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DOE OSTI2024

Structural transformation of dusty plasma crystal in dc discharge plasma by changing confinement ring bias

We report an experimental study of the structural transition of a stable complex plasma crystal to a solid-liquid phase coexistence by the controlled adjustment of the confinement potential, while keeping all other parameters constant. The experiments are carried out on a tabletop linear dusty plasma experimental device, which consists of a circular powered electrode and an extended grounded cathode plate. A stationary crystal of melamine formaldehyde particles is formed in a background of argon plasma inside a confining ring that is isolated from the cathode by a ceramic cover. The stable crystal structure breaks in the core region and transitions to a coexistent state by carefully changing the confining potential, thereby modifying the sheath structure. The transition is confirmed by evaluating the variation in different characteristic parameters such as the pair correlation function, local bond order parameter, and dust kinetic temperature as a function of confining bias potential. It is found that melting in the core is due to the onset of dust fluctuations in the layers beneath the topmost layer, which grow in amplitude as the confining bias potential is reduced below a threshold value. The present technique of changing confinement provides a unique feature to study structural transitions of plasma crystals without affecting the overall plasma parameters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Structural transformation of dusty plasma crystal in dc discharge plasma by changing confinement ring bias

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists

As part of our effort to discover drugs that target HIV-1 entry, we report the antiviral activity and crystal structures of two novel inhibitors in a complex with a gp120 core. NBD-14204 showed similar antiviral activity against all the clinical isolates tested. The IC50 values were in the range of 0.24–0.9 µM with an overall mean of 0.47 ± 0.03 µM, showing slightly better activity against the clinical isolates than against the lab-adapted HIV-1 HXB2 (IC 50 = 0.96 ± 0.1 µM). Moreover, the antiviral activity of NBD-14208 was less consistent, showing a wider range of IC 50 values (0.66–5.7 µM) with an overall mean of 3 ± 0.25 µM and better activity against subtypes B and D (Mean IC 50 2.2–2.5 µM) than the A, C and Rec viruses (Mean IC 50 2.9–3.9 µM). SI of NBD-14204 was about 10-fold higher than NBD-14208, making it a better lead compound for further optimization. In addition, we tested these compounds against S375Y and S375H mutants of gp120, which occurred in some clades and observed these to be sensitive to NBD-14204 and NBD-14208. These inhibitors also showed modest activity against HIV-1 reverse transcriptase. Furthermore, we determined the crystal structures of both inhibitors in complexes with gp120 cores. As expected, both NBD-14204 and NBD-14208 bind primarily within the Phe43 cavity. It is noteworthy that the electron density of the thiazole ring in both structures was poorly defined due to the flexibility of this scaffold, suggesting that these compounds maintain substantial entropy, even when bound to the Phe43 cavity.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Observation of the Y(4230) and a new structure in ${\boldsymbol e^+\boldsymbol e^- \boldsymbol\rightarrow \boldsymbol K^+\boldsymbol K^-\boldsymbol J/\boldsymbol\psi}$

The cross sections of $e^+e^- \rightarrow K^+K^-J/\psi$ at center-of-mass energies from 4.127 to 4.600 GeV are measured based on 15.6 fb -1 data collected with the BESIII detector operating at the BEPCII storage ring. Two resonant structures are observed in the line shape of the cross sections. The mass and width of the first structure are measured to be ($4225.3\pm2.3\pm21.5$) MeV and ($72.9\pm6.1\pm30.8$) MeV, respectively. They are consistent with those of the established $Y(4230)$. The second structure is observed for the first time with a statistical significance greater than 8σ, denoted as $Y(4500)$. Its mass and width are determined to be ($4484.7\pm13.3\pm24.1$) MeV and ($111.1\pm30.1\pm15.2$) MeV, respectively. The first presented uncertainties are statistical and the second ones are systematic. The product of the electronic partial width with the decay branching fraction $\Gamma(Y(4230)\to e^+ e^-) \mathcal{B}(Y(4230) \to K^+ K^- J/\psi)$ is reported.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Structural tuning of nonlinear terahertz metamaterials using broadside coupled split ring resonators

We present an experimental and numerical study of a terahertz metamaterial with a nonlinear response that is controllable via the relative structural arrangement of two stacked split ring resonator arrays. The first array is fabricated on an n-doped GaAs substrate, and the second array is fabricated vertically above the first using a polyimide spacer layer. Due to GaAs carrier dynamics, the on-resonance terahertz transmission at 0.4 THz varies in a nonlinear manner with incident terahertz power. The second resonator layer dampens this nonlinear response. In samples where the two layers are aligned, the resonance disappears, and the total nonlinear modulation of the on-resonance transmission decreases. The nonlinear modulation is restored in samples where an alignment offset is imposed between the two resonator arrays. Structurally tunable metamaterials and metasurfaces can therefore act as a design template for tunable nonlinear THz devices by controlling the coupling of confined electric fields to nonlinear phenomena in a complex material substrate or inclusion.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Instabilities of a vortex-ring-bright soliton in trapped binary three-dimensional Bose-Einstein condensates

Instabilities of vortex-ring-bright coherent structures in harmonically trapped two-component three-dimensional Bose-Einstein condensates are studied numerically within the coupled Gross-Pitaevskii equations and interpreted analytically. Interestingly, the filled vortex core with a sufficiently large amount of the bright component is observed to reduce the parametric interval of stability of the vortex ring. Here, we have identified the mechanisms of several linear instabilities and one nonlinear parametric instability in this connection. Two of the linear instabilities are qualitatively different from ones reported earlier and are associated with azimuthal modes of m = 0 and m = 1, i.e., deviations of the vortex from the stationary ring shape. Our nonlinear parametric resonance instability occurs between the m = 0 and m = 2 modes and signals the exchange of energy between them.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

First Sagittarius A* Event Horizon Telescope Results. VII. Polarization of the Ring

Abstract The Event Horizon Telescope observed the horizon-scale synchrotron emission region around the Galactic center supermassive black hole, Sagittarius A* (Sgr A*), in 2017. These observations revealed a bright, thick ring morphology with a diameter of 51.8 ± 2.3 μas and modest azimuthal brightness asymmetry, consistent with the expected appearance of a black hole with mass M ≈ 4 × 106 M ⊙. From these observations, we present the first resolved linear and circular polarimetric images of Sgr A*. The linear polarization images demonstrate that the emission ring is highly polarized, exhibiting a prominent spiral electric vector polarization angle pattern with a peak fractional polarization of ∼40% in the western portion of the ring. The circular polarization images feature a modestly (∼5%–10%) polarized dipole structure along the emission ring, with negative circular polarization in the western region and positive circular polarization in the eastern region, although our methods exhibit stronger disagreement than for linear polarization. We analyze the data using multiple independent imaging and modeling methods, each of which is validated using a standardized suite of synthetic data sets. While the detailed spatial distribution of the linear polarization along the ring remains uncertain owing to the intrinsic variability of the source, the spiraling polarization structure is robust to methodological choices. The degree and orientation of the linear polarization provide stringent constraints for the black hole and its surrounding magnetic fields, which we discuss in an accompanying publication.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet–triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The persistent shadow of the supermassive black hole of M 87. I. Observations, calibration, imaging, and analysis

In April 2019, the Event Horizon Telescope (EHT) Collaboration reported the first-ever event-horizon-scale images of a black hole, resolving the central compact radio source in the giant elliptical galaxy M 87. These images reveal a ring with a southerly brightness distribution and a diameter of ∼42 μas, consistent with the predicted size and shape of a shadow produced by the gravitationally lensed emission around a supermassive black hole. These results were obtained as part of the April 2017 EHT observation campaign, using a global very long baseline interferometric radio array operating at a wavelength of 1.3 mm. Here, we present results based on the second EHT observing campaign, taking place in April 2018 with an improved array, wider frequency coverage, and increased bandwidth. In particular, the additional baselines provided by the Greenland telescope improved the coverage of the array. Multiyear EHT observations provide independent snapshots of the horizon-scale emission, allowing us to confirm the persistence, size, and shape of the black hole shadow, and constrain the intrinsic structural variability of the accretion flow. We have confirmed the presence of an asymmetric ring structure, brighter in the southwest, with a median diameter of 43.3−3.1+1.5 μas. The diameter of the 2018 ring is remarkably consistent with the diameter obtained from the previous 2017 observations. On the other hand, the position angle of the brightness asymmetry in 2018 is shifted by about 30° relative to 2017. The perennial persistence of the ring and its diameter robustly support the interpretation that the ring is formed by lensed emission surrounding a Kerr black hole with a mass ∼6.5 × 109 M⊙. The significant change in the ring brightness asymmetry implies a spin axis that is more consistent with the position angle of the large-scale jet.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Tuning the Mechanical and Electric Properties of Conjugated Polymer Semiconductors: Side–Chain Design Based on Asymmetric Benzodithiophene Building Blocks

Understanding molecular design rules for stretchable polymer semiconductors is important for enabling next generation stretchable electronic circuits. To simultaneously improve both electrical properties and mechanical stretchability, a design strategy is reported in introducing conjugated rigid fused-rings with bulky side groups in semiconducting polymers. In this work, the understanding of this design concept is improved by systematically investigating the effect of different types of bulky side groups asymmetrically substituted on conjugated polymer semiconductor backbones. Specifically, four types of side groups are investigated, including naphthalene (NaPh), biphenyl (PhPh), thienylphenyl (ThPh), and alkylphenyl (C4Ph), asymmetrically substituted on benzodithiophene units, namely asy-BDT. With the four types of side groups installed on BDT-containing conjugated polymers in an asymmetrical fashion, it is observed that they reduced the polymer chain aggregation and film crystallinity, hence improving the film stretchability. Furthermore, the fully conjugated polymer back-bone allows maintenance of good charge carrier mobilities. Specifically, polymer PDPP-C4Ph (with C4Ph side groups) shows the highest mobility in the fully stretchable transistor and maintained its mobility even after being subjected to hundreds of stretching-releasing cycles at 25% strain. Altogether, the results provide anunderstanding of the use of asymmetrically substituted fused-ring conjugated polymer structures to tune mechanical and charge transport properties.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs

To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assay. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved longrange pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg 2+ - dependent, furthermore, the Mg 2+ -dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg 2+ to stabilize its folding, exhibits reduced conformational dynamics and strong Xrn1 resistance even at low Mg 2+ , and tolerates mutations at key tertiary motifs at high Mg 2+ , which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The Optical Corrector for the Dark Energy Spectroscopic Instrument

The Dark Energy Spectroscopic Instrument (DESI) is currently measuring the spectra of 40 million galaxies and quasars, the largest such survey ever made to probe the nature of cosmological dark energy. The 4 m Mayall telescope at Kitt Peak National Observatory has been adapted for DESI, including the construction of a 3$_{.}^{°}$2 diameter prime focus corrector that focuses astronomical light onto a 0.8 m diameter focal surface with excellent image quality over the DESI bandpass of 360–980 nm. The wide-field corrector includes six lenses, as large as 1.1 m in diameter and as heavy as 237 kilograms, including two counterrotating wedged lenses that correct for atmospheric dispersion over zenith angles from 0° to 60°. The lenses, cells, and barrel assembly all meet precise alignment tolerances on the order of tens of microns. The barrel alignment is maintained throughout a range of observing angles and temperature excursions in the Mayall dome by use of a hexapod, which is itself supported by a new cage, ring, and truss structure. In this paper we describe the design, fabrication, and performance of the new corrector and associated structure, focusing on how they meet DESI requirements. In particular, we describe the prescription and specifications of the lenses, design choices and error budgeting of the barrel assembly, stray light mitigations, and integration and test at the Mayall telescope. We conclude with some validation highlights that demonstrate the successful corrector on-sky performance, and we list some lessons learned during the multiyear fabrication phase.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restrains for non-protein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in Chlorophyll (Chl) proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C 2 symmetry of Photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and Cryogenic electron microscopy (CryoEM) PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restrains play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested, from cyanobacteria to algae. Furthermore, these results highlight both the opportunities and limitations inherent in the structure-based analysis of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

14 SOLAR ENERGY↗

DOE OSTI2022

How arsenic makes amorphous GeSe a robust chalcogenide glass for advanced memory integration

The 3D integration technology in semiconductor fabrication requires a key component, the ovonic threshold switching (OTS) selector, to suppress the current leakage. The As doped amorphous (a-) GeSe glass is a commercialized OTS material in 3D phase-change memory, but the understanding of such a doping mechanism is still inadequate. Here we systematically explore the effect of As doping on the structural, bonding, and dynamics properties of a-GeAsSe using ab initio molecular dynamics simulations. The results reveal that As atoms form strong bonds with both Ge and Se atoms. The distorted octahedral structures and the 5-fold rings linked by atoms are increased. All of these structural features lead to a more disordered configuration. Moreover, as atoms have notably slowed down the atomic mobility, rendering a-GeAsSe a high stability. Overall, our studies offer insightful understanding of As-doping in OTS materials, paving the way for the design and application of advanced selector devices.

36 MATERIALS SCIENCE↗

DOE OSTI2025

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif—a protective ring encircling the RNA’s 5′ end—despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

Biochemistry & Molecular Biology↗

DOE OSTI2020

Structures of fluoride containing aluminosilicate low activity nuclear waste glasses: A molecular dynamics simulations study

Fluorine and other halides commonly exist in nuclear waste forms, and due to their volatile nature, halide retention poses an issue affecting waste loading during vitrification. The compositional effect on fluorine incorporation in aluminosilicate glasses is investigated through molecular dynamics simulations. Oxygen and fluorine coordination numbers around glass former and modifier cations, bond angle distributions, and medium range structure features such as Q n distributions, ring size distributions and neutron diffraction structure factors were calculated. It was found that fluorine has higher preference to bond to Ca 2+ than to Na + , both in the melt and the glass, and there is no Si-F bond formation in the glass but they do exist in the melt. Consequently, CaO for Na 2 O substitution can be an effective way to help fluorine retention without significantly changing the glass chemistry. Furthermore, these results thus provide insights on fluorine incorporation in the aluminosilicate nuclear waste glasses and the strategy on how to improve fluorine retention both in the glass and the melt.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Capturing the generation and structural transformations of molecular ions

Molecular ions are ubiquitous and play pivotal roles in many reactions, particularly in the context of atmospheric and interstellar chemistry. However, their structures and conformational transitions, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that mega-electronvolt ultrafast electron diffraction (MeV-UED), used in conjunction with resonance-enhanced multiphoton ionization, can monitor the formation of 1,3-dibromopropane (DBP) cations and their subsequent structural dynamics forming a halonium ion. We find that the DBP + cation remains for a substantial duration of 3.6 ps in aptly named ‘dark states’ that are structurally indistinguishable from the DBP electronic ground state. The structural data, supported by surface-hopping simulations and ab initio calculations, reveal that the cation subsequently decays to iso-DBP + , an unusual intermediate with a four-membered ring containing a loosely bound bromine atom, and eventually loses the bromine atom and forms a bromonium ion with a three-membered-ring structure. We anticipate that the approach used here can also be applied to examine the structural dynamics of other molecular ions and thereby deepen our understanding of ion chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗