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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection

Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed “discontinuous transcription” that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex

From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the ’electron transfer’ (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes trans- formation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Level density within a micro-macroscopic approach

Statistical level density $ρ$($E, A$) is derived for nucleonic system with a given energy $E$, particle number $A$ and other integrals of motion in the micro-macroscopic approximation beyond the standard saddle-point method of the Fermi gas model. This level density reaches the two limits; the well-known Fermi gas grand-canonical ensemble limit for a large entropy $S$ related to large excitation energies, and the finite micro-canonical limit for a small combinatorical entropy $S$ at low excitation energies. In conclusion, the inverse level density parameter $K$ as function of the particle number $A$ in the semiclassical periodic orbit theory, taking into account the extended Thomas-Fermi and Strutinsky shell corrections, is calculated and compared with experimental data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Collision-energy dependence of deuteron cumulants and proton-deuteron correlations in Au+Au collisions at RHIC

We report the first measurements of cumulants, up to 4th order, of deuteron number distributions and proton-deuteron correlations in Au+Au collisions recorded by the STAR experiment in phase-I of Beam Energy Scan (BES) program at the Relativistic Heavy Ion Collider. Deuteron cumulants, their ratios, and proton-deuteron mixed cumulants are presented for different collision centralities covering a range of center-of-mass energy per nucleon pair $\sqrt{s_{NN}} = 7.7$ to 200 GeV. It is found that the cumulant ratios at lower collision energies favor a canonical ensemble over a grand canonical ensemble in thermal models. An anti-correlation between proton and deuteron multiplicity is observed across all collision energies and centralities, consistent with the expectation from global baryon number conservation. The UrQMD model coupled with a phase-space coalescence mechanism qualitatively reproduces the collision-energy dependence of cumulant ratios and proton-deuteron correlations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Single-cell RNA-seq revealed diverse cell types in the mouse placenta at mid-gestation

The mammalian placenta consists of a set of cells to ensure normal placental functions throughout gestation. Dysfunctional placentae are considered as the origin of a series of pregnancy complications. Therefore, it is urgent for detailed information about the molecular recipes of the cell types within the normal placenta. In the past years, gene expression analysis via single-cell RNA-seq (scRNA-seq) offers opportunities to identify new cell types in a variety of organs and tissues. In this study, scRNA-seq was used to explore the cell heterogeneity within the E10.5 mouse placenta and unravel their discrepancies in cell composition and communications. We identified sixteen cell clusters, including some cell clusters that originated from the maternal tissue. Moreover, we traced the developmental trajectories of trophoblasts and Hofbauer-like cells. Further analysis revealed cell connections between the endothelial cells and pericytes, syncytiotrophoblasts, as well as decidual cells. Besides, we highlighted several signaling pathways, such as the EGF, FGF, canonical, and non-canonical WNT signaling pathways, which mediated the potential crosstalk between different cell types within placenta. Our research provides an in-depth understanding of placental development, cellular composition, and communications at the maternal-fetal interface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Simulation and flow physics of a shocked and reshocked high-energy-density mixing layer

This work describes a computational investigation of multimode instability growth and multimaterial mixing induced by multiple shock waves in a high-energy-density (HED) environment, where pressures exceed 1 Mbar. The simulations are based on a series of experiments performed at the National Ignition Facility (NIF) and designed as an HED analogue of non-HED shock-tube studies of the Richtmyer–Meshkov instability and turbulent mixing. A three-dimensional computational modelling framework is presented. It treats many complications absent from canonical non-HED shock-tube flows, including distinct ion and free-electron internal energies, non-ideal equations of state, radiation transport and plasma-state mass diffusivities, viscosities and thermal conductivities. The simulations are tuned to the available NIF data, and traditional statistical quantities of turbulence are analysed. Integrated measures of turbulent kinetic energy and enstrophy both increase by over an order of magnitude due to reshock. Large contributions to enstrophy production during reshock are seen from both the baroclinic source and enstrophy–dilatation terms, highlighting the significance of fluid compressibility in the HED regime. Dimensional analysis reveals that Reynolds numbers and diffusive Péclet numbers in the HED flow are similar to those in a canonical non-HED analogue, but conductive Péclet numbers are much smaller in the HED flow due to efficient thermal conduction by free electrons. It is shown that the mechanism of electron thermal conduction significantly softens local spanwise gradients of both temperature and density, which causes a minor but non-negligible decrease in enstrophy production and small-scale mixing relative to a flow without this mechanism.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression

Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.

Coomey, Joshua↗
DOE OSTI2022

Improved accuracy in degenerate variational integrators for guiding centre and magnetic field line flow

First-order-accurate degenerate variational integration (DVI) was introduced in Ellison et al. ( Phys. Plasmas , vol. 25, 2018, 052502) for systems with a degenerate Lagrangian, i.e. one in which the velocity-space Hessian is singular. In this paper we introduce second-order-accurate DVI schemes, both with and without non-uniform time stepping. We show that it is not in general possible to construct a second-order scheme with a preserved two-form by composing a first-order scheme with its adjoint, and discuss the conditions under which such a composition is possible. We build two classes of second-order-accurate DVI schemes. We test these second-order schemes numerically on two systems having non-canonical variables, namely the magnetic field line and guiding centre systems. Variational integration for Hamiltonian systems with non-uniform time steps, in terms of an extended phase space Hamiltonian, is generalized to non-canonical variables. It is shown that preservation of proper degeneracy leads to single-step (one-step) methods without parasitic modes, i.e. to non-uniform time step DVIs. This extension applies to second-order-accurate as well as first-order schemes, and can be applied to adapt the time stepping to an error estimate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Phase transition to blob-hole coherent structure in the Hasegawa–Mima model for plasmas

An equilibrium statistical mechanics theory for the Hasegawa–Mima equations of toroidal plasmas, with canonical constraint on energy and microcanonical constraint on potential enstrophy, is solved exactly as a spherical model. The use of a canonical energy constraint instead of a fixed-energy microcanonical approach is justified by the preference for viewing real plasmas as an open system. A significant consequence of the results obtained from the partition function, free energy and critical temperature, is the condensation into a ground state exhibiting a blob-hole-like structure observed in real plasmas.

Physics↗
DOE OSTI2022

A gauge-compatible Hamiltonian splitting algorithm for particle-in-cell simulations using finite element exterior calculus

A particle-in-cell algorithm is derived with a canonical Poisson structure in the formalism of finite element exterior calculus. The resulting method belongs to the class of gauge-compatible splitting algorithms, which exactly preserve gauge symmetries and their associated conservation laws via the momentum map. We numerically demonstrate this time invariance of the momentum map and its usefulness in establishing precise initial conditions with a desired initial electric field and fixed background charge. The restriction of this canonical, finite element Poisson structure to the 1X2P $1\frac {1}{2}$ -dimensional phase space is also considered and simulated numerically.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Geometrical optics without singularities: using the ray time as the coordinate space

Geometrical optics (GO) is widely used for reduced modelling of waves in plasmas, but it fails near reflection points, where it predicts a spurious singularity of the wave amplitude. We show how to avoid this singularity by adopting a different representation of the wave equation. Instead of the physical coordinate 𝑥 and the wavevector 𝑘, we use the ray time 𝜏 as the new canonical coordinate and the ray energy ℎ as the associated canonical momentum. To derive the envelope equation in the 𝜏-representation, we construct the Weyl symbol calculus on the (𝜏,ℎ) space and show that the corresponding Weyl symbols are related to their (𝑥,𝑘) counterparts by the Airy transform. This allows us to express the coefficients in the envelope equation through the known properties of the original dispersion operator. When necessary, solutions of this equation can be mapped to the 𝑥-space using a generalised metaplectic transform. However, the field per se might not even be needed in practice. Instead, knowing the corresponding Wigner function usually suffices for linear and quasilinear calculations. As a Weyl symbol itself, the Wigner function can be mapped analytically, using the aforementioned Airy transform. We show that the standard Airy patterns that form in regions where conventional GO fails are successfully reproduced within metaplectic GO (MGO) simply by remapping the field from the 𝜏-space to the 𝑥-space. An extension to mode-converting waves is also presented. This formulation, which we call generalised MGO, can be particularly useful, for example, for reduced modelling of the O–X conversion in inhomogeneous plasma near the critical density, an effect that is important for fusion applications and also occurs in the ionosphere. Overall, MGO can replace GO for any practical purposes, because it better handles cutoffs and is similar otherwise.

plasma waves↗
DOE OSTI2024

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Density Matrix Implementation of the Fermi–Löwdin Orbital Self-Interaction Correction Method

The Fermi–Löwdin orbital self-interaction correction (FLOSIC) method effectively provides a transformation from canonical orbitals to localized Fermi–Löwdin orbitals which are used to remove the self-interaction error in the Perdew–Zunger (PZ) framework. This transformation is solely determined by a set of points in space, called Fermi–Löwdin descriptors (FODs), and the occupied canonical orbitals or the density matrix. In this work, we provide a detailed workflow for the implementation of the FLOSIC method for removal of self-interaction error in DFT calculations in an orbital-by-orbital basis that takes advantage of the unitary invariant nature of the FLOSIC method. In this way, it is possible to cast the self-consistent energy minimization at fixed FODs in the same manner than standard Kohn–Sham with one additional term in the Kohn–Sham Hamiltonian that introduces the PZ self-interaction correction. Each energy minimization iteration is divided in two substeps, one for the density matrix and one for the FODs. Expressions for the effective Kohn–Sham matrix and FOD gradients are provided such that its implementation is suitable for most electronic structure codes. Here, we analyze the convergence characteristics of the algorithm and present applications for the evaluation of NMR shielding constants and real-time time-dependent DFT simulations based on the Liouville–von Neumann equation to calculate excitation energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Hydride Accessibility and Reactivity in the Configurational and Stoichiometric Space of β-Ga 2 O 3 for CO 2 Hydrogenation

Understanding how surface species evolve under reaction conditions is essential for improving catalyst design for efficient CO 2 hydrogenation. This work combines systematic DFT calculations with grand canonical sampling to investigate the stability and reactivity of Ga–H species on β-Ga 2 O 3 across a range of reaction conditions. Initial DFT studies reveal that when Ga–H species are present, they facilitate formate formation via a low-barrier pathway, largely independent of the surface termination or hydrogen site. However, grand canonical sampling shows that under a broad range of reaction conditions─especially at high oxygen chemical potentials associated with high water content─Ga–H species are thermodynamically inaccessible. Furthermore, adsorbed water molecules can block reactive sites, inhibiting CO 2 activation even when hydrides are present. These findings suggest that the lack of accessible hydride species, rather than their intrinsic reactivity, could contribute to reduced catalytic performance of β-Ga 2 O 3 under more oxidizing, high-conversion conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

CO (2) Electroreduction on Borated Copper Surfaces: Boron Active Sites, Not Copper

Boron-doped copper has recently emerged as an active and stable catalyst for the electrochemical reduction of CO 2 to value-added C 2 products. Here, in this work, we develop a realistic model of CO electroreduction on surface borides of copper under operational conditions, taking into account the effects of electrode potential, electrolyte environment, and pH. We study the possible reconstruction of the electrocatalyst surface using grand canonical DFT and global optimization to obtain a potential-dependent grand canonical ensemble description of metastable, hydrogen-covered catalyst surfaces. Two key surface configurations, low H coverage (LC, −0.6 V SHE ) and high H coverage (HC, −0.8 V SHE ), dominate this ensemble, with the former being kinetically persistent and C 2 selective under strongly reducing conditions. Nonmetallic boron sites on the surface copper boride are found to bind CO more strongly than copper sites, and mechanistic investigation of CO electroreduction pathways presents a surprisingly unconventional case of boron-centered reactivity in contrast to typical copper-centered reactivity. Neighboring boron sites present along boron chains on the surface copper boride are found to facilitate C−C coupling, thereby driving the high C 2 selectivity of this electrocatalyst.

boron-doped copper↗
DOE OSTI2022

Modification at the C2'-O-Position with 2-Methylbenzothiophene Induces Unique Structural Changes and Thermal Transitions on Duplexes of RNA and DNA

Oligonucleotides can be chemically modified for a variety of applications that include their use as biomaterials, in therapeutics, or as tools to understand biochemical processes, among others. This work focuses on the functionalization of oligonucleotides of RNA and DNA (12- or 14-nucleotides long) with methylbenzothiophene (BT), at the C2'-O-position, which led to unique structural features. Circular dichroism (CD) analyses showed that positioning the BT units on one strand led to significant thermal destabilization, while duplexes where each strand contained 4-BT rings formed a distinct arrangement with cooperativity/interactions among the modifications (evidenced from the appearance of a band with positive ellipticity at 235 nm). Interestingly, the structural arrays displayed increased duplex stabilization (>10 °C higher than the canonical analogue) as a function of [Na + ] with an unexpected structural rearrangement at temperatures above 50 °C. Density functional theory–polarizable continuum model (DFT-PCM) calculations were carried out, and the analyses were in agreement with induced structural changes as a function of salt content. A model was proposed where the hydrophobic surface allows for an internal nucleobase rearrangement into a more thermodynamically stable structure, before undergoing full denaturation, with increased heat. While this behavior is not common, B- to Z-form duplex transitions can occur and are dependent on parameters that were probed in this work, i.e., temperature, nature of modification, or ionic content. To take advantage of this phenomenon, we probed the ability of the modified duplexes to be recognized by Zα (an RNA binding protein that targets Z-form RNA) via electrophoretic analysis and CD. Interestingly, the protein did not bind to canonical duplexes of DNA or RNA; however, it recognized the modified duplexes, in a [monovalent/divalent salt] dependent manner. Overall, the findings describe methodology to attain unique structural motifs of modified duplexes of DNA or RNA, and control their behavior as a function of salt concentration. While their affinity to RNA binding proteins, and the corresponding mechanism of action, requires further exploration, the tunable properties can be of potential use to study this, and other, types of modifications. The novel arrays that formed, under the conditions described herein, provide a useful way to explore the structure and behavior of modified oligonucleotides, in general.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Off-Stoichiometric Restructuring and Sliding Dynamics of Hexagonal Boron Nitride Edges in Conditions of Oxidative Dehydrogenation of Propane

Boron-containing materials, such as hexagonal boron nitride (h-BN), recently shown to be active and selective catalysts for the oxidative dehydrogenation of propane (ODHP), have been shown to undergo significant surface oxyfunctionalization and restructuring. Although experimental ex situ studies have probed the change in chemical environment on the surface, the structural evolution of it under varying reaction conditions has not been established. Herein, we perform global optimization structure search with a grand canonical genetic algorithm to explore the chemical space of off-stoichiometric restructuring of the h-BN surface under ambient as well as ODHP-relevant conditions. A grand canonical ensemble representation of the surface is established, and the predicted 11B solid-state NMR spectra are consistent with previous experimental reports. In addition, we investigated the relative sliding of h-BN sheets and how it influences the surface chemistry with ab initio molecular dynamics simulations. Furthermore, the B–O linkages on the edges are found to be significantly strained during the sliding, causing the metastable sliding configurations to have higher reactivity toward the activation of propane and water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Diaminopurine in Nonenzymatic RNA Template Copying

In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗