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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↗

DOE OSTI2024

AI-assisted detector design for the EIC (AID(2)E)

Artificial Intelligence is poised to transform the design of complex, large-scale detectors like ePIC at the future Electron Ion Collider. Featuring a central detector with additional detecting systems in the far forward and far backward regions, the ePIC experiment incorporates numerous design parameters and objectives, including performance, physics reach, and cost, constrained by mechanical and geometric limits. This project aims to develop a scalable, distributed AI-assisted detector design for the EIC (AID(2)E), employing state-of-the-art multiobjective optimization to tackle complex designs. Supported by the ePIC software stack and using G EANT 4 simulations, our approach benefits from transparent parameterization and advanced AI features. The workflow leverages the PanDA and iDDS systems, used in major experiments such as ATLAS at CERN LHC, the Rubin Observatory, and sPHENIX at RHIC, to manage the compute intensive demands of ePIC detector simulations. Tailored enhancements to the PanDA system focus on usability, scalability, automation, and monitoring. Ultimately, this project aims to establish a robust design capability, apply a distributed AI-assisted workflow to the ePIC detector, and extend its applications to the design of the second detector (Detector-2) in the EIC, as well as to calibration and alignment tasks. Additionally, we are developing advanced data science tools to efficiently navigate the complex, multidimensional trade-offs identified through this optimization process.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Hepatitis B e Antigen-Negative Single Hepatocyte Analysis Shows Transcriptional Silencing and Slow Decay of Infected Cells With Treatment

Background Nucleos(t)ide analogues (NUCs) rarely cure chronic hepatitis B (CHB) because they do not eliminate covalently closed circular deoxyribonucleic acid, the stable replication template. In hepatitis B e antigen (HBeAg)-positive CHB during NUCs, HBV-infected cells decline slowly and are transcriptionally silenced. Whether these occur in HBeAg-negative CHB is unknown. Methods Using paired liver biopsies separated by 2.7–3.7 years in 4 males with HIV and HBeAg-negative CHB at both biopsies and 1 male with HIV who underwent HBeAg seroconversion between biopsies, we quantified amounts of viral nucleic acids in hundreds of individual hepatocytes. Results In the 4 persistently HBeAg-negative participants, HBV-infected hepatocytes ranged from 6.2% to 17.7% (biopsy 1) and significantly declined in 3 of 4 by biopsy 2. In the HBeAg seroconverter, the proportion was 97.4% (biopsy 1) and declined to 81.9% at biopsy 2 (P < .05). Here, we extrapolated that HBV eradication with NUCs would take >100 years. At biopsy 1 in the persistently HBeAg-negative participants, 23%–56.8% of infected hepatocytes were transcriptionally inactive—higher than we observed in HBeAg-positive CHB—and significantly declined in 1 of 4 at biopsy 2. Conclusions In HBeAg-negative CHB on NUCs, the negligible decline in infected hepatocytes is similar to HBeAg-positive CHB, supporting the need for more potent therapeutics to achieve functional cure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp

Abstract Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Altering translation allows E. coli to overcome G-quadruplex stabilizers

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses reveal decreased protein and transcript levels, respectively, for ribosome assembly factors and proteins associated with translation in the presence of G4 stabilizer. Our results support a model in which reducing the rate of translation by altering translation initiation, translation elongation, or ribosome assembly can compensate for G4-related stress in E. coli.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Possible continuous transition from fractional quantum Hall to stripe phase at ν e = 7 / 3

We study the phase diagram of the ν e = 7/3 state in the N=1 Landau level in the presence of band mass anisotropy. Using the density matrix renormalization group on an infinite cylinder geometry, we find a continuous transition from the topologically ordered Laughlin fractional quantum Hall state to a stripe phase with a period of approximately five and a half magnetic lengths. The transition is driven by the condensation of the magnetoroton mode which becomes gapless at the critical point. We interpret the transition within the composite-boson theory as the onset of stripe order in a superfluid background, resulting from the roton mode going soft.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Measurement of the Li 7 ( γ , t ) He 4 ground-state cross section between E γ = 4.4 and 10 MeV

Here, the Li 7 ( γ , t ) He 4 ground state cross section was measured for the first time using monoenergetic γ rays with energies between 4.4 and 10 MeV at the High Intensity Gamma-ray Source. The reaction is important for the primordial Li problem and for testing our understanding of the mirror α -capture reactions H 3 ( α , γ ) Li 7 and He 3 ( α , γ ) Be 7 . Although over the last 30 years most measurements of the H 3 ( α , γ ) Li 7 reaction have concentrated in an energy range below E γ = 3.65 MeV, measurements at higher energies could potentially restrict the extrapolation to astrophysically important energies. The experimental arrangement for measuring the Li 7 ( γ , t ) He 4 reaction included a large-area silicon detector array and several beam characterization instruments. The experimental astrophysical S factor of H 3 ( α , γ ) calculated from the present data was fitted using the R -matrix formalism. The results are in disagreement with previous experimental measurements in the same energy range but the extrapolated S factor agrees with the potential model calculation and lower energy experimental data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

First measurement of the asymmetry and the Gerasimov-Drell-Hearn integrand from the 3 $\vec{H}$e ($\vec{γ},p$) 2 H reaction at an incident photon energy of 29 MeV

The first measurement of the 3 $\vec{H}$e ($\vec{γ},p$) 2 H process was performed at the High Intensity γ-ray Source ( HIγS ) facility at Triangle Universities Nuclear Laboratory using a circularly polarized, monoenergetic γ -ray beam and a longitudinally polarized 3 He target. The spin-dependent asymmetry and the contribution from the two-body photodisintegration to the 3 He Gerasimov-Drell-Hearn integrand are extracted and compared with state-of-the-art three-nucleon system calculations at the incident photon energy of 29 MeV. The data are in general agreement with the various theoretical predictions based on the Siegert theorem or on explicit inclusion of meson-exchange currents.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Accessing the gluon GTMD F 1 , 4 in exclusive π 0 production in e p collisions

We demonstrate that the longitudinal single target-spin asymmetry in exclusive π 0 production in e p collisions can give access to the imaginary part of the gluon generalized transverse momentum distribution (GTMD) F 1 , 4 . Such a longitudinal spin asymmetry that results from the Coulomb-nuclear interference effect, leads to a characteristic azimuthal angular correlation of sin 2 ϕ , where ϕ is the azimuthal angle between the scattered lepton transverse momentum and the recoil proton’s transverse momentum. We also present a numerical estimate of the asymmetry for the kinematics accessible at EIC and EicC. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Valley-Coherent Quantum Anomalous Hall State in AB-Stacked MoTe 2 / W S e 2 Bilayers

Moiré materials provide fertile ground for the correlated and topological quantum phenomena. Among them, the quantum anomalous Hall (QAH) effect, in which the Hall resistance is quantized even under zero magnetic field, is a direct manifestation of the intrinsic topological properties of a material and an appealing attribute for low-power electronics applications. The QAH effect has been observed in both graphene and transition metal dichalcogenide (TMD) moiré materials. It is thought to arise from the interaction-driven valley polarization of the narrow moiré bands. Here, we show that the newly discovered QAH state in AB-stacked MoTe 2 / W S e 2 moiré bilayers is not valley polarized but valley coherent. The layer- and helicity-resolved optical spectroscopy measurement reveals that the QAH ground state possesses spontaneous spin (valley) polarization aligned (antialigned) in two TMD layers. In addition, saturation of the out-of-plane spin polarization in both layers occurs only under high magnetic fields, supporting a canted spin texture. Our results call for a new mechanism for the QAH effect and highlight the potential of TMD moiré materials with strong electronic correlations and spin-orbit interactions for exotic topological states. Published by the American Physical Society 2024

2-dimensional systems↗

DOE OSTI2020

Atomically precise digital e-beam lithography

Hydrogen Depassivation Lithography (HDL) is a version of electron beam lithography that uses scanning tunneling microscope (STM) instrumentation to expose a self–developing resist that is a monolayer of H chemisorbed to a Si (100) 2x1 H-passivated surface. Developed in the 1990s it has been largely a laboratory tool used in research for nanofabrication. Here, the technique is capable of atomic resolution, the ability to remove single H atoms from the Si surface and has much higher precision than the best conventional e-beam lithography can possibly achieve exposing polymeric resists. However, its most promising attribute is that it can be used as a digital fabrication tool and is the first of a class of nanofabrication techniques that can be considered digital atomic scale fabrication technologies. Digital Atomic Scale Fabrication can be shown to have similar advantages over analog fabrication techniques that digital information technology has over analog information technology.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Interactions between terminal ribosomal RNA helices stabilize the E. coli large ribosomal subunit

The ribosome is a large ribonucleoprotein assembly that uses diverse and complex molecular interactions to maintain proper folding. In vivo assembled ribosomes have been isolated using MS2 tags installed in either the 16S or 23S ribosomal RNAs (rRNAs), to enable studies of ribosome structure and function in vitro. RNA tags in the Escherichia coli 50S subunit have commonly been inserted into an extended helix H98 in 23S rRNA, as this addition does not affect cellular growth or in vitro ribosome activity. Here, we find that E. coli 50S subunits with MS2 tags inserted in H98 are destabilized compared to wild-type (WT) 50S subunits. We identify the loss of RNA–RNA tertiary contacts that bridge helices H1, H94, and H98 as the cause of destabilization. Using cryogenic electron microscopy (cryo-EM), we show that this interaction is disrupted by the addition of the MS2 tag and can be restored through the insertion of a single adenosine in the extended H98 helix. This work establishes ways to improve MS2 tags in the 50S subunit that maintain ribosome stability and investigates a complex RNA tertiary structure that may be important for stability in various bacterial ribosomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Structure of the E. coli agmatinase, SPEB

Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E . coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P 3 1 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/R free values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.

59 BASIC BIOLOGICAL SCIENCES↗