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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Electronic Excitations in Complex Molecular Environments: Many-Body Green’s Functions Theory in VOTCA-XTP

Many-body Green’s functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identity techniques, the code is designed specifically for nonperiodic systems. Application to a small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2 to 8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a binucleobase CT exciton. Furthermore, the results show that VOTCA-XTP’s GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.

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

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Chemical Durability and Dissolution Kinetics of Iodoapatite in Aqueous Solutions

Understanding the long-term release of radionuclides from nuclear waste to the environment is critical for public acceptance and sustainability of nuclear energy. Iodoapatite, a synthetic material similar to mineral vanadinite proposed for radioactive iodine-129 immobilization, is employed in this study as a model system for iodine waste forms and ceramic waste forms in general to understand its long-term chemical durability. Semidynamic leaching experiments were performed in cap-sealed Teflon vessels to evaluate the chemical durability at temperatures from 20 to 90 degrees C and pH values from 4 to 9 using deionized water and pH buffer solutions. The leachates were analyzed using inductively coupled plasma-mass spectrometry. The leached surfaces were examined by X-ray diffraction, scanning electron microscopy, and Raman spectroscopy. Effects of test variables including surface-to-volume ratio, leachant replacement interval, and environmental variables including temperature and pH on the dissolution rate were systematically investigated. The activation energy of the dissolution was 16.9 ± 1.5 kJ/mol for the matrix elements and 34.4 ± 3.9 kJ/mol for the diffusive iodine release. The order of the pH effect on the dissolution rate as a power law exponent was 0.87 ± 0.08. The effect of the surface-to-volume ratio and replacement interval was approximated by a single exponential function rise to maximum. Fully parametrized models were then combined to predict iodine release rate under various conditions. The result suggests that the long-term iodine release is controlled by iodide diffusion when the matrix dissolution rate is very low in near neutral pH solutions and by matrix dissolution when the dissolution rate is high at low pH. The present study demonstrates a mechanistic approach to parametrize models that can be used to evaluate the performance of nuclear waste forms under various disposal environments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Engineering Robust Metallic Zero-Mode States in Olympicene Graphene Nanoribbons

Metallic graphene nanoribbons (GNRs) represent a critical component in the toolbox of low-dimensional functional materials technology serving as 1D interconnects capable of both electronic and quantum information transport. The structural constraints imposed by on-surface bottom-up GNR synthesis protocols along with the limited control over orientation and sequence of asymmetric monomer building blocks during the radical step-growth polymerization have plagued the design and assembly of metallic GNRs. Here, we report the regioregular synthesis of GNRs hosting robust metallic states by embedding a symmetric zero-mode (ZM) superlattice along the backbone of a GNR. Tight-binding electronic structure models predict a strong nearest-neighbor electron hopping interaction between adjacent ZM states, resulting in a dispersive metallic band. First-principles density functional theory-local density approximation calculations confirm this prediction, and the robust, metallic ZM band of olympicene GNRs is experimentally corroborated by scanning tunneling spectroscopy.

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

Structural phase transition, s ± -wave pairing, and magnetic stripe order in bilayered superconductor La 3 Ni 2 O 7 under pressure

Motivated by the recently discovered high-T c superconductor La 3 Ni 2 O 7 , we comprehensively study this system using density functional theory and random phase approximation calculations. At low pressures, the Amam phase is stable, containing the Y 2- mode distortion from the Fmmm phase, while the Fmmm phase is unstable. Because of small differences in enthalpy and a considerable Y 2- mode amplitude, the two phases may coexist in the range between 10.6 and 14 GPa, beyond which the Fmmm phase dominates. In addition, the magnetic stripe-type spin order with wavevector (π, 0) was stable at the intermediate region. Pairing is induced in the s ± -wave channel due to partial nesting between the M = (π, π) centered pockets and portions of the Fermi surface centered at the X = (π, 0) and Y = (0, π) points. This resembles results for iron-based superconductors but has a fundamental difference with iron pnictides and selenides. Moreover, our present efforts also suggest La 3 Ni 2 O 7 is qualitatively different from infinite-layer nickelates and cuprate superconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Machine-learning-based spectral methods for partial differential equations

Spectral methods are an important part of scientific computing’s arsenal for solving partial differential equations (PDEs). However, their applicability and effectiveness depend crucially on the choice of basis functions used to expand the solution of a PDE. The last decade has seen the emergence of deep learning as a strong contender in providing efficient representations of complex functions. In the current work, we present an approach for combining deep neural networks with spectral methods to solve PDEs. In particular, we use a deep learning technique known as the Deep Operator Network (DeepONet) to identify candidate functions on which to expand the solution of PDEs. We have devised an approach that uses the candidate functions provided by the DeepONet as a starting point to construct a set of functions that have the following properties: (1) they constitute a basis, (2) they are orthonormal, and (3) they are hierarchical, i.e., akin to Fourier series or orthogonal polynomials. We have exploited the favorable properties of our custom-made basis functions to both study their approximation capability and use them to expand the solution of linear and nonlinear time-dependent PDEs. The proposed approach advances the state of the art and versatility of spectral methods and, more generally, promotes the synergy between traditional scientific computing and machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

First-principles molecular dynamics simulation of the Ca 2 UO 2 (CO 3 ) 3 complex in water

Recent experiments have shown that the neutral Ca 2 UO 2 (CO 3 ) 3 complex is the dominant species of uranium in many uranyl-containing streams. However, the structure and solvation of such a species in water has not been investigated from first principles. Herein we present a first principles molecular dynamics perspective of the Ca 2 UO 2 (CO 3 ) 3 complex in water based on density functional theory and Born–Oppenheimer approximation. We find that the Ca 2 UO 2 (CO 3 ) 3 complex is very stable in our simulation timeframe for three different concentrations considered and that the key distances from our simulation are in good agreement with the experimental data from extended X-ray absorption fine structure (EXAFS) spectroscopy. More important, we find that the two Ca ions bind differently in the complex, as a result of the hydrogen-bonding network around the whole complex. Furthermore, this finding invites confirmation from time-resolved EXAFS and has implications in understanding the dissociative equilibrium of the Ca 2 UO 2 (CO 3 ) 3 complex in water.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Rational design of super-alkalis and their role in CO 2 activation

Super-alkalis are clusters of atoms. With ionization potentials smaller than those of the alkali atoms, they are playing an increasing role in chemistry as highlighted by recent applications in solar cells as well as in Li-ion batteries. For the past 40 years superalkalis were designed using inorganic elements with the sp orbital character. Here, we show that a large class of superalkalis composed of only simple metal atoms, transition metal complexes as well as organic molecules can be designed by making use of electron counting rules beyond the octet rule. Examples include Al3+, Mn(B3N3H6)2+, B9C3H12+, and C5NH6+ which obey the jellium shell closure rule, the 18-electron rule, the Wade–Mingos rule, and Hückel's aromatic rule, respectively. We further show that the ability of superalkalis to transfer an electron easily can be used to activate a CO2 molecule by transforming it from a linear to a bent structure. These results, based on density functional theory with generalized gradient approximation for exchange–correlation potential, open the door to a new class of catalysts for CO2 activation.

Zhao, Tianshan↗
DOE OSTI2016

Magnetic properties of bimetallic clusters composed of Gd and transition metals

Gadolinium, a rare earth metal, is ferromagnetic, while Mn, a transition metal atom, is antiferromagnetic in the bulk phase. Clusters of these elements, however, share some common properties; both exhibit ferrimagnetic behavior and maintain magnetic moments close to their free atomic value. Using density functional theory and generalized gradient approximation for exchange and correlation, we have studied the magnetic properties of bimetallic clusters composed of Gd and Mn to see if they show unusual behavior. The coupling between Gd and Mn spins is found to be antiferromagnetic, while that between Mn atoms is ferromagnetic. Moreover, the bonding between Gd and Mn atoms is stronger than that between the Gd atoms or Mn atoms, thus enabling the possibility of creating more stable magnetic particles. In conclusion, a systematic study of the magnetic and binding properties of clusters composed of Gd atom and other transition metal atoms such as V, Sc, Ti, Cr, Fe, and Co is also carried out to probe the effect of 3 d -orbital occupation on magnetic coupling.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Ultrarelativistic bound states in the spherical well

We address an eigenvalue problem for the ultrarelativistic (Cauchy) operator (−Δ){sup 1/2}, whose action is restricted to functions that vanish beyond the interior of a unit sphere in three spatial dimensions. We provide high accuracy spectral data for lowest eigenvalues and eigenfunctions of this infinite spherical well problem. Our focus is on radial and orbital shapes of eigenfunctions. The spectrum consists of an ordered set of strictly positive eigenvalues which naturally splits into non-overlapping, orbitally labelled E{sub (k,l)} series. For each orbital label l = 0, 1, 2, …, the label k = 1, 2, … enumerates consecutive lth series eigenvalues. Each of them is 2l + 1-degenerate. The l = 0 eigenvalues series E{sub (k,0)} are identical with the set of even labeled eigenvalues for the d = 1 Cauchy well: E{sub (k,0)}(d = 3) = E{sub 2k}(d = 1). Likewise, the eigenfunctions ψ{sub (k,0)}(d = 3) and ψ{sub 2k}(d = 1) show affinity. We have identified the generic functional form of eigenfunctions of the spherical well which appear to be composed of a product of a solid harmonic and of a suitable purely radial function. The method to evaluate (approximately) the latter has been found to follow the universal pattern which effectively allows to skip all, sometimes involved, intermediate calculations (those were in usage, while computing the eigenvalues for l ≤ 3).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Detecting coherent core-hole wave-packet dynamics in N 2 by time- and angle-resolved inner-shell photoelectron spectroscopy

Here, we introduce an imaging technique to follow core-hole wave-packet oscillations in the nitrogen molecule. In this scheme, an attosecond x-ray pulse core-ionizes the nitrogen molecule and a subsequent attosecond x-ray pulse probes the evolution of the electron dynamics. We can image the oscillation of the core-hole between the two atomic sites by measuring the angular correlation between photoelectrons. Analytical relations for the angular correlation are derived based on the plane-wave approximation for the photoelectron wave function. We confirm these results with a scattering calculation for the photoelectron wave function. The feasibility of the experimental realization of this scheme is discussed in light of current and future capabilities of x-ray free-electron lasers.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches

Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and their induced asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. In this work, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic timescale separation; the Franck-Condon method, which includes dynamical effects but only at the harmonic level; as well as the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.

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

PyFLOSIC: Python-based Fermi–Löwdin orbital self-interaction correction

We present pyflosic, an open-source, general-purpose python implementation of the Fermi–Löwdin orbital self-interaction correction (FLO-SIC), which is based on the python simulation of chemistry framework (pyscf) electronic structure and quantum chemistry code. Thanks to pyscf, pyflosic can be used with any kind of Gaussian-type basis set, various kinds of radial and angular quadrature grids, and all exchange-correlation functionals within the local density approximation, generalized-gradient approximation (GGA), and meta-GGA provided in the libxc and xcfun libraries. A central aspect of FLO-SIC is the Fermi-orbital descriptors, which are used to estimate the self-interaction correction. Importantly, they can be initialized automatically within pyflosic; they can also be optimized within pyflosic with an interface to the atomic simulation environment, a python library that provides a variety of powerful gradient-based algorithms for geometry optimization. Although pyflosic has already facilitated applications of FLO-SIC to chemical studies, it offers an excellent starting point for further developments in FLO-SIC approaches, thanks to its use of a high-level programming language and pronounced modularity.

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

Shock compression of single-crystal austenitic FeCr18Ni12.5 stainless steel to 60 GPa

We measured the austenitic FeCr18Ni12.5 stainless steel Hugoniot as a function of crystallographic direction to approximately 60 GPa. We shock-compressed FeCr18Ni12.5 samples oriented along $\langle$100$\rangle$, $\langle$110$\rangle$, and $\langle$111$\rangle$ to mean stresses ranging 30.5–58.1 GPa via Ta plate impact in a large-bore powder gun and measured the free-surface velocities with laser interferometry. We unambiguously observed the largest post-shock free-surface velocity along $\langle$100$\rangle$ in each experiment, which consequently produced the lowest shock velocity along that orientation. However, the propagation of experimental uncertainties through the impedance matching scheme used to compute the shock velocity produced sufficient uncertainty overlap to preclude definitive conclusion of Hugoniot anisotropy.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Effects of artificial collisions, filtering, and nonlocal closure approaches on Hermite-based Vlasov–Poisson simulations

Kinetic simulations of collisionless plasmas are computationally challenging due to phase-space mixing and filamentation, resulting in fine-scale velocity structures. This study compares three methods developed to reduce artifacts related to limited velocity resolution in Hermite-based Vlasov–Poisson simulations: artificial collisions, filtering, and nonlocal closure approaches. We evaluate each method's performance in approximating the linear kinetic response function and suppressing recurrence in linear and nonlinear regimes. Numerical simulations of Landau damping demonstrate that artificial collisions, particularly higher orders of the Lenard-Bernstein collisional operator, most effectively recover the correct damping rate across a range of wavenumbers. Moreover, Hou-Li filtering and nonlocal closures underdamp high wavenumber modes in linear simulations, and the Lenard-Bernstein collisional operator overdamps low wavenumber modes in both linear and nonlinear simulations. This study demonstrates that hypercollisions offer a robust approach to kinetic simulations, accurately capturing collisionless dynamics with limited velocity resolution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew–Burke–Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). In this work, we investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH 3 O) or hydroxymethyl (CH 2 OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C–H and O–H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C–H and O–H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C–H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C–H bond of methanol is more facile than the O–H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O–H bond activation is enhanced, becoming slightly more facile than C–H bond activation.

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

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Abstract Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

Salgado-Salazar, Catalina↗
DOE OSTI2021

Impacts of random filling on spin squeezing via Rydberg dressing in optical clocks

Here, we analyze spin squeezing via Rydberg dressing in optical lattice clocks with random fractional filling. We compare the achievable clock stability in different lattice geometries, including unity-filled tweezer clock arrays and fractionally filled lattice clocks with varying dimensionality. We provide practical considerations and useful tools in the form of approximate analytical expressions and fitting functions to aid in the experimental implementation of Rydberg-dressed spin squeezing. We demonstrate that spin squeezing via Rydberg dressing in one-, two-, and three-dimensional optical lattices can provide significant improvements in stability in the presence of random fractional filling.

74 ATOMIC AND MOLECULAR PHYSICS↗