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DOE OSTI2021

Tuning the critical Li intercalation concentrations for MoX 2 (X = S, Se, or Te) bilayer phase transitions

Transition metal dichalcogenides (TMDs), such as MoS 2 , are known to undergo a structural phase transformation as well as a change in the electronic conductivity upon Li intercalation. These properties make them candidates for charge-tunable ion-insertion materials that could be used in electro-chemical devices. In this work we study the phase stability and electronic structure of H and T’ Li-intercalated MoX 2 bilayers with X=S, Se, or Te. Here, using first-principles calculations in combination with classical and machine learning modeling approaches, we find that the H phase is more stable at low Li concentration for all X, and the critical Li concentration at which the T’→H transition occurs decreases with increasing mass of X. Furthermore the relative free energy of the two phases becomes less sensitive to Li insertion with increasing atomic mass of the chalcogen atom X. While the electronic conductivity increases with increasing ion concentration at low concentrations, we do not observe a (positive) conductivity jump at the phase transition from H to T’.

36 MATERIALS SCIENCE↗

DOE OSTI2016

The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2

Traditional marker-based mapping and next-generation sequencing was used to determine that the Arabidopsis (Arabidopsis thaliana) low cell wall arabinose mutant murus5 (mur5) encodes a defective allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 (RGP2). Marker analysis of 13 F2 confirmed mutant progeny from a recombinant mapping population gave a rough map position on the upper arm of chromosome 5, and deep sequencing of DNA from these 13 lines gave five candidate genes with G→A (C→T) transitions predicted to result in amino acid changes. Of these five, only insertional mutant alleles of RGP2, a gene that encodes a UDP-arabinose mutase that interconverts UDP-arabinopyranose and UDP-arabinofuranose, exhibited the low cell wall arabinose phenotype. The identities of mur5 and two SALK insertional alleles were confirmed by allelism tests and overexpression of wild-type RGP2 complementary DNA placed under the control of the 35S promoter in the three alleles. The mur5 mutation results in the conversion of cysteine-257 to tyrosine-257 within a conserved hydrophobic cluster predicted to be distal to the active site and essential for protein stability and possible heterodimerization with other isoforms of RGP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein

Determination of the nitrogenase MoFe protein from C. pasteurianum at 1.08 Å resolution and comparison to its distinct ortholog from A. vinelandii at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The X-ray crystal structure of the nitrogenase MoFe protein from Clostridium pasteurianum (Cp1) has been determined at 1.08 Å resolution by multiwavelength anomalous diffraction phasing. Cp1 and the ortholog from Azotobacter vinelandii (Av1) represent two distinct families of nitrogenases, differing primarily by a long insertion in the α-subunit and a deletion in the β-subunit of Cp1 relative to Av1. Comparison of these two MoFe protein structures at atomic resolution reveals conserved structural arrangements that are significant to the function of nitrogenase. The FeMo cofactors defining the active sites of the MoFe protein are essentially identical between the two proteins. The surrounding environment is also highly conserved, suggesting that this structural arrangement is crucial for nitrogen reduction. The P clusters are likewise similar, although the surrounding protein and solvent environment is less conserved relative to that of the FeMo cofactor. The P cluster and FeMo cofactor in Av1 and Cp1 are connected through a conserved water tunnel surrounded by similar secondary-structure elements. The long α-subunit insertion loop occludes the presumed Fe protein docking surface on Cp1 with few contacts to the remainder of the protein. This makes it plausible that this loop is repositioned to open up the Fe protein docking surface for complex formation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans

YidC, a membrane-protein chaperone/insertase from B. halodurans, was expressed, purified and crystallized in the lipidic cubic phase. An X-ray diffraction data set was collected to 2.4 Å resolution. YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P2{sub 1}, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

PRISTINE: An Emulation Platform for PCB-Level Hardware Trojans

Printed circuit Boards (PCBs) are becoming increasingly vulnerable to malicious design alteration, also known as Trojan attacks, due to a distributed business model that often involves various untrusted parties. Such attacks can be mounted at various stages in the PCB life cycle. The relative ease of alteration of PCB hardware even after fabrication (due to physical access to surface-mounted critical components and traces) makes them attractive for an adversary to manipulate their functional/physical behavior for malicious intent. There is a growing need to explore viable Trojan attacks in a PCB, analyze their functional and physical characteristics (e.g., impact on power or delay), and study the effectiveness of countermeasures against these attacks. While simulation-based approaches for PCB Trojan insertion are effective at creating a large population of possible Trojans, they fail to provide functional feasibility analysis with a realistic workload for a trigger circuit. Also, they cannot estimate a Trojan’s side-channel footprint due to the unavailability of physical models of diverse PCB components. To address these deficiencies, in this paper, we present PRISTINE, a PCB-level emulation system for any integrity or physical tampering issues, specifically, hardware Trojan insertion. The need for building such an emulation platform to resolve PCB trust issues in the supply chain is also surveyed and discussed. Both custom Hardware Hacking (HaHa) boards and multiple commercial PCBs are then used to test the ability of the proposed system to emulate various hardware Trojans specially designed to exploit board-specific hardware characteristics. Experimental results on emulated board-level Trojans show that a wide range of Trojans can be successfully activated, thus enabling the expected payload effects on both types of boards to be studied and quantified. The resulting data are further analyzed to create PCB-level Trojan benchmarks. In particular, a comparative evaluation of the experimental results is used to propose a risk level metric that quantifies the probability of detection and degree of payload impact of each Trojan on a given commercial PCB.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Power Plant Testing of Ultrasonic Measurements of Temperature Distributions and Heat Fluxes to Heat Exchange Surfaces

Extreme environmental conditions are common in energy conversion applications, in which the most hardened insertion sensors often do not perform reliably for long. On the other hand, ultrasonic measurements can be acquired noninvasively, with sensitive components kept away from the damaging environment. We have previously developed the ultrasonic method for measuring the spatial distribution of temperatures in solid materials applicable when large thermal gradients are present. In the developed approach, we use the echogenically segmented ultrasound propagation path, structured to contain engineered or naturally occurring echogenic features, to produce a train of echoes in response to an external pulse of ultrasonic excitation. This paper outlines the testing results of this approach applied to the temperature distribution measurements to a waterwall of a 500 MW power-plant utility boiler. The validation results obtained over the prolonged power plant test show that the estimated temperature profile is correctly captured, and the measurement accuracy can be comparable with traditional insertion sensors, such as thermocouples. Overall, the testing has confirmed that the developed approach has matured to become an attractive alternative to conventional sensing in solving challenging problems of long-term temperature measurements in extreme environments. Heat fluxes and thermal stresses in the structure can then be characterized noninvasively using the measured temperature distribution as the basis.

Walton, Kenneth↗

DOE OSTI2014

Atomic-Layer-Deposited Transparent Electrodes for Silicon Heterojunction Solar Cells

We examine damage-free transparent-electrode deposition to fabricate high-efficiency amorphous silicon/crystalline silicon heterojunction solar cells. Such solar cells usually feature sputtered transparent electrodes, the deposition of which may damage the layers underneath. Using atomic layer deposition, we insert thin protective films between the amorphous silicon layers and sputtered contacts and investigate their effect on device operation. We find that a 20-nm-thick protective layer suffices to preserve, unchanged, the amorphous silicon layers beneath. Insertion of such protective atomic-layer-deposited layers yields slightly higher internal voltages at low carrier injection levels. However, we identify the presence of a silicon oxide layer, formed during processing, between the amorphous silicon and the atomic-layer-deposited transparent electrode that acts as a barrier, impeding hole and electron collection.

14 SOLAR ENERGY↗

DOE OSTI2019

Test Results of the CERN HL-LHC low- Quadrupole Short Models MQXFS3c and MQXFS4

For the High Luminosity Upgrade of the CERN Large Hadron Collider, lower * quadrupole magnets based on advanced Nb3Sn conductors will be installed on each side of the ATLAS and CMS experiment insertion zones. As part of the technological developments needed to achieve the required field gradient of 132.6 T/m within a 150-mm aperture, short length model magnets, named MQXFS, are tested both at the CERN SM18 and FERMI Lab test facilities. The model magnets rely on two types of Nb3Sn conductors (RRP and PIT) and on an innovative bladders and keys design to provide mechanical support against the Lorentz forces. In 2016 and 2017, the powering tests of the first two models MQXFS3 (RRP) and MQXFS5 (PIT) proved that nominal performance (16.5 kA) could be reached with excellent memory of the quench current after thermal cycle. However both magnets showed a slow training behavior with clear observations of voltage disturbances before the quench. Besides MQXFS5 only could reach ultimate current (17.9 kA) whereas erratic behavior was observed on MQXFS3 due to conductor local degradation at the head of one of the coil. In 2018, this limiting coil was changed and the applied azimuthal pre-stress increased. If ultimate current could then be reached, no stable current could be maintained due to identified defect on the outer layer of the new coil. Finally the outcome of the test of the new model MQXFS4, featuring the final RRP conductors that will be used for the series production and variation on the inner layer quench heater designs are here reported in details.

43 PARTICLE ACCELERATORS↗

DOE OSTI2019

New Approach and Test Facility for High Field Accelerator Magnets R&D

This paper presents a new approach for developing and demonstrating high field magnet technology based on a magnet and test facility developed specifically for it. The traditional approach for carrying out high field magnet R&D has been building a new magnet to demonstrate a new design, new material or new technology. However, building a high field magnet is time consuming and expensive. To overcome this limitation, Brookhaven National Laboratory (BNL) built and successfully tested a 10 T Nb 3 Sn dipole DCC017 with large enough open or clear space (31 mm wide and 338 mm high) so that a pair of racetrack coils could be inserted into this opening without disassembling the magnet. The motivation be-hind this design was to facilitate a magnet R&D program where the new coils (with a large range in width and height accommodated) would reside in a high field region in direct contact with the existing coils (just as other magnet coils) and thus become an integral part of the magnet. We summarize the approach, the magnet, the test facility, past experiences, current and future test plans and planned up-grade. Here, the magnet facility is now available to service the needs of the wider community for testing cable and insert coils in a back-ground field of up to 10 T.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Application of Distributed Fiber Optic Strain Sensors to LMQXFA Cold Mass Welding

The future High Luminosity upgrade of the Large Hadron Collider (HL-LHC) at CERN will include the low-beta inner triplets (Q1, Q2a/b, Q3) for two LHC insertion regions. The Q1, Q3 components consist of eight 10 m-long LMQXFA cryo-assemblies fabricated by the HL-LHC Accelerator Upgrade Project. Each LMQXFA Cold mass contains two Nb 3 Sn magnets connected in series. A stainless-steel shell is welded around the two magnets before the insertion into the cryostat. There is a limit on how much coil preload increase induced by the shell welding is allowed. Distributed Rayleigh backscattering fiber optics sensors were used for the first time to obtain a strain map over a wide area of a Nb 3 Sn magnet cold mass shell. Finally, data were collected during welding of the first LMQXFA cold mass and the results confirm that the increase of the coil pole azimuthal pre-stress after welding do not exceed requirements.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

FEM Analysis of Hybrid LTS/HTS Cos-Theta Dipole Magnet With Heterogeneous Cable Model

The Lawrence Berkeley National Laboratory (LBNL) and the National High Magnetic Field Laboratory (NHMFL) have published results on Bi-2212 superconductive magnets realized and tested in the canted cosine-theta and solenoid designs, respectively. Fermilab is now preparing for the assembly of the first Bi-2212 stress-managed cosine-theta insert magnet. The insert will be part of the first hybrid cosine-theta magnet made of Nb$_3$Sn outer layers within the US-MDP effort to reach a 20 T bore field. This paper presents the analytical analysis of the cosine-theta Nb$_3$Sn/Bi-2212 hybrid magnet. We report the parameters, logic, and implementation method of the 2D electromagnetic and mechanical FEM analysis of the LTS/HTS hybrid magnet. Results from a detailed heterogeneous model are compared to the homogeneous model implemented in the past. A Python code has been developed to simulate the current degradation due to stresses in the detail-modeled conductor areas. The current degradation has been introduced in the simulation dynamics for the HTS conductor as an iteration process, updating the input load of Lorentz forces of the energization at each step. The magnetic and mechanical analysis results of the 2D cosine-theta LTS/HTS dipole magnet have been described and analyzed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Conceptual Design of a Scintillator-Based Fast-Ion Loss Detector for the Wendelstein 7-X Stellarator

Here, a conceptual design of a scintillator-based fast-ion loss detector (FILD) has been developed for the Wendelstein 7-X stellarator (W7-X). Simulations using the Monte Carlo codes ASCOT5 and BEAMS3D have been performed to calculate the expected flux of neutral beam injection (NBI)-generated fast hydrogen ions onto the conceptual detector probe head. These fast-ion loss fluxes have been calculated for several magnetic field configurations as well as probe insertion positions. At the maximum insertion position, both co-and counter-going losses with high incident pitch angles are observed; however, at retracted positions, only co-going fast ions reach the probe head. The FILDSIM code has been used to optimize the geometry of the detector entrance and collimating elements to achieve a wide velocity space coverage as well as a high velocity–space resolution. A synthetic FILD signal is calculated for the expected loss distribution via forward modeling using the instrument response function. The synthetic signal is found to largely retain the velocity space features of the loss distribution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2019

Ultrasonic Measurements of Temperature Distribution and Heat Fluxes Across Containments of Extreme Environments

Extreme conditions are common in energy conversion, material processing, nuclear, airspace, and military applications. In such environments, the most hardened insertion sensors do not perform reliably for long. Ultrasonic measurements, on the other hand, can be acquired noninvasively, with sensitive components kept away from the damaging environment. We have previously developed the ultrasonic method for measuring the spatial distribution of temperatures in solid materials applicable in the cases when large thermal gradients are present. In the developed approach, we use the echogenically segmented ultrasound propagation path, structured to contain engineered or naturally occurring echogenic features, to produce a train of echoes in response to an external pulse of ultrasonic excitation. The delays between the echoes, which encode the information on the temperature distribution in the corresponding segments, is used to reconstruct unknown temperature profile. In this paper, we outline the results of pilot-scale testing of the developed approach and demonstrate its application to the measurements of the temperature distribution across the containment of a high-temperature combustion process. The validation results show that the estimated temperature profile is correctly captured, and the measurement accuracy can be comparable with traditional insertion sensors, such as thermocouples. Overall, the testing has confirmed that the developed approach has matured to become an attractive alternative to conventional sensing in solving challenging problems of long-term temperature measurements in extreme environments. Heat fluxes and thermal stresses in the structure can then be characterized noninvasively using the measured temperature distribution as the basis.

Jia, Yunlu↗

DOE OSTI2024

Utilization of lasso peptides for biodegradation of polycyclic aromatic hydrocarbons

Abstract Many microbial genes involved in degrading recalcitrant environmental contaminants such as polycyclic aromatic hydrocarbons (PAHs) have been identified and characterized. However, all molecular mechanisms required for PAH utilization have not yet been elucidated. In this work, we demonstrate the proposed involvement of lasso peptides in the utilization of the PAH phenanthrene in Sphingomonas BPH. Transpositional mutagenesis of Sphingomonas BPH with the miniTn5 transposon yielded 3 phenanthrene utilization deficient mutants, #257, #1778, and #1782. In mutant #1782, Tn5 had inserted into the large subunit of the naph/bph dioxygenase gene. In mutant #1778, Tn5 had inserted into the B2 protease gene of a lasso peptide cluster. This finding is the first report on the role of lasso peptides in PAH utilization. Our studies also demonstrate that interruption of the lasso peptide cluster resulted in a significant increase in the amount of biosurfactant produced in the presence of glucose when compared to the wild‐type strain. Collectively, these results suggest that the mechanisms Sphingomonas BPH utilizes to degrade phenanthrene are far more complex than previously understood and that the #1778 mutant may be a good candidate for bioremediation when glucose is applied as an amendment due to its higher biosurfactant production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

KIN3 impacts arbuscular mycorrhizal symbiosis and promotes fungal colonisation in Medicago truncatula

Summary Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in four Medicago truncatula Tnt1 ‐insertion mutants affected in arbuscular mycorrhizal colonisation. We located their Tnt1 insertions and identified alleles for two genes known to be involved in mycorrhization, RAM1 and KIN3 . We compared the effects of the kin3‐2 and ram1‐4 mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting that RAM1 acts upstream of KIN3. Additionally, KIN3 appears to be involved in the suppression of plant defences in response to the fungal symbiont. KIN3 is located on the endoplasmic reticulum of arbuscule‐containing cortical cells, and kin3‐2 mutants plants hosted significantly fewer arbuscules than the wild type. KIN3 plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild‐type plants, the kin3‐2 mutant did not exhibit increased root colonisation under high nitrogen.

Irving, Thomas B.↗

DOE OSTI2018

Influence of charge motion and compression ratio on the performance of a combustion concept employing in-cylinder gasoline and natural gas

The present paper represents a small piece of an extensive experimental effort investigating the dual-fuel operation of a light-duty spark ignited engine. Natural gas (NG) was directly injected into the cylinder and gasoline was injected into the intake-port. Direct injection (DI) of NG was used in order to overcome the power density loss usually experienced with NG port-fuel injection (PFI) as it allows an injection after intake valve closing. Having two separate fuel systems allows for a continuum of in-cylinder blend levels from pure gasoline to pure NG operation. The huge benefit of gasoline is its availability and energy density, whereas NG allows efficient operation at high load due to improved combustion phasing enabled by its higher knock resistance. Furthermore, using NG allowed a reduction of carbon dioxide emissions across the entire engine map due to the higher hydrogen-to-carbon ratio. Exhaust gas recirculation (EGR) was used to (a) increase efficiency at low and part-load operation and (b) reduce the propensity of knock at higher compression ratios (CRs) thereby enabling blend levels with greater amount of gasoline across a wider operating range. Two integral engine parameters, CR and in cylinder turbulence levels, were varied in order to study their influence on efficiency, emissions, and performance over a specific speed and load range. Increasing the CR from 10.5 to 14.5 allowed an absolute increase in indicated thermal efficiency of snore than 3% for 7.5% NG (2.5% gasoline) operation at 8 bar net indicated mean effective pressure (IMEP) and 2500 rpm. However, as anticipated, the achievable peak load at CR 14.5 with 100% gasoline was greatly reduced due to its lower knock resistance. The in cylinder turbulence level was varied by means of tumble plates (TPs) as well as an insert for the NG injector that guides the injection "spray" to augment the tumble motion. The usage of TPs showed a significant increase in EGR dilution tolerance for pure gasoline operation, however, no such impact was found for blended operation of gasoline and NG.

Sevik, James↗

DOE OSTI2013

Ion optical effects in a low pressure rf plasma

Ion optical effects in low pressure gas discharges are introduced as a novel input into low pressure plasma technology. They are based on appropriate geometrical plasma confinements which enable a control of the shape of internal density and potential distributions and, hence, the ion motion in the plasma bulk. Such effects are exemplified for an electron cyclotron wave resonance plasma in Ar at 1–5 × 10{sup −3} millibars. The geometry of the plasma chamber is modified by a conical and a cylindrical insert. Computer simulations display spherical plasma density contours to be formed around the conical confinement. This effects an increase of the ratio of the ion currents into the conical and the cylindrical inserts which depends on the fourth power of the plasma electron temperature. A quantitative understanding of this behavior is presented. As another essential result, the shape of the internal plasma contours is found to be independent of the pressure controlled plasma parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗