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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The timbre of Hawking gravitons: an effective description of energy transport from holography

Planar black holes in AdS, which are holographically dual to compressible relativistic fluids, have a long-lived phonon mode that captures the physics of attenuated sound propagation and transports energy in the plasma. We describe the open effective field theory of this fluctuating phonon degree of freedom. The dynamics of the phonon is encoded in a single scalar field whose gravitational coupling has non-trivial spatial momentum dependence. This description fits neatly into the paradigm of classifying gravitational modes by their Markovianity index, depending on whether they are long-lived. The sound scalar is a non-Markovian field with index 3 - d for a d-dimensional fluid. We reproduce (and extend) the dispersion relation of the holographic sound mode to quartic order in derivatives, constructing in the process the effective field theory governing its attenuated dynamics and associated stochastic fluctuations. We also remark on the presence of additional spatially homogeneous zero modes in the gravitational problem, which remain disconnected from the phonon Goldstone mode.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Farysia magdalena sp. nov. and description of the anamorph of Anthracocystis heteropogonicola from the Americas

Several interesting Ustilaginaceae yeast morphs were isolated during ongoing surveys of phylloplane-associated fungi in Louisiana (USA) and Guyana. In this work, we describe Farysia magdalena sp. nov., a phylloplane yeast isolated in southern Louisiana, based on phylogenetic analyses, assimilation profiles and morphological characters, and discuss the yeast morphs in this genus. Additionally, we describe the anamorphic stage of Anthracocystis heteropogonicola, isolated from plant phylloplanes from the Americas. This is the first report of this fungus in the Western Hemisphere and the first description of the yeast morph for a species of Anthracocystis.

1 new taxon↗
DOE OSTI2024

Generalized grain boundary constitutive description implemented in a strain-gradient large-strain FFT-based formulation: Application to nano-metallic laminates

Herein this paper presents a general treatment of grain boundary constitutive behavior in the context of strain-gradient (SG) plasticity, and its numerical implementation in a large-strain (LS) elasto-viscoplastic (EVP) fast Fourier transform (FFT)-based micromechanical model. Two novel grain boundary constitutive equations are proposed, allowing for more accurate description of the Burgers vector flow at the grain boundary. The capabilities of the generalized SG-LS-EVPFFT formulation are illustrated for the case of kink-band formation during layer-parallel compression of nano-metallic laminates (NMLs), requiring consideration of the interaction between dislocations and interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Characterization and description of a spectrum unfolding method for the $\mathrm{CATRiNA}$ neutron detector array

We report the CATRiNA deuterated neutron detector array at Florida State University consists of 16 2" x 2" and 16 $" x 2" EJ-315 detectors with characteristic light output and pulse-shape discrimination capabilities. The unique properties of the detectors, in part due to the anisotropic nature of (d,n) scattering, are used to extract the energy of neutrons via pulse-height spectrum unfolding. The unfolding method uses the light output and response matrix of the detectors to extract neutron energies, independent of the traditional time-of-flight (ToF) technique. Detailed response matrices of the CATRiNA detectors were measured at the Edwards Accelerator Laboratory at Ohio University via the 9 Be(d,n) and 27 Al(d,n) reactions. Full characterization of the detectors using digital electronics, as well as a description of the unfolding method are reported.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Integrated Quantum-Classical Protocol for the Realistic Description of Solvated Multinuclear Mixed-Valence Transition-Metal Complexes and Their Solvatochromic Properties

Linear cyanide-bridged polymetallic complexes, which undergo photoinduced metal-to-metal charge transfer, represent prototypical systems for studying long-range electron-transfer reactions and understanding the role played by specific solute–solvent interactions in modulating the excited-state dynamics. Here, to tackle this problem, while achieving a statistically meaningful description of the solvent and of its relaxation, one needs a computational approach capable of handling large polynuclear transition-metal complexes, both in their ground and excited states, as well as the ability to follow their dynamics in several environments up to nanosecond time scales. Here, we present a mixed quantum classical approach, which combines large-scale molecular dynamics (MD) simulations based on an accurate quantum mechanically derived force field (QMD-FF) and self-consistent QMD polarized point charges, with IR and UV–vis spectral calculations to model the solvation dynamics and optical properties of a cyano-bridged trinuclear mixed-valence compound (trans-[(NC) 5 Fe III (μ-CN)Ru II (pyridine) 4 (μ-NC)Fe III (CN) 5 ] 4– ). We demonstrate the reliability of the QMD-FF/MD approach in sampling the solute conformational space and capturing the local solute–solvent interactions by comparing the results with higher-level quantum mechanics/molecular mechanics (QM/MM) MD reference data. The IR spectra calculated along the classical MD trajectories in different solvents correctly predict the red shift of the CN stretching band in the aprotic medium (acetonitrile) and the subtle differences measured in water and methanol, respectively. By explicitly including the solvent molecules around the cyanide ligands and calculating the thermal averaged absorption spectra using time-dependent density functional theory calculations within the Tamm–Dancoff approximation, the experimental solvatochromic shift is quantitatively reproduced going from water to methanol, while it is overestimated for acetonitrile. This discrepancy can likely be traced back to the lack of important dispersion interactions between the solvent cyano groups and the pyridine substituents in our micro solvation model. The proposed protocol is applied to the ground state in water, methanol, and acetonitrile and can be flexibly generalized to study excited-state nonequilibrium solvation dynamics.

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

Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu 2 O 2 Active Site of oxy-Tyrosinase

Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O 2 towards the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady state stopped-flow kinetics approach that allows direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu 2 O 2 core of oxy-tyrosinase. The correlation of these experimental results to quantum-mechanics/ molecular-mechanics calculations provides a detailed mechanistic description of this H-transfer step. Furthermore, these new mechanistic insights revise and expand our fundamental understanding Cu 2 O 2 active sites in biology.

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

Description of the Electronic Structure of Oxyhemoglobin Using Fe L-Edge X-ray Absorption Spectroscopy

The electronic structure of oxyhemoglobin has been controversial since the discovery of the compound’s diamagnetism in 1936. Here, this study uses partial fluorescence yield Fe L-edge X-ray absorption spectroscopy (XAS) in the 3s→2p fluorescence on oxyhemoglobin solutions, measured using a transition-edge sensor detector, to obtain a quantitative experimental description of the electronic structure of the O 2 -bound iron site. The spectrum is very different from typical low-spin Fe II and Fe III heme spectra, and multiplet simulations indicate a mixed ground configuration with ∼57% low-spin Fe III and ∼43% low-spin Fe II character. This is also very different from the Fe II character found for the picket-fence porphyrin model complex. The oxyhemoglobin L-edge XAS data further show that the O 2 ligand engages in a weak σ- but strong π-bond with the iron ion, leading to the overall strong Fe–O 2 bond required for O 2 transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Unifying Advective and Diffusive Descriptions of Bedform Pumping in the Benthic Biolayer of Streams

Abstract Many water quality and ecosystem functions performed by streams occur in the benthic biolayer, the biologically active upper (~5 cm) layer of the streambed. Solute transport through the benthic biolayer is facilitated by bedform pumping, a physical process in which dynamic and static pressure variations over the surface of stationary bedforms (e.g., ripples and dunes) drive flow across the sediment‐water interface. In this paper we derive two predictive modeling frameworks, one advective and the other diffusive, for solute transport through the benthic biolayer by bedform pumping. Both frameworks closely reproduce patterns and rates of bedform pumping previously measured in the laboratory, provided that the diffusion model's dispersion coefficient declines exponentially with depth. They are also functionally equivalent, such that parameter sets inferred from the 2D advective model can be applied to the 1D diffusive model, and vice versa. The functional equivalence and complementary strengths of these two models expand the range of questions that can be answered, for example, by adopting the 2D advective model to study the effects of geomorphic processes (such as bedform adjustments to land use change) on flow‐dependent processes and the 1D diffusive model to study problems where multiple transport mechanisms combine (such as bedform pumping and turbulent diffusion). By unifying 2D advective and 1D diffusive descriptions of bedform pumping, our analytical results provide a straightforward and computationally efficient approach for predicting, and better understanding, solute transport in the benthic biolayer of streams and coastal sediments.

Grant, Stanley B.↗
DOE OSTI2020

On the nonadiabatic collisional quenching of OH(A) by H 2 : a four coupled quasi-diabatic state description

A four-state diabatic potential energy matrix (DPEM), H d , for the description of the nonadiabatic quenching of OH(A 2 Σ + ) by collisions with H 2 is reported. The DPEM is constructed as a fit to adiabatic energies, energy gradients, and derivative couplings obtained exclusively from multireference configuration interaction wave functions. A four-adiabatic-electronic-state representation is used in order to describe all energetically accessible regions of the nuclear coordinate space. Partial permutation-inversion symmetry is incorporated into the representation. Here, the fit is based on electronic structure data at 42 882 points, described by over 1.6 million least squares equations with a root mean square (mean unsigned) error of 178(83) cm –1 . Comparison of ab initio and H d determined minima, saddle points, and energy minimized points on C 2v , C s , C ∞v , and C 1 (noncoplanar) portions of two conical intersection seams are used to establish the accuracy of the H d .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

A cautionary tale: Problems in the valence-CASSCF description of the ground state (X1Σ+) of BF

In the full optimized reaction space and valence-complete active space self-consistent field (vCAS) methods, a set of active orbitals is defined as the union of the valence orbitals on the atoms, all possible configurations involving the active orbitals are generated, and the orbitals and configuration coefficients are self-consistently optimized. Such wave functions have tremendous flexibility, which makes these methods incredibly powerful but can also lead to inconsistencies in the description of the electronic structure of molecules. In this paper, the problems that can arise in vCAS calculations are illustrated by calculations on the BH and BF molecules. BH is well described by the full vCAS wave function, which accounts for molecular dissociation and 2s–2p near-degeneracy in the boron atom. The same is not true for the full vCAS wave function for BF. There is mixing of core and active orbitals at short internuclear distances and swapping of core and active orbitals at large internuclear distances. In addition, the virtual 2π orbitals, which were included in the active space to account for the 2s–2p near degeneracy effect, are used instead to describe radial correlation of the electrons in the F2pπ-like pairs. Although the above changes lead to lower vCAS energies, they lead to higher vCAS+1+2 energies as well as irregularities and/or discontinuities in the potential energy curves. All of the above problems can be addressed by using the spin-coupled generalized valence bond-inspired vCAS wave function for BF, which includes only a subset of the atomic valence orbitals in the active space.

Xu, Lu T. (ORCID:0000000182064902)↗
DOE OSTI2021

A purely kinetic description of the evaporation of water droplets

The process of water evaporation, although deeply studied, does not enjoy a kinetic description that captures known physics and can be integrated with other detailed processes such as drying of catalytic membranes embedded in vapor-fed devices and chemical reactions in aerosol whose volumes are changing dynamically. In this work, we present a simple, three-step kinetic model for water evaporation that is based on theory and validated by using well-established thermodynamic models of droplet size as a function of time, temperature, and relative humidity as well as data from time-resolved measurements of evaporating droplet size. Additionally, the kinetic mechanism for evaporation is a combination of two limiting processes occurring in the highly dynamic liquid-vapor interfacial region: direct first order desorption of a single water molecule and desorption resulting from a local fluctuation, described using third order kinetics. The model reproduces data over a range of relative humidities and temperatures only if the interface that separates bulk water from gas phase water has a finite width, consistent with previous experimental and theoretical studies. The influence of droplet cooling during rapid evaporation on the kinetics is discussed; discrepancies between the various models point to the need for additional experimental data to identify their origin.

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

X-point effects on the ideal MHD modes in tokamaks in the description of dual-poloidal-region safety factor

The flux coordinates with dual-region safety factor (q) in the poloidal direction are developed in this work. The X-point effects on the ideal MHD modes in tokamaks are then analyzed using this coordinate system. Since the X-point effects mainly affect the edge region, the modes localized at the tokamak edge are particularly examined. Two types of modes are studied. The first is related to the conventional peeling or peeling-ballooning modes. The mode existence aligned with the local magnetic field in the poloidally core region as observed experimentally is confirmed. The X points are shown to contribute to a stabilizing effect for the conventionally treated modes with the surface-averaged q and with the tokamak edge portion truncated. The other is the axisymmetric modes localized in the vicinity of X points, which can affect the cross-field-line transport near the X points. The existence of axisymmetric modes points to the possibility of applying a toroidally axisymmetric resonant magnetic perturbation (RMP) in the X-point area for mitigating the edge localized modes, which can be an alternative to the current RMP design. The dual q description also has important implications for the existing non-axisymmetric RMP concept. It helps to understand why the RMP suppression of edge localized modes is difficult to achieve in the double-null tokamak configurations and points to the possibility of further improving the current RMP concept by considering the alignment to the local q.

Fourier analysis↗
DOE OSTI2021

Kinetic description of site ensembles on catalytic surfaces

Significance The kinetic assessment of catalytic reactions is essential to the design and application of thermochemical processes useful in petrochemical synthesis, energy conversion, and environmental remediation. We demonstrate that the ubiquitously used Langmuir–Hinshelwood formalism is incomplete and fails to correctly describe even simple catalytic reactions (e.g., A + A → A 2 ). An accurate kinetic description requires explicit rate equations for multisite configurations (e.g., A*–A* pairs) to account for the nonrandom clustering/isolation of surface species. We rigorously describe clustering/isolation phenomena by derivation of coverage-dependent stoichiometric coefficients, which capture the distinct influence each elementary step exerts on each catalytic site ensemble—thereby overcoming limitations of the mean-field (i.e., Hinshelwood) assumption in describing reactions of mobile Langmuirian adsorbates on catalytic surfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Self-consistent description of the halo nature of 31 Ne with continuum and pairing correlations

Here a relativistic structure model has previously been used to predict a halo structure for 31 Ne, consistent with halo signatures from measured reaction cross sections of Ne isotopes bombarding Carbon targets. However, previous attempts to calculate those cross sections with reaction models were missing contributions from resonances and pairing correlations in their structure input. Use a reaction model with our relativistic fully microscopic structure model input to predict these cross sections and momentum distributions and analyze for possible halo signatures. Structure input for exotic Ne isotopes were obtained via the analytical continuation of the coupling constant (ACCC) method based on the relativistic mean field (RMF) theory with Bardeen - Cooper - Schrieffer (BCS) pairing approximation, the RAB approach. Total reaction cross sections, one-neutron removal cross sections, and momentum distributions of breakup reaction products were calculated with a Glauber model using our relativistic structure input. Our predictions of total reaction and one-neutron removal cross sections of 31 Ne on a Carbon target were significantly enhanced compared with those of neighboring Neon isotopes, agreeing with measurements at 240 MeV/nucleon and consistent with a single neutron halo. Furthermore, our calculations of the inclusive longitudinal momentum distribution of the 30 Ne and valence neutron residues from the 31 Ne breakup reaction indicate a dilute density distribution in coordinate space, another halo signature. We give a full description of the halo nature of 31 Ne that includes a self-consistent use of pairing and continuum contributions that makes predictions consistent with reaction cross section measurements. This approach can be utilized to determine the halo structure of other exotic nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Connection between classical and quantum descriptions of spin waves using quantum circuits

A quantum computing circuit is presented that approximates a single spin wave quantum on a linear chain of spin 1/2 particles described by a Heisenberg Hamiltonian. The circuit is a product state where each qubit represents a spin. The spin wave motion is represented by opening the cone angle using Y rotations and then adding progressive Z rotations along the chain to represent wave propagation. We show analytically that this product state yields the correct dispersion relation in the limit of an unbounded chain. This observation is confirmed using both a simulator and various quantum processors. The use of the quantum computing paradigm in this case does not lead to a computational advantage, but rather leads to a novel conceptual connection between classical and quantum descriptions of spin waves, and may also be useful for characterizing the error in quantum processors.

magnons↗
DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A comprehensive framework to assess elemental mercury in the Department of Energy: A descriptive analysis

Objective: This study investigated the relationship between personal breathing zone air samples and associated biological monitoring urine samples collected in the U.S. Department of Energy Operations. Methods: We performed standard descriptive analyses of the air sample and BEI monitoring data. We also provide a list of direct-reading instruments used in mercury field assessments. Results: A total of 2,330 air samples and 265 BEI data were analyzed. These data were grouped into 16 job titles, excluding categories with fewer than 10 samples, which resulted in 11 job titles. Conclusions: We conclude that industrial hygiene airborne sample data alone may not provide a complete assessment in exposure determination. We suggested the necessity of incorporating biological monitoring to determine the exposure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Towards a Quintic Ginzburg-Landau Description of the (2,7) Minimal Model

We discuss dimensional continuation of the massless scalar field theory with the 𝑖⁢𝜙 5 interaction term. It preserves the so-called 𝒫⁢𝒯 symmetry, which acts by 𝜙 →−𝜙 accompanied by 𝑖 →−𝑖. Below its upper critical dimension 10/3, this theory has interacting infrared fixed points. We argue that the fixed point in 𝑑 = 2 describes the nonunitary minimal conformal model 𝑀⁡(2,7). We identify the operators 𝜙 and 𝜙 2 with the Virasoro primaries 𝜙 1,2 and 𝜙 1,3 , respectively, and 𝑖⁢𝜙 3 with a quasiprimary operator, which is a Virasoro descendant of 𝜙 1,3 . Our identifications appear to be consistent with the operator product expansions and with considerations based on integrability. Using constrained Padé extrapolations, we provide estimates of the critical exponents in 𝑑 = 3. We also comment on possible lattice descriptions of 𝑀⁡(2,7) and discuss RG flows to and from this conformal field theory (CFT). Finally, we conjecture that the minimal models 𝑀⁡(2,2⁢𝑛 +1) are described by the massless scalar field theories with the 𝑖⁢𝜙 2⁢𝑛−1 interaction terms.

Conformal field theory↗