest beam powers, and a newfound quasi-steady response is revealed at intermediate beam conditions. A quantitative window for the successful conduction of e-beam studies with minimal electronic degradation is revealed by evaluating induced current response over a wide range of perovskite devices, which invites broader use of SEM-based characterization techniques, including EBIC, as powerful techniques for correlative microscopy investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

High-Resolution Three-Dimensional Sculpting of Two-Dimensional Graphene Oxide by E-Beam Direct Write

On demand switchable additive/subtractive patterning of 2D nanomaterials is an essential capability for developing new concepts of functional nanomaterials and their device realizations. Traditionally, this is performed via a multi-step process using photoresist coating and patterning by conventional photo or electron beam lithography, which is followed by bulk dry/wet etch or deposition. This limits the range of functionalities and structural topologies that can be achieved, as well as increases the complexity, cost, and possibility of contamination which are significant barriers to device fabrication from highly sensitive 2D materials. Focused electron beam induced processing (FEBIP) enables a material chemistry/site-specific, high-resolution multi-mode atomic scale processing and provides unprecedented opportunities for direct-write, single-step surface patterning of 2D nanomaterials with an in-situ imaging capability. It allows for realizing a rapid multi-scale/multi-mode approach, ranging from an atomic scale manipulation (e.g., via targeted defect introduction as an active site) to a large-area surface modification on nano and micro scales, including patterned doping and material removal/deposition with 2D (in-plane)/3D (out-of-plane) control. In this work, we report on a new capability of FEBIP for nanoscale patterning of graphene oxide via removal of oxygenated carbon moieties with no use of reactive gas required for etching complemented by carbon atom deposition using focused electron beam. The mechanism of experimentally observed phenomena is explored using the density functional theory (DFT) calculations, revealing that interactions of e-beam liberated reactive oxygen radicals with carbon atoms on graphene basal plane lead to creation of atomic vacancies in the material. The reaction by-products are volatile carbon di-oxides, which are dissociated and volatilized from the graphene oxide surface functional groups by interactions with an energetic focused electron beam. Along with selective “subtractive” patterning of graphene oxide, the same electron beam with increased irradiation doses can deposit out-of-plane 3D carbon nanostructures on top of or around the 2D etched pattern, thus forming a hybrid 2D/3D nanocomposite with feature control down to a few nanometers. Furthermore, this in-operando dual nanofabrication capability of FEBIP is unmatched by any other nanopatterning techniques and opens a new design window for forming 2D/3D complex nanostructures and functional nanodevices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog

New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the development of agents that selectively target bacterial pathogens. 1-Deoxy- D -xylulose 5-phosphate synthase (DXPS) converts pyruvate and d-glyceraldehyde 3-phosphate ( D -GAP) to DXP, which is required for synthesis of essential vitamins and isoprenoids in bacterial pathogens. Thus, DXPS is a promising antimicrobial target. Toward this goal, our lab has demonstrated selective inhibition of Escherichia coli DXPS by alkyl acetylphosphonate (alkylAP)-based bisubstrate analogs that exploit the requirement for ternary complex formation in the DXPS mechanism. Here, we present the first DXPS structure with a bisubstrate analog bound in the active site. Insights gained from this cocrystal structure guided structure–activity relationship studies of the bisubstrate scaffold. A low nanomolar inhibitor (compound 8) bearing a gem-dibenzyl glycine moiety conjugated to the acetylphosphonate pyruvate mimic via a triazole-based linker emerged from this study. Compound 8 was found to exhibit slow, tight-binding inhibition, with contacts to E. coli DXPS residues R99 and R478 demonstrated to be important for this behavior. This work has discovered the most potent DXPS inhibitor to date and highlights a new role of R99 that can be exploited in future inhibitor designs toward the development of a novel class of antimicrobial agents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Media Robustness and Scalability of Phosphate Regulated Promoters Useful for Two-Stage Autoinduction in E. coli

A key challenge in synthetic biology is the successful utilization of characterized parts, such as promoters, in different biological contexts. We report the evaluation of the media robustness of a small library of E. coli PhoB regulated promoters that enable heterologous protein production in two-stage cultures. Expression levels were measured both in a rich Autoinduction Broth as well as a minimal mineral salts media. Expression was both media and promoter dependent. Of the 16 promoters tested, 4 were identified to have tightly controlled expression, which was also robust to media formulation. Improved promoter robustness led to more predictable scale up and consistent expression in instrumented bioreactors. Furthermore, this subset of PhoB activated promoters, useful for two-stage autoinduction, highlights the impact of the environment on the performance of biological parts and the importance of robustness testing in synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C–H and C=C Bonds

The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. Here we show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cryo-EM structures provide insight into how E. coli F 1 F o ATP synthase accommodates symmetry mismatch

F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Engineering regulatory networks for complex phenotypes in E. coli

Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli , with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5

Abstract Penicillin-binding proteins (PBPs) are essential for the formation of the bacterial cell wall. They are also the targets of β-lactam antibiotics. In Enterococcus faecium , high levels of resistance to β-lactams are associated with the expression of PBP5, with higher levels of resistance associated with distinct PBP5 variants. To define the molecular mechanism of PBP5-mediated resistance we leveraged biomolecular NMR spectroscopy of PBP5 – due to its size (>70 kDa) a challenging NMR target. Our data show that resistant PBP5 variants show significantly increased dynamics either alone or upon formation of the acyl-enzyme inhibitor complex. Furthermore, these variants also exhibit increased acyl-enzyme hydrolysis. Thus, reducing sidechain bulkiness and expanding surface loops results in increased dynamics that facilitates acyl-enzyme hydrolysis and, via increased β-lactam antibiotic turnover, facilitates β-lactam resistance. Together, these data provide the molecular basis of resistance of clinical E. faecium PBP5 variants, results that are likely applicable to the PBP family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

E(n)-Equivariant cartesian tensor message passing interatomic potential

Machine learning potential (MLP) has been a popular topic in recent years for its capability to replace expensive first-principles calculations in some large systems. Meanwhile, message passing networks have gained significant attention due to their remarkable accuracy, and a wave of message passing networks based on Cartesian coordinates has emerged. However, the information of the node in these models is usually limited to scalars, and vectors. In this work, we propose High-order Tensor message Passing interatomic Potential (HotPP), an E(n) equivariant message passing neural network that extends the node embedding and message to an arbitrary order tensor. By performing some basic equivariant operations, high order tensors can be coupled very simply and thus the model can make direct predictions of high-order tensors such as dipole moments and polarizabilities without any modifications. The tests in several datasets show that HotPP not only achieves high accuracy in predicting target properties, but also successfully performs tasks such as calculating phonon spectra, infrared spectra, and Raman spectra, demonstrating its potential as a tool for future research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide

Capsular polysaccharides are important virulence factors in pathogenic bacteria. Characterizing the structural components and biosynthetic pathways for these polysaccharides is key to our ability to design vaccines and other preventative therapies that target encapsulated pathogens. Many gramnegative pathogens such as Neisseria meningitidis and Escherichia coli express acidic capsules. The E. coli K15 serotype has been identifed as both an enterotoxigenic and uropathogenic pathogen. Despite its relevance as a disease-causing serotype, the associated capsular polysaccharide remains poorly characterized. We describe in this report the chemical structure of the K15 polysaccharide, based on chemical analysis and nuclear magnetic resonance (NMR) data. The repeating structure of the K15 polysaccharide consists of 4)-α-GlcpNAc-(1→5)-α-KDOp-(2→partially O-acetylated at 3-hydroxyl of GlcNAc. We also report, the organization of the gene cluster responsible for capsule biosynthesis. We identify genes in this cluster that potentially encode an O-acetyltransferase, an N-acetylglucosamine transferase, and a KDO transferase consistent with the structure we report.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7

The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP

F 1 F o ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F o motor that is transferred to the F 1 motor to catalyze ATP production, with flexible F 1 /F o coupling required for efficient catalysis. F 1 F o ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F 1 F o ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F ο motor. This highlights the importance of the central rotor for flexible coupling of the F 1 and F o motors and provides further insight into the regulatory mechanism mediated by subunit ε.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Physics of E × B discharges relevant to plasma propulsion and similar technologies

This paper provides perspectives on recent progress in understanding the physics of devices in which the external magnetic field is applied perpendicular to the discharge current. This configuration generates a strong electric field that acts to accelerate ions. The many applications of this set up include generation of thrust for spacecraft propulsion and separation of species in plasma mass separation devices. These “E × B” plasmas are subject to plasma–wall interaction effects and to various micro- and macroinstabilities. In many devices we also observe the emergence of anomalous transport. This perspective presents the current understanding of the physics of these phenomena and state-of-the-art computational results, identifies critical questions, and suggests directions for future research.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Electric field measurements of DC-driven positive streamer coronas using the E-FISH method

This paper reports on electric field measurements, using the electric field-induced second harmonic (E-FISH) method, sampling the spatial structure and temporal development of DC-driven positive streamer coronas in atmospheric-pressure air at relevant timescales to examine the self-pulsating behavior of the discharge. The discharge is triggered from a point-to-plate geometry and consists of transient coronas, which bridge the inter-electrode gap and pulsate at about 3 kHz, superimposed with a persisting glow corona. The measurements presented challenge the phenomenological explanation for the pulsations based on field recovery at the anode driven by the evacuation of positive ions by electric drift effects and hint at a propagating wave-like feature from the plate-cathode to the tip-anode.

42 ENGINEERING↗
DOE OSTI2025

Mode transitions and spoke structures in E × B Penning discharge

Two-dimensional particle-in-cell simulations in the (radial-azimuthal) plane perpendicular to the axial direction of a cylindrical $E$ x $B$ Penning discharge are presented. The low-pressure discharge is self-consistently supported by plasma ionization from the electron beam injected axially, along the direction of the external magnetic field. It is shown that with the increasing strength of the external magnetic field, the discharge undergoes a sequence of transitions between several azimuthal modes. Azimuthal m > 1 spiral arm structures are excited at low magnetic field values as plasma confinement improves and the radial density profile becomes peaked. With a larger field, spiral arms with m > 1 are replaced by the m = 1 spoke mode, most clearly seen in plasma density. A transition from spiral arms to the spoke regime occurs when the plasma potential in the center changes from weakly positive (or zero) to negative. Further increase in the magnetic field results in a well-developed m = 1 spoke mode with additional small-scale higher-frequency m > 1 structures inside and around the spoke. It is shown that while ionization and collisions affect some characteristics of the observed fluctuations, the basic features of the spoke and m > 1 spiral structure remained similar without ionization. The role of energy conservation in small-scale high-frequency modes and spoke dynamics is discussed. It is demonstrated that in regimes with the m = 1 spoke mode, additional m = 4 harmonics of the ion and electron fluxes to the wall appear due to the square boundary. The frequency of the m = 1 mode is weakly affected by the geometry of the boundary.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

A new mechanism for filament disconnection at the X-point: poloidal shear in radial E × B velocity

Plasma filaments generated by turbulence in the scrape-off layer are sometimes observed in experiments and simulations to disconnect from the target plate in the vicinity of the X-point, resulting in a ‘quiescent zone’ with reduced fluctuations, possibly affecting the fluctuating part of the divertor heat loads. This phenomena is usually explained by the flux tubes squeezing, induced by flux expansion, down to scales where collisions dominate. In this work, we consider an additional mechanism spontaneously arising at the X-point: the poloidal shear in radial E × B velocity. Through a simple model, tested against 3D global turbulence simulations, herein we quantify the effectiveness of this disconnection mechanism and identify ways to control it.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

New insights on divertor parallel flows,E × B drifts, and fluctuations from in situ, two-dimensional probe measurement in the Tokamak à Configuration Variable

Abstract In situ , two-dimensional (2D) Langmuir probe measurements across a large part of the TCV outer divertor are reported in L-mode discharges with and without divertor baffles. This provides detailed insights into time averaged profiles, particle fluxes, and fluctuation behavior in different divertor regimes. The presence of the baffles is shown to substantially increase the divertor neutral pressure for a given upstream density and to facilitate the access to detachment, an effect that increases with plasma current. The detailed, 2D probe measurements allow for a divertor particle balance, including ion flux contributions from parallel flows and E × B drifts. The poloidal flux contribution from the latter is often comparable or even larger than the former, and the divertor parallel flow direction reverses in some conditions, pointing away from the target. In most conditions, the integrated particle flux at the outer target can be predominantly ascribed to ionization along the outer divertor leg, consistent with a closed-box approximation of the divertor. The exception is a strongly detached divertor, achieved here only with baffles, where the total poloidal ion flux even decreases towards the outer target, indicative of significant plasma recombination. The most striking observation from relative density fluctuation measurements along the outer divertor leg is the transition from poloidally uniform fluctuation levels in attached conditions to fluctuations strongly peaking near the X-point when approaching detachment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Geometric dependencies of the mean E × B shearing rate in negative triangularity tokamaks

Abstract This paper presents a comparative study of the poloidal distribution of the mean E × B shearing rate for positive triangularity (PT) and negative triangularity (NT) tokamaks. The effects of flux surface up–down asymmetry due to asymmetric upper and lower triangularities are also considered. Both direct eddy straining and the effects on Shafranov shift feedback loops are examined. Shafranov shift increases the shearing rate at all poloidal angles for all triangularities, due to flux surface compression. The maximum shearing rate bifurcates at a critical triangularity δ crit ( ≲ 0 ) . Thus, the shearing rate is maximal off the outboard midplane for NT, while it is maximal on the outboard midplane for PT. For up–down asymmetric triangularity, the usual up–down symmetry of the shearing rate is broken. The shearing rate at the outboard midplane is lower for NT than for PT, suggesting that the shearing efficiency in NT is reduced. Implications for turbulence stabilisation and confinement improvement in high- β p NT and internal transport barrier discharges are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗