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At least 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

K-LL Auger transition probabilities for elements with low and intermediate atomic numbers

Radiationless K-LL transition probabilities have been calculated nonrelativistically in j-j coupling and in intermediate coupling, without and with configuration interaction, for elements with atomic numbers from 13 to 47. The system is treated as a coupled two-hole configuration. The single-particle radial wave functions required in the calculation of radial matrix elements, and in the calculation of mixing coefficients in the intermediate-coupling scheme, were obtained from Green's atomic independent-particle model. Comparison with previous theoretical work and with experimental data is made. The effects of intermediate coupling, configuration interaction, and relativity are noted.

Chen, M. H.↗
NASA NTRS1986

Automated Design Synthesis

Automated Design Synthesis (ADS) program is general-purpose numerical optimization program containing wide variety of algorithms. Assumed user prepares analysis problem capable of computing objective function and constraints. Program able to accept as part of input design variable quantities. Optimization process carried out by ADS coupled with user's program. ADS used for constrained and unconstrained function minimization. Solution of general problem separated into three basic levels: Strategy, Optimizer, and One-Dimensional Search. Already significant applications in area of structural synthesis (minimum-weight design).

Vanderplaats, G. N.↗
NASA NTRS1996

On the Reaction of FNO2 with CH3, t-butyl, and C13H21

Theoretical studies are reported for the reaction of FN02 with the radicals CH3, t-butyl, and C13H21, which are templates for the radical site of a hydrogenated diamond surface. All structures axe fully optimized using density functional theory (DFT) based on the B3LYP functional. Calibration calculations axe performed for CH3 + FNO2 using the coupled cluster approach, the the internally contracted multireference configuration. interaction method, and second order perturbation theory based upon complete active space SCF (CASSCF) reference wave function. These calibration calculations support the B3LYP approach for the calculation of bond energies, but show the B3LYP barrier is too low. Combining the calibration calculations with the larger clusters yields our best estimate of a barrier of about 10 kcal/mol. for the reaction of FNO2 with a radical site on hydrogenated diamond.

Thuemmel, H. T.↗
DOE OSTI2025

Softening of dd excitation in the resonant inelastic x-ray scattering spectra as a signature of Hund's coupling in nickelates

We investigate the effects of Hund's coupling on the resonant x-ray absorption spectra of the recently discovered family of layered nickelate superconductors. We contrast two scenarios depending on the relative strength of the ratio of the effective Hund's coupling ( J H ) to the crystal fields ( Δ ) in these systems. We carry out the cluster and DFT + DMFT simulations of the RIXS signal at the Ni L edge for different values of Hund's coupling. We find the latter dominates for the parent compound while the former becomes important for sufficiently large doping. Our results are consistent with the observations of a softening of a RIXS peak as a function of doping by Rossi [], only when the Hund coupling is sizable. To interpret the results, we separate the theoretical RIXS signal into spin conserving and nonspin conserving channels and conclude that the infinite layer nickelates are in a regime where Δ and J compete effectively and suggest further experimental tests of the theory. Published by the American Physical Society 2025

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

A Lumped Stochastic Model of Coupled Neutronic Assemblies

The objective of the present work is to apply the Harris ansatz to coupled assemblies in a lumped setting, i.e., ignoring the neutron phase dependence, which hitherto has not been considered. A Master equation for the single-time joint distribution of neutron number in each assembly, accounting for transfer of neutrons from one assembly to another via leakage transition probabilities and intercept or view factors is derived from which equations for the mean and variance in each assembly are developed. Because of the neutronic coupling, it is necessary to additionally compute the correlation function between pairs of assemblies which gives an expanded set of moment equations to solve. The reactivity of each assembly is allowed to vary with time, although a formal mechanism that is responsible for reactivity coupling between assemblies is not considered or proposed. Following Harris, it is then hypothesized that the number distribution in each assembly is a gamma distribution with assembly-specific mean and variance computed exactly from the moment equations. Illustrative numerical results are presented for the moments of a system of four coupled assemblies under various reactivity and neutronic coupling scenarios. The gamma distribution is then used to compute the probability that the neutron population exceeds a threshold value in any assembly. The report concludes with a discussion of recommended further work on this problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Metal–Organic Framework Integrating Ionic Framework and Bimetallic Coupling Effect for Highly Efficient Oxygen Evolution Reaction

Metal–organic frameworks (MOFs) are recognized as promising electrocatalysts for the oxygen evolution reaction (OER) because of their permanent porosity and rich architectural diversity; however, ionic MOFs enabling fast ions exchange during OER are rarely explored. Here, an ionic MOF (Ni-btz) constructed with an azolate ligand is selected, and continuous 3D bimetallic MOF (NiFe-btz) films deriving from high-degree intergrowth of microsized MOFs particles are fabricated. The as-prepared NiFe-btz/NF-OH electrode exhibits excellent OER performance with a low overpotential of 239 mV at 10 mA cm –2 under alkaline condition. The OER charge transfer process and bimetallic coupling effect in ionic NiFe-btz are probed by density functional theory calculations and confirmed via X-ray photoelectron spectroscopy and in situ Raman measurements. The partial density of states of NiFe-btz indicates that the main contribution for electron density around the Fermi level is from Cl ions clarifying the profitable impact of ionic MOF framework. This work systematically demonstrates the relationship of electronic structure and OER activity in ionic, bimetallic MOFs and expands the scope of 3D MOF films for efficient OER.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Fermi–Löwdin orbital self-interaction correction of adsorption energies on transition metal ions

Density functional theory (DFT)-based descriptions of the adsorption of small molecules on transition metal ions are prone to self-interaction errors. Here, we show that such errors lead to a large over-estimation of adsorption energies of small molecules on Cu + , Zn + , Zn 2+ , and Mn + in local spin density approximation (LSDA) and Perdew, Burke, Ernzerhof (PBE) generalized gradient approximation calculations compared to reference values computed using the coupled-cluster with single, doubles, and perturbative triple excitations method. These errors are significantly reduced by removing self-interaction using the Perdew–Zunger self-interaction correction (PZ-SIC) in the Fermi–Löwdin Orbital (FLO) SIC framework. In the case of FLO-PBE, typical errors are reduced to less than 0.1 eV. Furthermore, analysis of the results using DFT energies evaluated on self-interaction-corrected densities [DFT(@FLO)] indicates that the density-driven contributions to the FLO-DFT adsorption energy corrections are roughly the same size in DFT = LSDA and PBE, but the total corrections due to removing self-interaction are larger in LSDA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Magnetic states of the quasi-one-dimensional iron chalcogenide Ba 2 FeS 3

Quasi-one-dimensional iron-based ladders and chains, with the 3d iron electronic density n=6, are attracting considerable attention. Recently, a new iron chain system Ba 2 FeS 3 , also with n=6, was prepared under high-pressure and high-temperature conditions. Here the magnetic and electronic phase diagrams are theoretically studied for this quasi-one-dimensional compound. Based on first-principles calculations, a strongly anisotropic one-dimensional electronic band behavior near the Fermi level was observed. In addition, a three-orbital electronic Hubbard model for this chain was constructed. Introducing the Hubbard and Hund couplings and studying the model via the density matrix renormalization group (DMRG) method, we studied the ground-state phase diagram. A robust staggered ↑-↓-↑-↓ AFM region was unveiled in the chain direction, consistent with our density functional theory (DFT) calculations. Furthermore, at intermediate Hubbard U coupling strengths, this system was found to display an orbital selective Mott phase (OSMP) with one localized orbital and two itinerant metallic orbitals. At very large U/W (W=bandwidth), the system displays Mott insulator characteristics, with two orbitals half-filled and one doubly occupied. Our results for high pressure Ba 2 FeS 3 provide guidance to experimentalists and theorists working on this one-dimensional iron chalcogenide chain material.

1-dimensional systems↗
DOE OSTI2022

Automating Component-Level Stress Measurements for Inverter Reliability Estimation

In the near future, grid operators are expected to regularly use advanced distributed energy resource (DER) functions, defined in IEEE 1547-2018, to perform a range of grid-support operations. Many of these functions adjust the active and reactive power of the device through commanded or autonomous operating modes which induce new stresses on the power electronics components. In this work, an experimental and theoretical framework is introduced which couples laboratory-measured component stress with advanced inverter functionality and derives a reduction in useful lifetime based on an applicable reliability model. Multiple DER devices were instrumented to calculate the additional component stress under multiple reactive power setpoints to estimate associated DER lifetime reductions. A clear increase in switch loss was demonstrated as a function of irradiance level and power factor. This is replicated in the system-level efficiency measurements, although magnitudes were different—suggesting other loss mechanisms exist. Using an approximate Arrhenius thermal model for the switches, the experimental data indicate a lifetime reduction of 1.5% when operating the inverter at 0.85 PF—compared to unity PF—assuming the DER failure mechanism thermally driven within the H-bridge. If other failure mechanisms are discovered for a set of power electronics devices, this testing and calculation framework can easily be tailored to those failure mechanisms.

Flicker, Jack (ORCID:0000000212232154)↗
NASA NTRS2010

Direct Observations of PMC Local Time Variations by Aura OMI

The Ozone Monitoring Instrument (OMI) on the Aura satellite obtains unique measurements for polar mesospheric cloud (PMC) analysis. Its wide cross-track viewing swath and high along-track spatial resolution makes it possible to directly evaluate PMC occurrence frequency and brightness variations between 6S" and 8S' latitude as a function of local time over a 12-14 h continuous period. OMI PMC local time variations are closely coupled to concurrent variations in measurement scattering angle, so that ice phase function effects must be considered when interpreting the observations. Two different phase functions corresponding to bright and faint clouds are examined in this analysis. OMI observations show maximum frequency and albedo values at 8-10 h local time in the Northern Hemisphere, with decreasing amplitude at higher latitudes. Southern Hemisphere values reach a minimum at 18-20 h LT. Larger variations are seen in Northern Hemisphere data. No statistically significant longitudinal dependence was seen.

DeLand, Matthew T.↗
DOE OSTI2022

Isogeometric large-eddy simulations of turbulent particle-laden flows

In recent years, isogeometric analysis (IGA) has attracted significant attention from the computational mechanics community due to its ability to integrate design and analysis. Besides, IGA is also a higher-order discretization technique for solving partial differential equations, showing high approximation capability per degree of freedom. In this paper, we extend the application realm of IGA to particle-laden flows based on Eulerian–Eulerian description that couples Navier–Stokes equations with a density transport equation through a Boussinesq approximation. The coupled systems are solved by using quadratic non-uniform rational B-spline (NURBS) functions and a recently developed residual-based variational multiscale (VMS) formulation, which introduces coupling between the fine velocity scales and density equation residuals. We deploy the proposed approach to perform large-eddy simulations (LES) of dilute particle-laden flows over a flat surface at Reynolds number = 10,000. We compare the simulation results against direct numerical simulation (DNS) results from the literature. We find that combining VMS and IGA, the proposed approach enables accurate prediction of a wide range of flow/particle statistics with a relatively lower mesh resolution.

Mathematics↗
DOE OSTI2023

Infrared fixed point of the SU(3) gauge theory with 𝑁 𝑓 = 10 flavors

We use lattice simulations and the continuous renormalization group method, based on the gradient flow, to calculate the 𝛽 function and anomalous dimensions of the SU(3) gauge theory with 𝑁 𝑓 = 10 flavors of fermions in the fundamental representation. We employ several improvements to extend the range of available renormalized couplings, including the addition of heavy Pauli-Villars bosons to reduce cutoff effects and the combination of a range of gradient flow transformations. While in the weak coupling regime our result is consistent with those of earlier studies, our techniques allow us to study the system at much stronger couplings than previously possible. We find that the renormalization group 𝛽 function develops a zero, corresponding to an infrared-stable fixed point, at gradient-flow coupling 𝑔 2 = 15.0⁢(5). We also determine the mass and tensor anomalous dimensions: At the fixed point we find 𝛾 𝑚 ≃0.6, suggesting that this system might be deep inside the conformal window.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Tuning the reactivity of carbon surfaces with oxygen-containing functional groups

Oxygen-containing carbons are promising supports and metal-free catalysts for many reactions. However, distinguishing the role of various oxygen functional groups and quantifying and tuning each functionality is still difficult. Here we investigate the role of Brønsted acidic oxygen-containing functional groups by synthesizing a diverse library of materials. By combining acid-catalyzed elimination probe chemistry, comprehensive surface characterizations, 15N isotopically labeled acetonitrile adsorption coupled with magic-angle spinning nuclear magnetic resonance, machine learning, and density-functional theory calculations, we demonstrate that phenolic is the main acid site in gas-phase chemistries and unexpectedly carboxylic groups are much less acidic than phenolic groups in the graphitized mesoporous carbon due to electron density delocalization induced by the aromatic rings of graphitic carbon. The methodology can identify acidic sites in oxygenated carbon materials in solid acid catalyst-driven chemistry.

Zhou, Jiahua↗
NASA NTRS1993

The quantum dynamics of electronically nonadiabatic chemical reactions

Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally adiabatic functions in various quantum scattering algorithms.

Truhlar, Donald G.↗
DOE OSTI2025

Reversible Modification of Rashba States in Topological Insulators at Room Temperature by Edge Functionalization

Quantum materials with novel spin textures from strong spin-orbit coupling (SOC) are essential components for a wide array of proposed spintronic devices. Topological insulators have a necessary strong SOC that imposes a unique spin texture on topological states and Rashba states that arise on the boundary, but there is no established methodology to control the spin texture reversibly. Here, it is demonstrated that functionalizing Bi 2 Se 3 films by altering the step-edge termination directly changes the strength of SOC and thereby modifies the Rashba strength of 1D edge states. Scanning tunneling microscopy/spectroscopy shows that these Rashba edge states arise and subsequently vanish through the Se functionalization and reduction process of the step edges. The observations are corroborated by density functional theory calculations, which show that a subtle chemical change of edge termination fundamentally alters the underlying electronic structure. Importantly, fully reversible and repeatable switching of Rashba edge states across multiple cycles at room temperature is experimentally demonstrated. The results imply Se functionalization as a practical method to control SOC and spin texture of quantum states in topological insulators.

Rashba edge states↗
DOE OSTI2020

Molecular-Scale Characterization of Photoinduced Charge Separation in Mixed-Dimensional InSe–Organic van der Waals Heterostructures

Layered indium selenide (InSe) is an emerging two-dimensional semiconductor that has shown significant promise for high-performance transistors and photodetectors. The range of optoelectronic applications for InSe can potentially be broadened by forming mixed-dimensional van der Waals heterostructures with zero-dimensional molecular systems that are widely employed in organic electronics and photovoltaics. Here, we report the spatially resolved investigation of photoinduced charge separation between InSe and two molecules (C 70 and C 8 -BTBT) using scanning tunneling microscopy combined with laser illumination. We experimentally and computationally show that InSe forms type-II and type-I heterojunctions with C 70 and C 8 -BTBT, respectively, due to an interplay of charge transfer and dielectric screening at the interface. Laser-excited scanning tunneling spectroscopy reveals a ~0.25 eV decrease in the energy of the lowest unoccupied molecular orbital of C 70 with optical illumination. Furthermore, photoluminescence spectroscopy and Kelvin probe force microscopy indicate that electron transfer from InSe to C 70 in the type-II heterojunction induces a photovoltage that quantitatively matches the observed downshift in the tunneling spectra. In contrast, no significant changes are observed upon optical illumination in the type-I heterojunction formed between InSe and C 8 -BTBT. Density functional theory calculations further show that, despite the weak coupling between the molecular species and InSe, the band alignment of these mixed-dimensional heterostructures strongly differs from the one suggested by the ionization potential and electronic affinities of the isolated components. Self-energy-corrected density functional theory indicates that these effects are the result of the combination of charge redistribution at the interface and heterogeneous dielectric screening of the electron–electron interactions in the heterostructure. In addition to providing specific insight for mixed-dimensional InSe–organic van der Waals heterostructures, this work establishes a general experimental methodology for studying localized charge transfer at the molecular scale that is applicable to other photoactive nanoscale systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1976

A numerical study of the radiative-dynamic interaction in the stratosphere by a time-dependent zonal mean circulation model

The response of a zonal mean circulation model was compared to different heating functions used to simulate the interannual climate cycle. Two heating functions were used: A simple Newtonian heating function and a sophisticated heating function (Ramanathan, 1976). The emphasis was on the coupling between radiative transfer and the circulation in the stratosphere. The model was formulated in terms of primitive equations with 10 deg latitudinal resolution and 18 levels in pressure. Eddy transport of heat in the stratosphere was treated by the Reed and German (1965) formulation, while Stone's (1973) formulation is used in the troposphere. Momentum eddy fluxes are specified by climate statistics after Harwood and Pyle (1975). The model dynamics resulting from the two runs are compared to demonstrate the benefits of using detailed heating functions.

Turner, R. E.↗