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DOE OSTI2018

Aberrantly expressed lncRNAs identified by microarray analysis in CD4+T cells in asthmatic patients

Highlights: • Long noncoding RNAs may be potential biomarkers to diagnose asthma. • Long noncoding RNAs may regulate the expression of cytokines in CD4+T cells in asthma. • Specific long noncoding RNAs are related with the characteristics of asthmatic patients. The aim of the study was to determine the expression profiles of message RNAs and long non-coding RNAs in CD4{sup +}T cells of asthmatic patients and to explore the clinical value and biological function. Expression profiles in CD4{sup +}T cells of asthmatic patients and healthy controls were analyzed by microarray. We found 2725 lncRNAs and 3167 mRNAs differentially expressed. The data were validated by quantitative real time polymerase chain reaction, with 3 up-regulated (ENST00000444682, ENST00000566098, ENST00000583179) and 1 down-regulated (ENST00000579468) lncRNAs found. Receiver operating characteristic curve analysis showed the area under the curve was 0.7058, 0.9026, 0.8361, 0.8316, respectively. Spearman correlation analysis showed that ENST00000566098 was positively related with IL-13 and ENST00000579468 was positively related with peak expiratory flow. Bioinformatics analyses were performed to explore the function of lncRNAs. Specific lncRNAs aberrantly expressed in CD4{sup +}T cells may take part in the development of asthma and may be used as biomarkers for diagnosis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

The impact of mixed solvents on the complexation thermodynamics of Eu(III) by simple carboxylate and amino carboxylate ligands

To gain insight on the role of mixed solvents on the thermodynamic driving forces for the complexation between trivalent f-elements and organic ligands, solution phase thermodynamic parameters were determined for Eu(III) complexation with 2-hydroxyisobutyric acid (HIBA) and 2-aminoisobutyric acid (AIBA) in mixed methanol (MeOH)-water and N,N-dimethylformamide (DMF)-water solvents. Included in this study were the determination of mixed solvent autoprotolysis constants (pK α ) as well as the thermodynamic formation constants: log β, ΔG, ΔH, and ΔS, for ligand protonation and Eu(III)-ligand complexation utilizing potentiometry and calorimetry techniques. The results presented are conditional thermodynamic values determined at an ionic strength of 1.0 M NaClO 4 and a temperature of 298 K. It was found that moving from an aqueous solution to a binary aqueous-organic solvent affected all solution equilibria to some degree and that the extent of change depended on both the type of mixed solvent and the ligand in each study. Here, the ability to understand and predict these changes in thermodynamic values as a function of solvent composition provides important information about the chemistry of the trivalent f-elements.

2-aminoisobutyric acid↗

DOE OSTI2020

A comparative study of the effectiveness of empirical potentials for molecular dynamics simulations of borosilicate glasses

Despite their practical importance, atomistic modeling of B 2 O 3 containing glasses have been challenging due to the lack of reliable empirical potentials. Fortunately, a few recent developments have shown promises to simulate these glasses where the boron coordination has complex and non-linear dependence on glass composition. This work aims to provide an evaluation of the effectiveness of three recently developed potentials by a systematic study of a series (~20) of sodium borosilicate glasses with constant K (ratio of [SiO 2 ]/[B 2 O 3 ]) =2 and varying R (ratio of [Na 2 O]/[B 2 O 3 ] ranging from 0.1 to 4) values and several sodium boroaluminosilicate glasses. A comparative assessment was established on the basis of the short- and medium-range structure features, such as boron N 4 values, total correlation functions, bond angle distribution, oxygen speciation, and mechanical properties using experimental or well-established models as criteria. Furthermore, this work provides insights on the choices of empirical potentials for MD simulations of borosilicate glasses and gives directions of future potential development and refining.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Thermodynamic properties of Ca–Pb electrodes determined by electromotive force measurements

Thermodynamic properties of Ca–Pb alloys are investigated by electromotive force (emf) measurements to determine equilibrium cell potentials and phase properties for their application in energy storage systems such as liquid metal batteries. Using the electrochemical cell Ca(s) | CaF 2 (s) | Ca(in Pb) at 700–1060 K, cell emf is measured for thirteen Ca–Pb alloys at mole fractions, x Ca = 0.06–0.80. At 873 K, the equilibrium potentials of liquid Ca–Pb alloys are 0.57–0.62 V versus Ca and the activity values are as low as a Ca = 6.2 × 10 -8 at x Ca = 0.06. In addition, the emf values as a function of temperature provide partial molar quantities (entropy and enthalpy) as well as phase transitions which are corroborated by determining transition temperatures and phase constituents using differential scanning calorimetry (DSC) and powder X-ray diffraction (XRD). This study establishes the fundamental data necessary for the design of Pb-containing liquid metal electrodes through the integration of electrochemical, thermal, and structural properties of Ca–Pb electrodes.

25 ENERGY STORAGE↗

DOE OSTI2018

In situ monitoring of hydrogen loss during pyrolysis of wood by neutron imaging

Hydrogen is an element of fundamental importance for energy but hard to quantify in bulk materials. Neutron radiography was used to map in situ loss of elemental hydrogen from beech tree wood samples during pyrolysis. The samples consisted of three wood cylinders (finished dowel or cut branch) of approximately 1 cm in length. The samples were pyrolyzed under vacuum in a furnace vessel that was placed inside a cold neutron imaging beamline using a temperature ramp of 5 °C/min from ambient up to 400 °C. Neutron radiographs with exposures of 30 s were sequentially recorded with a charge-coupled device over the course of the experiment. Relative absorbance/scattering of the neutron beam by each sample was based on intensity (or brightness) values as a function of pixel position. The much larger neutron cross section for hydrogen compared to carbon and oxygen enables almost direct conversion of neutron attenuation into sample hydrogen content for each time step during the pyrolysis experiment. Target and vessel temperatures were recorded concurrently with collection of the radiographs so that changes could be directly correlated to different states of pyrolysis. The most visible change appeared at the initial phase of the 400 °C plateau as evidenced by strong hydrogen loss and primarily diametric shrinking of the samples. In conclusion, the loss of elemental hydrogen between initial and final states of pyrolysis was estimated to be about 70%.

08 HYDROGEN↗

DOE OSTI2021

Excited-State Dynamics and Nonlinear Optical Properties of Hyperpolarizable Chromophores Based on Conjugated Bis(terpyridyl)Ru(II) and Palladium and Platinum Porphyrinic Components: Impact of Heavy Metals upon Supermolecular Electro-Optic Properties

A new series of strongly coupled oscillators based upon (porphinato)Pd, (porphinato)Pt, and bis(terpyridyl)-ruthenium(II) building blocks is described. These RuPPd, RuPPt, RuPPdRu, and RuPPtRu chromophores feature bis- (terpyridyl)Ru(II) moieties connected to the (porphinato)metal unit via an ethyne linker that bridges the 4!-terpyridyl and porphyrin macrocycle meso-carbon positions. Pump–probe transient optical data demonstrate sub-picosecond excited singlet-to-triplet-state relaxation. The relaxed lowest-energy triplet (T 1 ) excited states of these chromophores feature absorption manifolds that span the 800–1200 nm spectral region, microsecond triplet-state lifetimes, and large absorptive extinction coefficients [ε(T 1 → T n ) > 4 × 10 4 M –1 cm –1 ]. Dynamic hyperpolarizability (β λ ) values were determined from hyper-Rayleigh light scattering (HRS) measurements carried out at several incident irradiation wavelengths over the 800–1500 nm spectral region. Relative to benchmark RuPZn and RuPZnRu chromophores which showed large βHRS values over the 1200–1600 nm range, RuPPd, RuPPt, RuPPdRu, and RuPPtRu displayed large βHRS values over the 850–1200 nm region. Generalized Thomas–Kuhn sum (TKS) rules and experimental hyperpolarizability values were utilized to determine excited state-to-excited state transition dipole terms from experimental electronic absorption data and thus assessed frequency-dependent β λ values, including two- and three-level contributions for both β zzz and β xzx tensor components to the RuPPd, RuPPt, RuPPdRu, and RuPPtRu hyperpolarizability spectra. Furthermore, these analyses qualitatively rationalize how the βzzz and βxzx tensor elements influence the observed irradiation wavelength-dependent hyperpolarizability magnitudes. The TKS analysis suggests that supermolecules related to RuPPd, RuPPt, RuPPdRu, and RuPPtRu will likely feature intricate dependences of experimentally determined βHRS values as a function of irradiation wavelength that derive from substantial singlet–triplet mixing, and complex interactions among multiple different β tensor components that modulate the long wavelength regime of the nonlinear optical response.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Predicting Elastic Properties of Materials from Electronic Charge Density Using 3D Deep Convolutional Neural Networks

Materials representation plays a key role in machine learning-based prediction of materials properties and new materials discovery. Currently both graph and three-dimensional (3D) voxel representation methods are based on the heterogeneous elements of the crystal structures. Here, we propose to use electronic charge density (ECD) as a generic unified 3D descriptor for materials property prediction with the advantage of possessing close relation with the physical and chemical properties of materials. We developed an ECD-based 3D convolutional neural networks (CNNs) for predicting the elastic properties of materials, in which CNNs can learn effective hierarchical features with multiple convolving and pooling operations. Extensive benchmark experiments over 2170 $Fm\bar3m$ face-centered-cubic materials show that our ECD-based CNNs can achieve good performance for elasticity prediction. Especially, our CNN models based on the fusion of elemental Materials-Agnostic Platform for Informatics and Exploration features and ECD descriptors achieved the best fivefold cross-validation performance. More importantly, we showed that our ECD-based CNN models can achieve significantly better extrapolation performance when evaluated over nonredundant data sets, where there are few neighbor-training samples around test samples. As an additional validation, we evaluated the predictive performance of our models on 329 materials of space group $Fm\bar3m$ by comparing to density functional theory calculated values, which shows a better prediction power of our model for bulk modulus than shear modulus. Because of the unified representation power of ECD, it is expected that our ECD-based CNN approach can also be applied to predict other physical and chemical properties of crystalline materials.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Influence of Longer Range Transfer of Vapor Interface Modified Caging Constraints on the Spatially Heterogeneous Dynamics of Glass-Forming Liquids

Based on the elastically collective nonlinear Langevin equation (ECNLE) theory of bulk relaxation in glass-forming liquids, and our recent ideas of how interface-nucleated modification of caging constraints are spatially transferred into the interior of a thick film, we present a force-based theory for dynamical gradients in thick films with one vapor interface that includes collective elasticity effects. Quantitative applications to the foundational hard sphere fluid and polymer melts of diverse fragilities are presented. In this work, we predict a roughly exponential spatial variation of the total activation barrier which is nonperturbatively modified to similar to 10 particle diameters into the film. This leads, to leading order, to the prediction of a reduced alpha relaxation time gradient of a double-exponential form characterized by a nearly constant spatial decay length, in qualitative accord with simulations. The relaxation acceleration at the surface grows exponentially with increasing packing fraction or decreasing temperature. The rate of increase with cooling of the alpha time strongly weakens upon approaching the vapor interface, with the top two layers remaining liquid-like down to similar to ~80-85% of the bulk glass transition temperature. These spatially heterogeneous changes of the temperature variation of the alpha time result in a large and long-range gradient of the local glass transition temperature. An average interfacial layer thickness relevant to ensemble-averaged dielectric and other experiments is also computed. It is predicted to be rather large at the bulk glass transition temperature, decreasing roughly linearly with heating. Remarkably, to leading order the ratio of this layer-averaged interfacial relaxation time to its bulk analogue is invariant to chemistry, volume fraction, and temperature and of modest absolute magnitude. Spatially inhomogeneous power law decoupling of the alpha relaxation time from its bulk value is predicted, with an effective exponent that decays to zero with distance from the free surface in a nearly exponential manner, trends which are in qualitative accord with recent simulations. Finally, this behavior and the double-exponential alpha time gradient are related and can be viewed as consequences of an effective quasi-universal factorization of the total barrier in films into the product of its bulk-temperature-dependent value times a function solely of location in the film.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Self-testing of a single quantum system from theory to experiment

Abstract Self-testing allows one to characterise quantum systems under minimal assumptions. However, existing schemes rely on quantum nonlocality and cannot be applied to systems that are not entangled. Here, we introduce a robust method that achieves self-testing of individual systems by taking advantage of contextuality. The scheme is based on the simplest contextuality witness for the simplest contextual quantum system—the Klyachko-Can-Binicioğlu-Shumovsky inequality for the qutrit. We establish a lower bound on the fidelity of the state and the measurements as a function of the value of the witness under a pragmatic assumption on the measurements. We apply the method in an experiment on a single trapped 40 Ca + using randomly chosen measurements and perfect detection efficiency. Using the observed statistics, we obtain an experimental demonstration of self-testing of a single quantum system.

Physics↗

DOE OSTI2019

Symmetry breaking charge transfer as a means to study electron transfer with no driving force

Symmetry breaking charge transfer (SBCT) is a process where a symmetrically disposed pair of identical chromophores forms a charge transfer excited state with the hole and electron on different chromophores, i.e. chr–chr + hν → chr + –chr – . Herein we explore this process in two dipyrrin-based bichromophoric systems. One of these bisdipyrrins involved a pair of BODIPY chromophores linked by a single bond at their meso-positions (compound 1) and the other involved two dipyrrin ligands coordinated in a tetrahedral geometry at the Zn 2+ ion (compound 2). Both compounds show rapid SBCT in polar solvents and only dipyrrin based emission in nonpolar solvents, the latter arising from a dipyrrin localized excited sate (LE). By “tuning” the solvent polarity the equilibrium between the LE and SBCT states can be shifted to favor either state. Ultrafast transient absorption spectroscopy (TA) was used to probe the kinetics of the charge transfer for 2 in solvents where the electron transfer is endergonic, exergonic and has a ΔG close to zero. Our TA derived rates were used to predict fluorescence efficiencies in each of the different solvent systems and showed a good correspondence to measured values. Detailed density functional theory (DFT) and time dependent DFT were used to model the ground states as well as the LE and SBCT states of 1 and 2, in both polar and nonpolar media. Lastly, the ground and LE excited states show small dipole moments, while the SBCT states show dipole moments of 16.4 and 20.3 D for 1 and 2, respectively.

14 SOLAR ENERGY↗

DOE OSTI2024

Statistical properties of filaments in the cosmic web

ABSTRACT In the context of the cosmological and constrained Exploring the Local Universe with the reConstructed Initial Density field (ELUCID) simulation, this study explores the statistical characteristics of filaments within the cosmic web, focussing on aspects such as the distribution of filament lengths and their radial density profiles. Using the classification of the cosmic web environment through the Hessian matrix of the density field, our primary focus is on how cosmic structures react to the two variables $R_{\rm s}$ and $\lambda _{\rm th}$. The findings show that the volume fractions of knots, filaments, sheets, and voids are highly influenced by the threshold parameter $\lambda _{\rm th}$, with only a slight influence from the smoothing length $R_{\rm s}$. The central axis of the cylindrical filament is pinpointed using the medial-axis thinning algorithm of the COsmic Web Skeleton (COWS) method. It is observed that median filament lengths tend to increase as the smoothing lengths increase. Analysis of filament length functions at different values of $R_{\rm s}$ indicates a reduction in shorter filaments and an increase in longer filaments as $R_{\rm s}$ increases, peaking around $2.5R_{\rm s}$. The study also shows that the radial density profiles of filaments are markedly affected by the parameters $R_{\rm s}$ and $\lambda _{\rm th}$, showing a valley at approximately $2R_{\rm s}$, with increases in the threshold leading to higher amplitudes of the density profile. Moreover, shorter filaments tend to have denser profiles than their longer counterparts.

Zhang, Youcai (ORCID:0000000319674091)↗

DOE OSTI2018

Survey geometry and the internal consistency of recent cosmic shear measurements

We explore the impact of an update to the typical approximation for the shape noise term in the analytic covariance matrix for cosmic shear experiments that assumes the absence of survey boundary and mask effects. We present an exact expression for the number of galaxy pairs in this term based on the survey mask, which leads to more than a factor of three increase in the shape noise on the largest measured scales for the Kilo-Degree Survey (KiDS-450) real-space cosmic shear data. We compare the result of this analytic expression to several alternative methods for measuring the shape noise from the data and find excellent agreement. This update to the covariance resolves any internal model tension evidenced by the previously large cosmological best-fitting χ 2 for the KiDS-450 cosmic shear data. The best-fitting χ 2 is reduced from 161 to 121 for 118 degrees of freedom. We also apply a correction to how the multiplicative shear calibration uncertainty is included in the covariance. This change shifts the inferred amplitude of the correlation function to higher values. In conclusion, we find that this improves agreement of the KiDS-450 cosmic shear results with Dark Energy Survey Year 1 and Planck results.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Quantitative surface studies of moiré intercalated Pb structures under Gr/SiC

Quantitative growth studies using surface diffraction and scanning tunneling microscopy are carried out to determine the intercalation conditions for Pb under Gr/SiC, with initial phase a mixture of buffer-layer and single-layer graphene. Intercalation is a kinetically complex, multistage process with intercalated Pb moving between different subsurface locations with annealing, eventually to the location of higher stability. The transfer is determined by monitoring the difference of a given spot intensity from its clean value, as a function of growth parameters. In addition, a broad, low-intensity (10×10) gr moiré phase is observed exclusively originating from intercalated Pb. Well-defined growth conditions are identified for the moiré spot to be observed reversibly. The (10×10) gr phase follows changes of the Pb(10) spot during growth and annealing experiments, instead of changes of the other Gr/SiC spots indicating preferred nucleation of Pb islands on the (10×10) gr domains. These structural results are discussed in connection to different models proposed for the (10×10) gr supercell and the subsurface Pb coverage. In conclusion, mass transport of subsurface Pb is unusually high, possibly because of the very high compression of the intercalated Pb, when compared to metallic Pb(111).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Temperature Measurement of Laser-Irradiated Metals Using Hyperspectral Imaging

Accurate noncontact surface-temperature measurements during laser-based materials processing remain challenging due to the difficulty of establishing reliable emissivity values as a function of temperature and wavelength. Direct measurement of emissivity is difficult, as the emissivity may be changing constantly in the laser-material interaction region, where the temperature gradients are extreme and surface displacement can complicate the measurement. Here, we present a hyperspectral imaging method using a multiwavelength camera to capture the spectral radiance in eight different bands and fit the wavelength-dependent radiance to Planck’s law. Time-resolved temperature measurements during microsecond pulsed-laser irradiation of a metal plate made of the titanium alloy Ti -6 Al -4 V provide temperature information about the irradiated surface with an estimated accuracy of ± 10 % . The extracted wavelength-dependent emissivity slope compares well with reported results for macroscale titanium melts obtained using IR spectroscopy, which measure temperature without any built-in assumptions about the emissivity. The results are directly applicable to temperature monitoring during welding, additive manufacturing, and semiconductor growth.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Analysis of over-magnetization of elemental transition metal solids from the SCAN density functional

Current investigations have revealed that the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation exchange-correlation functional significantly over-magnetizes elemental Fe, Co, and Ni solids. For the paradigmatic case, bcc Fe, the error relative to experiment is ≳ 20 % . A comparative analysis of magnetization results from SCAN and its deorbitalized counterpart, SCAN-L, leads to identification of the source of the discrepancy. It is not from the difference between Kohn-Sham (SCAN-L) and generalized Kohn-Sham (SCAN) procedures. The key is the iso-orbital indicator α (the ratio of the local Pauli and Thomas-Fermi kinetic energy densities). Its deorbitalized counterpart α L has more dispersion in both spin channels with respect to magnetization in an approximate region between 0.6 and 1.2 bohrs around an Fe nucleus. The overall effect is that the SCAN switching function evaluated with α L reduces the energetic disadvantage of the down channel with respect to up compared to the original α , which in turn reduces the magnetization. This identifies the origin of the SCAN magnetization error as insensitivity of the SCAN switching function to α values in the approximate range 0.5 ≲ α ≲ 0.8 and oversensitivity for α ≳ 0.8 .

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electronic and topological properties of the van der Waals layered superconductor PtTe

We report the crystal growth and structural and electronic properties of superconducting, van der Waals layered PtTe. Easily cleavable crystals with a platelike morphology consistent with the layered structure were grown from a platinum-rich flux. A consistent determination of T c = 0.57 K is made from the onset of diamagnetism, the zero of resistivity, and the midpoint of the heat-capacity jump. The observed behavior is consistent with type-II superconductivity, with upper critical field at T = 0 estimated using the Werthamer-Helfand-Hohenberg theory to be 143 and 65 Oe for fields out of and in the plane, respectively. The heat-capacity discontinuity is close to the weak-coupling BCS value. Density-functional theory calculations and analysis of the electronic structure finds that PtTe is a topological semimetal with numerous surface states but suggests that the superconducting state itself may be topologically trivial. Additionally, angle-resolved photoemission spectroscopy reveals a normal-state Fermi surface in remarkable agreement with theory and confirms the overall topological nature of the material by experimental identification of the surface bands. Together, these findings identify PtTe as an interesting example of a cleavable, topological, and superconducting material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Isovector charges of the nucleon from 2+1-flavor QCD with clover fermions

Here, we present high-statistics estimates of the isovector charges of the nucleon from four 2 + 1-flavor ensembles generated using Wilson-clover fermions with stout smearing and tree-level tadpole improved Symanzik gauge action at lattice spacings 𝑎 ≈ 0.127 and 0.09 fm and with 𝑀 𝜋 ≈ 280 and 170 MeV. The truncated solver method with bias correction and the coherent source sequential propagator construction are used to cost-effectively achieve 𝑂⁡(1⁢0 5 ) measurements on each ensemble. Using these data, the analysis of two-point correlation functions is extended to include four states in the fits, and of three-point functions to three states. Control over excited-state contamination in the calculation of the nucleon mass, the mass gaps between excited states, and in the matrix elements is demonstrated by the consistency of estimates using this multistate analysis of the spectral decomposition of the correlation functions and from simulations of the three-point functions at multiple values of the source-sink separation. The results for all three charges, 𝑔 𝐴 , 𝑔 𝑆 , and 𝑔 𝑇 , are in good agreement with calculations done using the clover-on-HISQ lattice formulation with similar values of the lattice parameters.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Rainbow Scattering of Inert Gas Atoms on Aluminum and Silver Crystal Surfaces

Particle trajectories are calculated to study the rainbow scattering and the focusing of Ar atoms on the Al(111) and Ag(111) crystal surfaces and Ne, Ar, and Kr atoms on the Al(001) crystal surface. The rainbow-scattering-induced features in spectra are used to determine the thermal vibration amplitudes of atoms for the Al(111) and Ag(111) targets. These data agree with the data of independent measurements. The dependence of the position of a rainbow peak on the initial energy of atoms is used to find the atom–surface interaction potentials in the energy range of 0.3–70 eV for the case Ar–Ag and 3–45 eV for other cases. The values and the functional dependences of the potentials on the internuclear distance differ strongly from the well-known pair potential models. This difference is associated with the interaction of a projectile atom with the conduction electrons in a metal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗