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DOE OSTI2024

Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes

It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin’s role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

V‐Groove Si Nanopatterning for the Direct Epitaxy of Orientation‐Patterned III–V Nonlinear Optical Crystals

Orientation‐patterned (OP) III–V semiconductors—used as quasi‐phase‐matched crystals for nonlinear optics applications—are typically epitaxially grown on expensive III–V substrates using a complex process requiring three separate epitaxy steps. In this work, a method is demonstrated for growing orientation‐patterned III–V crystals on Si substrates through V‐groove nanopatterning and a single epitaxial growth. V‐groove Si allows for suppression of random antiphase domain formation that is typical of III–V growth on (001)‐oriented Si through the use of (111)‐faceted trenches patterned on (001)‐oriented Si substrates. By alternating the directions of the V‐groove trenches between [110] and [10], antiphase boundaries can be selectively induced at the boundaries between the two directions of trenches due to the difference in symmetry between the III–V material and Si. This approach allows for a greatly simplified process for growing OP‐III‐Vs and more broadly is a new, robust approach for precisely patterning antiphase boundaries of arbitrary shape and length scales down to 50 nm.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Atomic masses with machine learning for the astrophysical r process

The astrophysical r process plays a vital role in the production of heavy elements. Modeling of the r process is sensitive to masses and further requires knowledge of masses beyond current experimental reach. Therefore, simulations of the r process offer a unique test bed for predicting mass extrapolations. We take a Machine-Learning (ML) approach to model the masses across the entire chart of nuclides. For the first time, we simulate r-process nucleosynthesis with a physics-based ML mass model. We compare simulated abundances to solar data in order to evaluate the model's performance far from stability. The resulting r-process abundances up to thorium and uranium qualitatively match those of the observed solar system abundance pattern, with the characteristic peaks well positioned. We propagate the mass uncertainties obtained from the ML model to r-process abundance yields to estimate an uncertainty band associated with our approach. The size of the uncertainty band is approximately one order of magnitude which aligns with the uncertainty reported using alternative techniques.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Confident detection of doubly ionized thorium in the extreme Ap star CPD-62° 2717

Despite the Universe containing primordial thorium (Th) of sufficient abundance to appear in stellar spectra, detection of Th has to date been tentative and based on just a few weak and blended lines. Here, we present convincing evidence not only for the first Th detection in a magnetic chemically peculiar Ap star but also for the first detection of Th iii in a stellar spectrum. CPD-62° 2717 was initially recognized as a highly magnetized Ap star due to resolved magnetically split lines captured in H-band spectra from the SDSS/APOGEE survey. The star was subsequently pinpointed as extraordinarily peculiar when careful inspection of the H-band line content revealed the presence of five lines of Th iii, none of which are detected in the other ∼1500 APOGEE-observed Ap stars. Follow-up with the VLT + UVES confirmed a similarly peculiar optical spectrum featuring dozens of Th iii lines, among other peculiarities. Unlike past claims of Th detection, and owing to high-resolution observations of the strong (∼8–12 kG) magnetic field of CPD-62° 2717, the detection of Th iii can in this case be supported by matches between the observed and theoretical magnetic splitting patterns. Comparison of CPD-62° 2717 to stars for which Th overabundances have been previously reported (e.g. Przybylski’s Star) indicates that only for CPD-62° 2717 is the Th detection certain. Along with the focus on Th iii, we use time series measurements of the magnetic field modulus to constrain the rotation period of CPD-62° 2717 to ∼4.8 yr, thus establishing it as a new example of a superslowly rotating Ap star.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Macroscopic Nonuniformities in Metal Grids Formed by Cracked Film Lithography Result in 19.3% Efficient Solar Cells

Cracked film lithography (CFL) is an emerging method for patterning transparent conductive metal grids. CFL can be vacuum- and Ag-free, and it forms more durable grids than nanowire approaches. In spite of CFL’s promising transmittance/grid sheet resistance/wire spacing tradeoffs, previous solar cell demonstrations have had relatively low performance. This work introduced macroscopic nonuniformities in the grids to improve the short-circuit current density/fill factor tradeoff in small area Cu(In,Ga)Se2 cells. Furthermore, the performance of optimized baseline grids was matched by CFL grids with microscopic openings and macroscopic patterns, culminating in a 19.3%-efficient cell. Simulations show that uniform CFL grids are enhanced by patterning because it leads to better balance among shadowing, grid resistance and transparent conductive oxide resistance losses. Thin-film module efficiency calculations were performed to highlight the performance gains that metal grids can enable by eliminating the transparent conductive oxide losses and widening monoliths. Adding the patterned CFL grids demonstrated in this work to CIGS modules is predicted to reach 0.7% higher efficiency (absolute) than screen-printed grids.

14 SOLAR ENERGY↗

DOE OSTI2021

Strain-Induced Lateral Heterostructures in Patterned Semiconductor Nanomembranes for Micro- and Optoelectronics

The ability to tailor the energy band lineup of semiconductor materials plays a key role in the development of many electronic and optoelectronic devices and normally relies on heteroepitaxy. In this work, we report a different method, based on strain engineering, for the controlled introduction of variations in bandgap energy with lateral position in thin films. External stress is applied on Ge nanomembranes stacked with an array of amorphous-Si pillars in order to create a non-uniform strain (and therefore bandgap energy) distribution commensurate with the sample thickness variations. The resulting strain profiles are mapped using Bragg diffraction with a hard X-ray probe featuring nanoscale spatial resolution. Compared with traditional heterostructures grown by epitaxial techniques, these strain-engineered samples involve a single chemical composition and are not limited in the choice of compatible materials by any restriction imposed by lattice-matching requirements. Furthermore, their energy band lineups can be patterned in nearly arbitrary shapes using nanolithography to control the thickness profile and can be tuned actively by varying the applied stress. As a result, these structures are attractive for a wide range of device applications (including lasers, LEDs, solar cells, and thermoelectrics) that require complex heterostructure lineups with multiple bandgap energies.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Collection of fluorescence from an ion using trap-integrated photonics

Spontaneously emitted photons are entangled with the electronic and nuclear degrees of freedom of the emitting atom, so interference and measurement of these photons can entangle separate matter-based quantum systems as a resource for quantum information processing. Since confinement in a single-mode facilitates the photon interference needed for generating entanglement, the dipole emission patterns relevant in spontaneous emission present a mode-matching challenge. Current demonstrations rely on bulk photon-collection and manipulation optics that suffer from large component size and system-to-system variability—factors that impede scaling to the large numbers of entangled pairs needed for quantum information processing. To address these limitations, we demonstrate a collection method that enables passive phase stability, straightforward photonic manipulation, and intrinsic reproducibility. Specifically, we engineer a waveguide-integrated grating to couple photons emitted from a trapped ion into a single optical mode within a microfabricated ion-trap chip. Using the integrated collection optic, we characterize the collection efficiency, image the ion, and detect the ion’s quantum state. The integrated optic covers 2.18% of the solid angle and collects 1.97 ± 0.3% of the spontaneously emitted light incident on the grating for a total collection efficiency of 0.043% into a single-mode waveguide. This proof-of-principle demonstration lays the foundation for leveraging the inherent stability and reproducibility of integrated photonics to create, manipulate, and measure multipartite quantum states in arrays of quantum emitters.

Optical physics↗

DOE OSTI2022

Reshaped Weyl fermionic dispersions driven by Coulomb interactions in MoTe 2

In this work, we report the direct evidence of impacts of the Coulomb interaction in a prototypical Weyl semimetal, MoTe 2 , that alter its bare bands in a wide range of energy and momentum. Our quasiparticle interference patterns measured using scanning tunneling microscopy are shown to match the joint density of states of quasiparticle energy bands including momentum-dependent self-energy corrections, while electronic energy bands based on the other simpler local approximations of the Coulomb interaction fail to explain neither the correct number of quasiparticle pockets nor the shape of their dispersions observed in our spectrum. With this, we predict a transition between type-I and type-II Weyl fermions with doping and resolve its disparate quantum oscillation experiments, thus highlighting the critical roles of Coulomb interactions in layered Weyl semimetals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

On-chip spectroscopic sensors with optical fringe suppression

An on-chip spectroscopic sensor includes a tunable diode laser. A laser driver for drives the tunable diode laser. An analyte test cavity receives a chemical sample and exposes the received chemical sample to light from the tunable diode laser. An optical detector detects light emerging from the analyte test cavity as a result of the laser exposure. A spectral analyzer determines a spectrum of the emerging light, matches and removes one or more known optical fringe patterns from the determined spectrum, and determines a composition or concentration of the chemical sample from the optical fringe pattern-removed spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

On-chip spectroscopic sensors with optical fringe suppression

Green, William↗

DOE OSTI2023

A reference-area-free strain mapping method using precession electron diffraction data

Here, in this work, we developed a method using precession electron diffraction data to map the residual elastic strain at the nano-scale. The diffraction pattern of each pixel was first collected and denoised. Template matching was then applied using the center spot as the mask to identify the positions of the diffraction disks. Statistics of distances between the selected diffracted disks enable the user to make an informed decision on the reference and to generate strain maps. Strain mapping on an unstrained single crystal sapphire shows the standard deviation of strain measurement is 0.5%. With this method, we were able to successfully measure and map the residual elastic strain in VO 2 on sapphire and martensite in a Ni 50.3 Ti 29.7 Hf 20 shape memory alloy. This approach does not require the user to select a “strain-free area” as a reference and can work on datasets even with the crystals oriented away from zone axes. This method is expected to provide a robust and more accessible alternative means of studying the residual strain of various material systems that complements the existing algorithms for strain mapping.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

CICE on a C-grid: new momentum, stress, and transport schemes for CICEv6.5

Abstract. This article presents the C-grid implementation of the CICE sea ice model, including the C-grid discretization of the momentum equation, the boundary conditions (BCs), and the modifications to the code required to use the incremental remapping transport scheme. To validate the new C-grid implementation, many numerical experiments were conducted and compared to the B-grid solutions. In idealized experiments, the standard advection method (incremental remapping with C-grid velocities interpolated to the cell corners) leads to a checkerboard pattern. A modal analysis demonstrates that this computational noise originates from the spatial averaging of C-grid velocities at corners. The checkerboard pattern can be eliminated by adjusting the departure regions to match the divergence obtained from the solution of the momentum equation. We refer to this novel approach as the edge flux adjustment (EFA) method. The C-grid discretization with edge flux adjustment allows for transport in channels that are one grid cell wide – a capability that is not possible with the B-grid discretization nor with the C-grid and standard remapping advection. Simulation results match the predicted values of a novel analytical solution for one-grid-cell-wide channels.

Lemieux, Jean-François (ORCID:0000000320845759)↗

DOE OSTI2021

Validation of the Sentinel-5 Precursor TROPOMI cloud data with Cloudnet, Aura OMI O 2 –O 2 , MODIS, and Suomi-NPP VIIRS

Accurate knowledge of cloud properties is essential to the measurement of atmospheric composition from space. In this work we assess the quality of the cloud data from three Copernicus Sentinel-5 Precursor (S5P) TROPOMI cloud products: (i) S5P OCRA/ROCINN_CAL (Optical Cloud Recognition Algorithm/Retrieval of Cloud Information using Neural Networks;Clouds-As-Layers), (ii) S5P OCRA/ROCINN_CRB (Clouds-as-Reflecting Boundaries), and (iii) S5P FRESCO-S (Fast Retrieval Scheme for Clouds from Oxygen absorption bands – Sentinel). Target properties of this work are cloud-top height and cloud optical thickness (OCRA/ROCINN_CAL), cloud height (OCRA/ROCINN_CRB and FRESCO-S), and radiometric cloud fraction (all three algorithms). The analysis combines (i) the examination of cloud maps for artificial geographical patterns, (ii) the comparison to other satellite cloud data (MODIS, NPP-VIIRS, and OMI O2–O2), and (iii) ground-based validation with respect to correlative observations (30 April 2018 to 27 February 2020) from the Cloudnet network of ceilometers, lidars, and radars. Zonal mean latitudinal variation of S5P cloud properties is similar to that of other satellite data. S5P OCRA/ROCINN_CAL agrees well with NPP VIIRS cloud-top height and cloud optical thickness and with Cloudnet cloud-top height, especially for the low (mostly liquid) clouds. For the high clouds, S5P OCRA/ROCINN_CAL cloud-top height is below the cloud-top height of VIIRS and of Cloudnet, while its cloud optical thickness is higher than that of VIIRS. S5P OCRA/ROCINN_CRB and S5P FRESCO cloud height are well below the Cloudnet cloud mean height for the low clouds but match on average better with the Cloudnet cloud mean height for the higher clouds. As opposed to S5P OCRA/ROCINN_CRB and S5P FRESCO, S5P OCRA/ROCINN_CAL is well able to match the lowest CTH mode of the Cloudnet observations. Peculiar geographical patterns are identified in the cloud products and will be mitigated in future releases of the cloud data products.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

PIP-II 800 MeV Proton Linac Beam Pattern Generator

The PIP2 IT Beam Pattern Generator is the system that synchronizes beam injection and the RF systems between the PIP2 LINAC to the Booster. The RF frequencies of these two accelerator systems are not harmonically related. Synchronization is accomplished by controlling two MEBT Beam Choppers, which select 162.5MHz beam bunches from the LEBT and RFQ to produce an appropriate reduced beam bunch pattern that enables bucket-to-bucket transfer to the Booster RF at 46.46MHz (84th harmonic). This chopping pattern also reduces the beam current to an average of 2mA over the Booster injection, matching the Linac nominal beam current. The BPG also generates the RF frequency/phase reference which the Booster will phase lock to during injection. The BPG is fully programmable, allowing for arbitrary beam patterns with adjustable timing parameters, having a fine adjustment resolution of 38ps. The latter is accomplished using digital signal processing techniques. This paper discusses the design of the BPG, its construction, test results, and operational experience after being integrated into the PIP2 IT test accelerator and concludes with a discussion of the system’s performance and future plans.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching

An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.

3D imaging↗

DOE OSTI2024

Dual-Image Color Normalization to Enable High-Performance Concentrating Solar Optical Metrology

Concentrating Solar Power (CSP) requires precision mirrors, and these in turn require metrology systems to measure their optical slope. In this project we studied a color-based approach to the correspondence problem, which is the association of points on an optical target with their corresponding points seen in a reflection. This is a core problem in deflectometry-based metrology, and a color solution would enable important new capabilities. We modeled color as a vector in the [R,G,B] space measured by a digital camera, and explored a dual-image approach to compensate for inevitable changes in illumination color. Through a series of experiments including color target design and dual-image setups both indoors and outdoors, we collected reference/measurement image pairs for a variety of configurations and light conditions. We then analyzed the resulting image pairs by selecting example [R,G,B] pixels in the reference image, and seeking matching [R,G,B] pixels in the measurement image. Modulating a tolerance threshold enabled us to assess both match reliability and match ambiguity, and for some configurations, orthorectification enabled us to assess match accuracy. Using direct-direct imaging, we demonstrated color correspondence achieving average match accuracy values of 0.004 h, where h is the height of the color pattern. We found that wide-area two-dimensional and linear one-dimensional color targets outperformed hybrid linear/lateral gradient targets in the cases studied. Introducing a mirror degraded performance under our current techniques, and we did not have time to evaluate whether matches could be reliably achieved despite varying light conditions. Nonetheless, our results thus far are promising.

14 SOLAR ENERGY↗

DOE OSTI2021

Dynamic electron correlations with charge order wavelength along all directions in the copper oxide plane

In strongly correlated systems the strength of Coulomb interactions between electrons, relative to their kinetic energy, plays a central role in determining their emergent quantum mechanical phases. We perform resonant x-ray scattering on Bi 2 Sr 2 CaCu 2 O 8+δ , a prototypical cuprate superconductor, to probe electronic correlations within the CuO 2 plane. We discover a dynamic quasi-circular pattern in the x-y scattering plane with a radius that matches the wave vector magnitude of the well-known static charge order. Along with doping- and temperature-dependent measurements, our experiments reveal a picture of charge order competing with superconductivity where short-range domains along x and y can dynamically rotate into any other in-plane direction. This quasi-circular spectrum, a hallmark of Brazovskii-type fluctuations, has immediate consequences to our understanding of rotational and translational symmetry breaking in the cuprates. We discuss how the combination of short- and long-range Coulomb interactions results in an effective non-monotonic potential that may determine the quasi-circular pattern.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

The influence of permeability anisotropy in the upper ocean crust on advective heat transport by a ridge-flank hydrothermal system

Here, in this study, we highlight the importance of permeability anisotropy on the hydrogeological regime of a ridge-flank hydrothermal system. Our study site, North Pond, is a marine sediment pond on ~8 Ma seafloor in the North Atlantic, and represents a low-temperature, end-member ridge-flank hydrothermal system. Previous simulations of North Pond elucidated long-standing hypotheses concerning hydrothermal fluid and heat transport in the upper volcanic crust but failed to fully explain observed patterns of seafloor heat flux in this area. Here we use variography, a geostatistical method, to quantify relations between seafloor heat-flux measurements, and coupled numerical simulations of fluid and heat flow to simulate the hydrogeologic regime. Directional variography shows that heat-flux observations are correlated along-strike of the regional crustal fabric. Three-dimensional simulations that include permeability anisotropy are able to replicate seafloor heat-flux patterns across North Pond. The simulations that result in the best match to thermal data incorporate permeability anisotropy in the horizontal plane. We find that the feedback between permeability anisotropy and the asymmetric geometry of North Pond combine to promote advective removal of heat and mass within the crustal aquifer. These findings suggest that permeability anisotropy in the oceanic crust may influence ridge-flank hydrothermal circulation more broadly.

58 GEOSCIENCES↗