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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo -7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA

Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neural Network Solver for Small Quantum Clusters

Machine learning approaches have recently been applied to the study of various problems in physics. Most of these studies are focused on interpreting the data generated by conventional numerical methods or the data on an existing experimental database. An interesting question is whether it is possible to use a machine learning approach, in particular a neural network, for solving the many-body problem. In this paper, we present a neural network solver for the single impurity Anderson model, the paradigm of an interacting quantum problem in small clusters. We demonstrate that the neural-network-based solver provides quantitative accurate results for the spectral function as compared to the exact diagonalization method. This opens the possibility of utilizing the neural network approach as an impurity solver for other many-body numerical approaches, such as the dynamical mean field theory.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Hydrogen irradiation-driven computational surface chemistry of lithium oxide and hydroxide

We have investigated, using molecular dynamics, the surface chemistry of hydrogen incident on the amorphous and crystalline lithium oxide and lithium hydroxide surfaces upon being slowed down by a collision cascade and retained in the amorphous surface of either Li 2 O or LiOH. We looked for the bonding of H to the resident structures in the surface to understand a possible chain of chemical reactions that can lead to surface transformation upon H atom impact. Our findings, using Density-Functional Theory (DFT) trained ReaxFF force field/electronegativity equalization method potentials, stress the importance of inclusion of polarization in the dynamics of a Li–O–H system, which is also illustrated by DFT energy minimization and quantum–classical molecular dynamics using tight binding DFT. The resulting polar-covalent chemistry of the studied systems is complex and very sensitive to the instantaneous positions of all atoms as well as the ratio of concentrations of various resident atoms in the surface.

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

Bayesian analysis of nucleon-nucleon scattering data in pionless effective field theory

We perform Bayesian model calibration of two-nucleon (NN) low-energy constants (LECs) appearing in an NN interaction based on pionless effective field theory (πEFT). The calibration is carried out for potentials constructed using naive dimensional analysis in NN relative momenta (p) up to next-to-leading order [NLO, O(p 2 )] and next-to-next-to-next-to-leading order [N3LO, O(p 4 )]. We consider two classes of pionless πEFT potential: one that acts in all partial waves and another that is dominated by s-wave physics. The two classes produce broadly similar results for calibrations to NN data up to E lab = 5 MeV. Our analysis accounts for the correlated uncertainties that arise from the truncation of the pionless πEFT. We simultaneously estimate both the πEFT LECs and the parameters that quantify the truncation error. This permits the first quantitative estimates of the pionless πEFT breakdown scale, Λ b : the 95% intervals are Λ b ∈[50.11,63.03] MeV at NLO and Λ b ∈[72.27,88.54] MeV at N3LO. Furthermore, invoking naive dimensional analysis for the NN potential, therefore, does not lead to consistent results across orders in pionless πEFT. This exemplifies the possible use of Bayesian tools to identify inconsistencies in a proposed EFT power counting.

Bayesian methods↗
DOE OSTI2022

Polyakov model in ’t Hooft flux background: a quantum mechanical reduction with memory

We construct a compactification of Polyakov model on T 2 × $\mathbb{R}$ down to quantum mechanics which remembers non-perturbative aspects of field theory even at an arbitrarily small area. Standard compactification on small T 2 × $\mathbb{R}$ possesses a unique perturbative vacuum (zero magnetic flux state), separated parametrically from higher flux states, and the instanton effects do not survive in the Born-Oppenheimer approximation. By turning on a background magnetic GNO flux in co-weight lattice corresponding to a non-zero ’t Hooft flux, we show that N-degenerate vacua appear at small torus, and there are N - 1 types of flux changing instantons between them. We construct QM instantons starting with QFT instantons using the method of replicas. For example, SU(2) gauge theory with flux reduces to the double-well potential where each well is a fractional flux state. Despite the absence of a mixed anomaly, the vacuum structure of QFT and the one of QM are continuously connected. We also compare the quantum mechanical reduction of the Polyakov model with the deformed Yang-Mills, by coupling both theories to TQFTs. In particular, we compare the mass spectrum for dual photons and energy spectrum in the QM limit. We give a detailed description of critical points at infinity in the semi-classical expansion, and their role in resurgence structure.

nonperturbative effects↗
DOE OSTI2024

(2 + δ)-dimensional theory of the electromechanics of lipid membranes: Electrostatics

The coupling of electric fields to the mechanics of lipid membranes gives rise to intriguing electromechanical behavior, as, for example, evidenced by the deformation of lipid vesicles in external electric fields. Electromechanical effects are relevant for many biological processes, such as the propagation of action potentials in axons and the activation of mechanically gated ion channels. Currently, a theoretical framework describing the electromechanical behavior of arbitrarily curved and deforming lipid membranes does not exist. Purely mechanical models commonly treat lipid membranes as two-dimensional surfaces, ignoring their finite thickness. While holding analytical and numerical merit, this approach cannot describe the coupling of lipid membranes to electric fields and is thus unsuitable for electromechanical models. In a sequence of articles, we derive an effective surface theory of the electromechanics of lipid membranes, called the (2 + δ)-dimensional theory, which has the advantages of surface descriptions while accounting for finite thickness effects. The present article proposes a generic dimension reduction procedure relying on low-order spectral expansions. This procedure is applied to the electrostatics of lipid membranes to obtain the (2 + δ)-dimensional theory that captures potential differences across and electric fields within lipid membranes. Finally, this model is tested on different geometries relevant for lipid membranes, showing good agreement with the corresponding three-dimensional electrostatics theory.

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

Heat transport in liquid water from first-principles and deep neural network simulations

In this work, we compute the thermal conductivity of water within linear response theory from equilibrium molecular dynamics simulations, by adopting two different approaches. In one, the potential energy surface (PES) is derived on the fly from the electronic ground state of density functional theory (DFT) and the corresponding analytical expression is used for the energy flux. In the other, the PES is represented by a deep neural network (DNN) trained on DFT data, whereby the PES has an explicit local decomposition and the energy flux takes a particularly simple expression. By virtue of a gauge invariance principle, established by Marcolongo, Umari, and Baroni, the two approaches should be equivalent if the PES were reproduced accurately by the DNN model. We test this hypothesis by calculating the thermal conductivity, at the GGA (PBE) level of theory, using the direct formulation and its DNN proxy, finding that both approaches yield the same conductivity, in excess of the experimental value by approximately 60%. Besides being numerically much more efficient than its direct DFT counterpart, the DNN scheme has the advantage of being easily applicable to more sophisticated DFT approximations, such as meta-GGA and hybrid functionals, for which it would be hard to derive analytically the expression of the energy flux. We find in this way that a DNN model, trained on meta-GGA (SCAN) data, reduces the deviation from experiment of the predicted thermal conductivity by about 50%, leaving the question open as to whether the residual error is due to deficiencies of the functional, to a neglect of nuclear quantum effects in the atomic dynamics, or, likely, to a combination of the two.

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

Theoretical Analysis of Resonant Tunneling Enhanced Field Emission

In this paper, we develop an exact analytical quantum theory for field emission from surfaces with a nearby quantum well, by solving the one-dimensional time-independent Schrödinger equation. The quantum well, which may be introduced by ions, atoms, nanoparticles, etc., is simplified as a square potential well with depth H, width d, and distance to the surface L. The theory is used to analyze the effects of the quantum well (d, H, and L), the cathode properties (work function W and Fermi energy E F ), and dc field F. It is found that the quantum well can lead to resonant tunneling enhanced field emission up to several orders of magnitude larger than that from bare cathode surfaces. In the meantime, the electron-emission-energy spectrum is significantly narrowed. The strong enhancement region is bounded by the conditions eFL + H ≥ W + C and eFL ≤ W, with e being the elementary charge (positive) and C a constant dependent on dc field F. It is also found that the linear shift of resonance peaks in the electron-emission-energy spectrum with dc field F follows ε p =ε p⁢0 –e⁢FL, with ε p⁢0 being approximately the eigenenergies for electrons confined in a square potential well without a dc field. Finally, the theory provides insights for the design of high-efficiency field emitters, which can produce a high current and highly collimated electron beams.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

A new interatomic potential for mixed Mg-Al-Ga-In spinels

While density functional theory (DFT) has become the de facto approach for accurate simulation of materials at the atomic scale, there are many aspects of materials that are simply out of reach of DFT methods. In particular, finite temperature properties such as diffusivities, the structure and properties of grain boundaries and interfaces, and the study of defect properties in complex alloys are computationally challenging for DFT methods. Recently, a new class of spinels in which three cations order over two sublattices was discovered. In order to predict the properties of these types of structures, classical potentials are a must. Here, in this work, we derive a new classical potential for Mg-bearing spinels in which the B cations are Al, Ga, and/or In. The potential does well in describing the DFT energetics of various spinel structures as a function of chemistry and inversion. In particular, it reproduces the thermodynamically favorable MgAlGaO 4 structure while correctly predicting that neither MgAlInO 4 nor MgGaInO 4 are stable. Further, it reproduces physical trends in elastic properties as compared against experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The Importance of a Moving Boundary Approach for Modeling the SEI Layer Growth to Predict Capacity Fade

One of the contributing factors to the aging of lithium-ion batteries is the growth of the solid-electrolyte interphase (SEI) layer. The growth of the SEI layer leads to the irreversible loss of lithium available for cycling and increases the resistance of the battery. Physics-based models in literature model the kinetically limited or solvent diffusion-limited growth. In such models, the interface resistance is a constant, and the contribution to the overpotential of the intercalation reaction from the SEI layer is considered to be ohmic. In this study, we propose a model that describes the growth of the SEI layer on the electrode surface as a moving interface. The transport of lithium ions and the solvent in the electrolyte are affected by this moving interface. The equations that govern the species transport and the potential drop across the SEI layer are derived from dilute solution theory and solved by transforming the coordinates of the moving boundary. The ion transport induces changes in the conductivity across the SEI layer, which affects the potential drop that arises due to its growth. The effects of this potential on capacity fade are studied over cycling the battery.

25 ENERGY STORAGE↗
DOE OSTI2025

Stable, Efficient Iron Electrodeposition via Anion-Directed Control of Fe(II) Coordination

Traditional steelmaking processes consume about 7% of the world’s energy supply, with reduction of iron oxides into iron via blast furnaces representing the most energy-demanding and capital-intensive step. To economize and modularize iron reduction processes, we aim to develop an electrodeposition technique to reduce aqueous iron ions to metallic iron. However, the hydrogen reduction reaction (HER) occurs at a more positive standard reduction potential than the iron reduction reaction. In addition, aqueous Fe(II) cations easily precipitate at mildly acidic conditions (pH ≥ 3), which limits the deposition efficiency and degrades deposit quality. To address these challenges, we first search for anions that have intermediate coordination strength with Fe(II) based on the hard-soft acid-base theory, trading a slightly more negative Fe(II) reduction potential for a considerably broader pH stability range. We select citrate with predicted intermediate coordination strength, in combination with more weakly coordinating anions (e.g., SO 4 2- , Cl - ) to control the coordination structure of Fe 2+ for improved electrolyte stability and electrodeposition behavior. We find that citrate coordination stabilizes Fe 2+ -based electrolytes at higher pH conditions (4.8–5.5), significantly extending their shelf life while also suppressing HER during Fe electrodeposition by orders of magnitude. To measure Faradaic efficiencies (FE), we developed a straightforward, titration-based methodology to quantify the amount of deposited iron regardless of the rate of concurrent HER. Although coordination between citrate and Fe 2+ decreases the reduction potential of Fe(II), high FE (≥98%) was achieved at 10 mA cm -2 . FE and achievable deposition rates are tunable by both concentration and the ratio of Fe 2+ to citrate. In all cases, Raman spectroscopy and X-ray diffraction (XRD) reveal that iron deposition in citrate-containing electrolytes suppresses iron oxide/hydroxide precipitation, in contrast to deposits generated in citrate-free electrolytes. Altogether, this work demonstrates that citrate-mediated anion coordination enables high-purity iron electrodeposition with increased FE, high current density, and improved electrolyte stability. This multi-anion coordination strategy provides a versatile framework for designing stable electrolyte and efficient metal electrodeposition.

coordination↗
DOE OSTI2023

Exact and Model Exchange-Correlation Potentials for Open-Shell Systems

The conventional approaches to the inverse density functional theory problem typically assume nondegeneracy of the Kohn–Sham (KS) eigenvalues, greatly hindering their use in open-shell systems. Here, we present a generalization of the inverse density functional theory problem that can seamlessly admit degenerate KS eigenvalues. Additionally, we allow for fractional occupancy of the Kohn–Sham orbitals to also handle noninteracting ensemble-v-representable densities, as opposed to just noninteracting pure-v-representable densities. We present the exact exchange-correlation (XC) potentials for six open-shell systems–four atoms (Li, C, N, and O) and two molecules (CN and CH 2 )–using accurate ground-state densities from configuration interaction calculations. We compare these exact XC potentials with model XC potentials obtained using nonlocal (B3LYP, SCAN0) and local/semilocal (SCAN, PBE, PW92) XC functionals. Although the relative errors in the densities obtained from these DFT functionals are of $O$(10 –3 to 10 –2 ), the relative errors in the model XC potentials remain substantially large–$O$(10 –1 to 10 0 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations

Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.

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

Laser spectroscopy of indium Rydberg atom bunches by electric field ionization

This work reports on the application of a novel electric field-ionization setup for high-resolution laser spectroscopy measurements on bunched fast atomic beams in a collinear geometry. In combination with multi-step resonant excitation to Rydberg states using pulsed lasers, the field ionization technique demonstrates increased sensitivity for isotope separation and measurement of atomic parameters over previous non-resonant laser ionization methods. The setup was tested at the Collinear Resonance Ionization Spectroscopy experiment at ISOLDE-CERN to perform high-resolution measurements of transitions in the indium atom from the 5s 2 5d 2 D 5/2 and 5s 2 5d 2 D 3/2 states to 5s 2 np 2 P and 5s 2 nf 2 F Rydberg states, up to a principal quantum number of n=72 . The extracted Rydberg level energies were used to re-evaluate the ionization potential of the indium atom to be 46,670.107(4)cm -1 . The nuclear magnetic dipole and nuclear electric quadrupole hyperfine structure constants and level isotope shifts of the 5s 2 5d 2 D 5/2 and 5s 2 5d 2 D 3/2 states were determined for 113,115 In. The results are compared to calculations using relativistic coupled-cluster theory. A good agreement is found with the ionization potential and isotope shifts, while disagreement of hyperfine structure constants indicates an increased importance of electron correlations in these excited atomic states. With the aim of further increasing the detection sensitivity for measurements on exotic isotopes, a systematic study of the field-ionization arrangement implemented in the work was performed at the same time and an improved design was simulated and is presented. The improved design offers increased background suppression independent of the distance from field ionization to ion detection.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

A tail of eternal inflation

Non-trivial inflaton self-interactions can yield calculable signatures of primordial non-Gaussianity that are measurable in cosmic surveys. We calculate the non-Gaussian corrections to Stochastic Inflation within the framework of Soft de Sitter Effective Theory, from which we derive the associated probability distribution for the scalar fluctuations. As a consequence of this new result, we show that the phase transition to slow-roll eternal inflation is often incalculable in these models. Instead, this transition is sensitive to the non-Gaussian tail of the distribution of scalar fluctuations, which probes physics inside the horizon, potentially beyond the cutoff scale of the Effective Field Theory of Inflation. We delineate the parameter space consistent with current observations and weak coupling at horizon crossing in which the large fluctuations relevant for eternal inflation can only be determined by appealing to a UV completion. We also argue that this breakdown of the perturbative description is required for the de Sitter entropy to reflect the number of de Sitter microstates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Glauber-theory analysis of nuclear reactions on a 12 C target with variational Monte Carlo wave functions

The application of Glauber theory has been playing an increasingly important role with the study of unstable or exotic nuclei. Its adaptation to medium and high-energy nucleus-nucleus collisions is severely limited because one has to evaluate the matrix elements of multiple-scattering operators. The extraction of physical observables has been done using ‘approximate’ Glauber theory whose validity is hard to evaluate. Here, we perform a full calculation of the matrix elements using Monte Carlo integration and analyze the elastic differential cross sections and the total reaction cross sections for p+¹²C, ⁴,⁶He+¹²C, and ¹²C+¹²C collisions. We use the variational Monte Carlo wave functions for ⁴,⁶He and ¹²C obtained by using realistic two- and three-nucleon potentials. We demonstrate the performance of the Glauber-theory calculations by comparing with available experimental data. We further discuss the accuracy of the conventional approximate methods in the light of the cumulant expansion for Glauber’s phase-shift function.

Horiuchi, W. [Osaka Metropolitan University (Japan↗
DOE OSTI2020

Identifying and Tuning the In Situ Oxygen-Rich Surface of Molybdenum Nitride Electrocatalysts for Oxygen Reduction

Rigorous in situ studies of electrocatalysts are required to enable the design of higher performing materials. Nonplatinum group metals for oxygen reduction reaction (ORR) catalysis containing light elements such as O, N, and C are known to be susceptible to both ex situ and in situ oxidation, leading to challenges associated with ex situ characterization methods. We have previously shown that the bulk O content plays an important role in the activity and selectivity of Mo–N catalysts, but further understanding of the role of composition and morphological changes at the surface is needed. Here, we report the measurement of in situ surface changes to a molybdenum nitride (MoN) thin film under ORR conditions using grazing incidence X-ray absorption and reflectivity. We show that the half-wave potential of MoN can be improved by ~90 mV by potential conditioning up to 0.8 V versus RHE. Utilizing electrochemical analysis, dissolution monitoring, and surface-sensitive X-ray techniques, we show that under moderate polarization (0.3–0.7 V vs RHE) there is local ligand distortion, O incorporation, and amorphization of the MoN surface, without changes in roughness. Furthermore, with a controlled potential hold procedure, we show that the surface changes concurrent with potential conditioning are stable under ORR relevant potentials. Conversely, at higher potentials (≥0.8 V vs RHE), the film incorporates O, dissolves, and roughens, suggesting that in this higher potential regime, the performance enhancements are due to increased access to active sites. Density functional theory calculations and Pourbaix analysis provide insights into film stability and O incorporation as a function of potential. These findings coupled with in situ electrochemical surface-sensitive X-ray techniques demonstrate an approach to studying nontraditional surfaces in which we can leverage our understanding of surface dynamics to improve performance with the rational, in situ tuning of active sites.

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

Thermal quasiparticle theory

The widely used thermal Hartree–Fock (HF) theory is generalized to include the effect of electron correlation while maintaining its quasi-independent-particle framework. An electron-correlated internal energy (or grand potential) is postulated in consultation with the second-order finite-temperature many-body perturbation theory (MBPT), which then dictates the corresponding thermal orbital (quasiparticle) energies in such a way that all fundamental thermodynamic relations are obeyed. The associated density matrix is of a one-electron type, whose diagonal elements take the form of the Fermi–Dirac distribution functions, when the grand potential is minimized. The formulas for the entropy and chemical potential are unchanged from those of Fermi–Dirac or thermal HF theory. The theory thus stipulates a finite-temperature extension of the second-order Dyson self-energy of one-particle many-body Green’s function theory and can be viewed as a second-order, diagonal, frequency-independent, thermal inverse Dyson equation. At low temperatures, the theory approaches finite-temperature MBPT of the same order, but it may outperform the latter at intermediate temperatures by including additional electron-correlation effects through orbital energies. Here, a physical meaning of these thermal orbital energies is proposed (encompassing that of thermal HF orbital energies, which has been elusive) as a finite-temperature version of Janak’s theorem.

74 ATOMIC AND MOLECULAR PHYSICS↗