Search NASA⌕ Search

SEARCH · Search NASA

Results for “ground structure”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11

A General Framework to Learn Tertiary Structure for Protein Sequence Characterization

During the past five years, deep-learning algorithms have enabled ground-breaking progress towards the prediction of tertiary structure from a protein sequence. Very recently, we developed SAdLSA, a new computational algorithm for protein sequence comparison via deep-learning of protein structural alignments. SAdLSA shows significant improvement over established sequence alignment methods. In this contribution, we show that SAdLSA provides a general machine-learning framework for structurally characterizing protein sequences. By aligning a protein sequence against itself, SAdLSA generates a fold distogram for the input sequence, including challenging cases whose structural folds were not present in the training set. About 70% of the predicted distograms are statistically significant. Although at present the accuracy of the intra-sequence distogram predicted by SAdLSA self-alignment is not as good as deep-learning algorithms specifically trained for distogram prediction, it is remarkable that the prediction of single protein structures is encoded by an algorithm that learns ensembles of pairwise structural comparisons, without being explicitly trained to recognize individual structural folds. As such, SAdLSA can not only predict protein folds for individual sequences, but also detects subtle, yet significant, structural relationships between multiple protein sequences using the same deep-learning neural network. The former reduces to a special case in this general framework for protein sequence annotation.

59 BASIC BIOLOGICAL SCIENCES↗

Lattice disorder effect on magnetic ordering of iron arsenides

This study investigates magnetic ordering temperature in nano- and mesoscale structural features in an iron arsenide. Although magnetic ground states in quantum materials can be theoretically predicted from known crystal structures and chemical compositions, the ordering temperature is harder to pinpoint due to potential local lattice variations that calculations may not account for. In this work we find surprisingly that a locally disordered material can exhibit a significantly larger Néel temperature (T N ) than an ordered material of precisely the same chemical stoichiometry. Here, a EuFe 2 As 2 crystal, which is a ‘122’ parent of iron arsenide superconductors, is found through synthesis to have ordering below T N = 195 K (for the locally disordered crystal) or T N = 175 K (for the ordered crystal). In the higher T N crystals, there are shorter planar Fe-Fe bonds [2.7692(2) Å vs. 2.7745(3) Å], a randomized in-plane defect structure, and diffuse scattering along the [00 L] crystallographic direction that manifests as a rather broad specific heat peak. For the lower T N crystals, the a-lattice parameter is larger and the in-plane microscopic structure shows defect ordering along the antiphase boundaries, giving a larger T N and a higher superconducting temperature (T c ) upon the application of pressure. First-principles calculations find a strong interaction between c-axis strain and interlayer magnetic coupling, but little impact of planar strain on the magnetic order. Neutron single-crystal diffraction shows that the low-temperature magnetic phase transition due to localized Eu moments is not lattice or disorder sensitive, unlike the higher-temperature Fe sublattice ordering. This study demonstrates a higher magnetic ordering point arising from local disorder in 122.

36 MATERIALS SCIENCE↗

Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery

Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.

3D structural interaction fingerprints↗

Nature of Excitons and Their Ligand-Mediated Delocalization in Nickel Dihalide Charge-Transfer Insulators

The fundamental optical excitations of correlated transition-metal compounds are typically identified with multielectronic transitions localized at the transition-metal site, such as d d transitions. In this vein, intense interest has surrounded the appearance of sharp, below-band-gap optical transitions, i.e., excitons, within the magnetic phase of correlated Ni 2 + van der Waals magnets. The interplay of magnetic and charge-transfer insulating ground states in Ni 2 + systems raises intriguing questions on the roles of long-range magnetic order and of metal-ligand charge transfer in the exciton nature, which inspired microscopic descriptions beyond typical d d excitations. Here we study the impact of charge transfer and magnetic order on the excitation spectrum of the nickel dihalides ( Ni X 2 , X = Cl , Br, and I) using Ni- L 3 edge resonant inelastic x-ray scattering (RIXS). In all compounds, we detect sharp excitations, analogous to the recently reported excitons, and assign them to spin-singlet multiplets of octahedrally coordinated Ni 2 + stabilized by intra-atomic Hund’s exchange. Additionally, we demonstrate that these excitons are dispersive using momentum-resolved RIXS. Our data evidence a ligand-mediated multiplet dispersion, which is tuned by the charge-transfer gap and independent of the presence of long-range magnetic order. This reveals the mechanisms governing nonlocal interactions of on-site d d excitations with the surrounding crystal or magnetic structure, in analogy to ground-state superexchange. These measurements thus establish the roles of magnetic order, self-doped ligand holes, and intersite-coupling mechanisms for the properties of d d excitations in charge-transfer insulators. Published by the American Physical Society 2024

2-dimensional systems↗

Controlling Noncollinear Ferromagnetism in van der Waals Metal–Organic Magnets

Van der Waals (vdW) magnets both allow exploration of fundamental 2D physics and offer a route toward exploiting magnetism in next generation information technology, but vdW magnets with complex, noncollinear spin textures are currently rare. We report here the syntheses, crystal structures, magnetic properties and magnetic ground states of four bulk vdW metal–organic magnets (MOMs): FeCl 2 (pym), FeCl 2 (btd), NiCl 2 (pym), and NiCl 2 (btd), pym = pyrimidine and btd = 2,1,3-benzothiadiazole. Using a combination of neutron diffraction and bulk magnetometry we show that these materials are noncollinear magnets. Although only NiCl 2 (btd) has a ferromagnetic ground state, we demonstrate that low-field hysteretic metamagnetic transitions produce states with net magnetization in zero-field and high coercivities for FeCl 2 (pym) and NiCl 2 (pym). By combining our bulk magnetic data with diffuse scattering analysis and broken-symmetry density-functional calculations, we probe the magnetic superexchange interactions, which when combined with symmetry analysis allow us to suggest design principles for future noncollinear vdW MOMs. These materials, if delaminated, would prove an interesting new family of 2D magnets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing correlated states with plasmons

Understanding the nature of strongly correlated states in flat-band materials (such as moiré heterostructures) is at the forefront of both experimental and theoretical pursuits. While magnetotransport, scanning probe, and optical techniques are often very successful in investigating the properties of the underlying order, the exact nature of the ground state often remains unknown. Here, we propose to leverage strong light-matter coupling present in the flat-band systems to gain insight through dynamical dielectric response into the structure of the many-body ground state. We argue that because of the enlargement of the effective lattice of the system arising from correlations, conventional long-range plasmon becomes “folded” to yield a multiband plasmon spectrum. We detail several mechanisms through which the structure of the plasmon spectrum and that of the dynamical dielectric response is susceptible to the underlying order, revealing valued insights such as the interaction-driven band gaps, spin-structure, and the order periodicity.

36 MATERIALS SCIENCE↗

Lifetime measurements in the even-even Cd 102 – 108 isotopes

The heaviest T z = 0 doubly-magic nucleus, Sn 100 , and the neighboring nuclei offer unique opportunities to investigate the properties of nuclear interaction. For instance, the structure of light-Sn nuclei has been shown to be affected by the delicate balance between nuclear-interaction components, such as pairing and quadrupole correlations. From Cd to Te, many common features and phenomena have been observed experimentally along the isotopic chains, leading to theoretical studies devoted to a more general and comprehensive study of the region. In this context, having only two proton holes in the Z = 50 shell, the Cd isotopes are expected to present properties similar to those found in the Sn isotopic chain. The aim of this work was to measure lifetimes of excited states in neutron-deficient nuclei in the vicinity of Sn 100 . Here, the neutron-deficient nuclei in the N ≈ Z ≈ 50 region were populated using a multinucleon transfer reaction with a Cd 106 beam and a Mo 92 target. The beamlike products were identified by the VAMOS + + spectrometer, while the γ rays were detected using the AGATA array. Lifetimes of excited states were determined using the recoil distance Doppler-shift method, employing the Cologne differential plunger. Lifetimes of low-lying states were measured in the even-mass Cd 102 – 108 isotopes. In particular, multiple states with excitation energy up to ≈ 3 MeV, belonging to various bands, were populated in Cd 106 via inelastic scattering. The transition strengths corresponding to the measured lifetimes were compared with those resulting from state-of-the-art beyond-mean-field calculations using the symmetry-conserving configuration-mixing approach. Conclusions: Despite the similarities in the electromagnetic properties of the low-lying states, there is a fundamental structural difference between the ground-state bands in the Z = 48 and Z = 50 isotopes. The comparison between experimental and theoretical results revealed a rotational character of the Cd nuclei, which have prolate-deformed ground states with β 2 ≈ 0.2 . At this deformation Z = 48 becomes a closed-shell configuration, which is favored with respect to the spherical one.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Entanglement and seniority

In quantum mechanics entanglement is the most striking phenomenon which has no counterpart in classical systems. Although, different approaches have already been developed to study correlations in the case of indistinguishable particles, the exploration of the so-called mode entanglement is still in its initial stage in nuclear physics. Study of mode-entanglement in the seniority model, derivation of analytic formulas for the one-body reduced density matrix of states with seniority $ν$ = 0, 1, 2, and $ν$ = 3, and also determination of the particle number dependence of the one-body reduced density matrix for arbitrary seniority. In addition, comparison of the predictions of the seniority model with the results of the shell model to gain insight into the structure and correlations of the ground and lowest yrast states. In the seniority model the analytic results are calculated using the quasi-spin formalism. The numerical shell model calculations are carried out in the standard shell model framework using an inert core. The applied realistic effective interactions are derived earlier using the $G$-matrix formalism. The density matrix renormalization group method is also applied in order to directly calculate the mode entropies. In the seniority model simple analytical expressions are given for the mode entropies. The peculiar behavior of the half-filled shells and the seniority-zero states are revealed. Numerical results are presented for the lightest stable calcium isotopes and for 94 Ru nucleus. For 94 Ru, the seniority model accounts for the 0$g$ 9/2 mode entropies, but seniority mixing is important for certain yrast states. Furthermore, interaction induced quantum fluctuations decrease the occupation of the 0$f$ 5/2 , 1$p$ 3/2 and 1$p$ 1/2 shells, and amount in non-negligible mode entropies on these shells, too, clearly outside the scope of the simple (0$g$ 9/2 ) 4 seniority model. The 0$f$ 7/2 shell-based seniority model is more accurate for the Ca isotopes, but seniority mixing is substantial for some 44 Ca yrast states, too. Mode and one-body entanglement entropies are useful tools to investigate the structure of quantum correlations in nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

TAMM: Tensor algebra for many-body methods

Tensor algebra operations such as contractions in computational chemistry consume a significant fraction of the computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. TAMM decouples the specification of the computation from the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM, whereas high-performance computing developers can direct their attention to various optimizations on the underlying constructs, such as efficient data distribution, optimized scheduling algorithms, and efficient use of intra-node resources (e.g., graphics processing units). The modular structure of TAMM allows it to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to the sustainable development of scalable ground- and excited-state electronic structure methods. We present case studies highlighting the ease of use, including the performance and productivity gains compared to other frameworks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simultaneous Optimization of Nuclear–Electronic Orbitals

Accurate modeling of important nuclear quantum effects, such as nuclear delocalization, zero-point energy, and tunneling, as well as non-Born-Oppenheimer effects, requires treatment of both nuclei and electrons quantum mechanically. The nuclear–electronic orbital (NEO) method provides an elegant framework to treat specified nuclei, typically protons, on the same level as the electrons. In conventional electronic structure theory, finding a converged ground state can be a computationally demanding task; converging NEO wavefunctions, due to their coupled electronic and nuclear nature, is even more demanding. Herein, we present an efficient simultaneous optimization method that uses the direct inversion in the iterative subspace method to simultaneously converge wavefunctions for both the electrons and quantum nuclei. In conclusion, benchmark studies show that the simultaneous optimization method can significantly reduce the computational cost compared to the conventional stepwise method for optimizing NEO wavefunctions for multicomponent systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Precise Modulation of CO 2 Sorption in Ti 8 Ce 2 –Oxo Clusters: Elucidating Lewis Acidity of the Ce Metal Sites and Structural Flexibility

Investigating the structure-property correlation in porous materials is a fundamental and consistent focus in various scientific domains, especially within sorption research. Metal oxide clusters with capping ligands, characterized by intrinsic cavities formed through specific solid-state packing, demonstrate significant potential as versatile platforms for sorption investigations due to their precisely tunable atomic structures and inherent long-range order. This study presents a series of Ti 8 Ce 2 -oxo clusters with subtle variations in coordinated linkers and explores their sorption behavior. Notably, Ti 8 Ce 2 -BA (BA denotes benzoic acid) manifests a distinctive two-step profile during CO 2 adsorption, accompanied by a hysteresis loop. This observation marks a new instance within the metal oxide cluster field. Of intrigue, the presence of unsaturated Ce(IV) sites was found to be correlated with the stepped sorption property. Moreover, the introduction of an electrophilic fluorine atom, positioned ortho or para to the benzoic acid, facilitated precise control over gate pressure and stepped sorption quantities. Advanced in-situ techniques systematically unraveled the underlying mechanism behind this unique sorption behavior. The findings elucidate that robust Lewis base-acid interactions are established between CO 2 molecules and Ce ions, consequently altering the conformation of coordinated linkers. Conversely, the F atoms primarily contribute to gate pressure variation by influencing the Lewis acidity of the Ce sites. This research advances the understanding in fabricating metal-oxo clusters with structural flexibility and provides profound insights into their host-guest interaction motifs. Furthermore, these insights hold substantial promise across diverse fields and offer valuable guidance for future adsorbent designs grounded in fundamental theories of structure-property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrical control of topological 3Q state in intercalated van der Waals antiferromagnet Co x -TaS 2

Van der Waals (vdW) magnets have opened a new avenue of opportunities encompassing various interesting phases. Co 1/3 TaS 2 –an intercalated metallic vdW antiferromagnet–is one of the latest additions to this growing list of materials due to its unique topologically nontrivial triple-Q (3Q) ground state. This 3Q tetrahedral structure, which critically depends on the Co content, yields the highest-density Skyrmion lattice with scalar spin chirality, resulting in a noticeable anomalous Hall effect. In this work, we demonstrate control of this topological phase via ionic gating. Using four Co x TaS 2 devices with different Co compositions, we show that ionic gating can cover the entire 3Q topological phase and reveal the nature of the thermodynamically inaccessible phase space. Another striking finding in our data is the existence of an adiabatic discontinuity in the phase boundary between the 3Q and 1Q phases. Our work constitutes one of the first examples of electrical control of scalar spin chirality using an antiferromagnetic metal.

Magnetic properties and materials↗

Phonon mixing in the charge density wave state of ScV6Sn6

Abstract Kagomé metals are widely recognized, versatile platforms for exploring topological properties, unconventional electronic correlations, magnetic frustration, and superconductivity. In the R V 6 Sn 6 family of materials ( R = Sc, Y, Lu), ScV 6 Sn 6 hosts an unusual charge density wave ground state as well as structural similarities with the A V 3 Sb 5 system ( A = K, Cs, Rb). In this work, we combine Raman scattering spectroscopy with first-principles lattice dynamics calculations to reveal phonon mixing processes in the charge density wave state of ScV 6 Sn 6 . In the low temperature phase, we find at least four new peaks in the vicinity of the V-containing totally symmetric mode near 240 cm −1 suggesting that the density wave acts to mix modes of P 6/ m m m and $$R\bar{3}m$$ R 3 ¯ m symmetry - a result that we quantify by projecting phonons of the high symmetry state onto those of the lower symmetry structure. We also test the stability of the short-range ordered density wave state under compression and propose that both physical and chemical pressure quench the effect. We discuss these findings in terms of symmetry and the structure-property trends that can be unraveled in this system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Complexity-calibrated benchmarks for machine learning reveal when prediction algorithms succeed and mislead

Abstract Recurrent neural networks are used to forecast time series in finance, climate, language, and from many other domains. Reservoir computers are a particularly easily trainable form of recurrent neural network. Recently, a “next-generation” reservoir computer was introduced in which the memory trace involves only a finite number of previous symbols. We explore the inherent limitations of finite-past memory traces in this intriguing proposal. A lower bound from Fano’s inequality shows that, on highly non-Markovian processes generated by large probabilistic state machines, next-generation reservoir computers with reasonably long memory traces have an error probability that is at least $$\sim 60\%$$ ∼ 60 % higher than the minimal attainable error probability in predicting the next observation. More generally, it appears that popular recurrent neural networks fall far short of optimally predicting such complex processes. These results highlight the need for a new generation of optimized recurrent neural network architectures. Alongside this finding, we present concentration-of-measure results for randomly-generated but complex processes. One conclusion is that large probabilistic state machines—specifically, large $$\epsilon$$ ϵ -machines—are key to generating challenging and structurally-unbiased stimuli for ground-truthing recurrent neural network architectures.

97 MATHEMATICS AND COMPUTING↗

Synthesis pathways to thin films of stable layered nitrides

Controlled synthesis of metastable materials away from equilibrium is of interest in materials chemistry. Thin-film deposition methods with rapid condensation of vapour precursors can readily synthesize metastable phases but often struggle to yield the thermodynamic ground state. Growing thermodynamically stable structures using kinetically limited synthesis methods is important for practical applications in electronics and energy conversion. Here, in this study, we reveal a synthesis pathway to thermodynamically stable, ordered layered ternary nitride materials, and discuss why disordered metastable intermediate phases tend to form. We show that starting from elemental vapour precursors leads to a 3D long-range-disordered MgMoN 2 thin-film metastable intermediate structure, with a layered short-range order that has a low-energy transformation barrier to the layered 2D-like stable structure. This synthesis approach is extended to ScTaN 2 , MgWN 2 and MgTa 2 N 3 , and may lead to the synthesis of other layered nitride thin films with unique semiconducting and quantum properties.

36 MATERIALS SCIENCE↗

Metamagnetism of few-layer topological antiferromagnets

MnBi 2 Te 4 (MBT) materials are a promising class of antiferromagnetic topological insulators whose films provide access to novel and technologically important topological phases, including quantum anomalous Hall states and axion insulators. MBT device behavior is expected to be sensitive to the various collinear and noncollinear magnetic phases that are accessible in applied magnetic fields. Here, we use classical Monte Carlo simulations and electronic structure models to calculate the ground state magnetic phase diagram as well as topological and optical properties for few-layer films with up to six septuple layers. Using magnetic interaction parameters appropriate for MBT, we find that it is possible to prepare a variety of different magnetic stacking sequences, some of which have sufficient symmetry to disallow nonreciprocal optical response and Hall transport coefficients. Other stacking arrangements do yield large Faraday and Kerr signals, even when the ground state Chern number vanishes.

36 MATERIALS SCIENCE↗

Importance of finite-size corrections for accurate ab initio modeling of carrier capture at semiconductor defects: A case study of substitutional C N in GaN

In ab initio studies of carrier-capture processes in defective semiconductor materials, the single-effective-mode formalism and the static-coupling approximation have become the predominant theoretical approaches for determining carrier-capture coefficients. The single-mode formalism relies on accurate nonequilibrium defect energies obtained from density-functional theory (DFT), where required inputs are a series of configurationally displaced, defect-containing supercells obtained using an interpolative ansatz, and where the DFT outputs are corresponding total energies that have traditionally been postprocessed using a long-established ground-state formulation of finite-size corrections and defect-formation energies. This formulation remains commonly used even though the defects that form a configuration-coordinate (CC) diagram typically exist as structures that are displaced from the ground state. To remedy this inconsistency, Kumagai has recently proposed novel methods for implementing finite-size corrections specifically intended for DFT calculations of the defect energies used to construct CC diagrams and implement the single-mode formalism [Y. Kumagai, Phys. Rev. B 107, L220101 (2023)]. Kumagai's approach builds on the latest finite-size-correction methods introduced to describe vertical charge-state transitions for charge-localizing point defects in semiconductors and insulators [T. Gake et al., Phys. Rev. B 101, 020102 (2020); S. Falletta et al., Phys. Rev. B 102, 041115 (2020)]. The newly identified finite-size artifact treated in these studies is the polarization charge induced on a configurationally frozen defect and its subsequent interaction with a vertical transition in charge state. In this work, we evaluate Kumagai's proposed methodology by applying it in a high-precision DFT study of carrier capture by substitutional C N in GaN, a well-characterized and technologically relevant defect and material. We have rigorously calculated C N defect energies across various supercell sizes for each defect configuration and charge state on the hole-capture CC diagram of C N (𝑞=−1), enabling a direct comparison of the slopes of the defect energies versus inverse cell size with those predicted by Kumagai. The most consequential prediction of Kumagai's method is that these slopes distinctly vary as the square of the linear-interpolation parameter used to construct the nonequilibrium defect configurations. Our results quantitatively support this prediction. Moreover, with these new finite-size corrections and multiple-cell-size DFT calculations in place, we find that the classical energy barrier for hole capture by C N (𝑞=−1) in GaN decreases to 0.092–0.127 eV. This finding confirms the recent ≈ 0.1 eV prediction of Reshchikov based on the weak temperature dependence for hole capture observed in photoluminescence experiments [M. A. Reshchikov, J. Appl. Phys. 129, 121101 (2021)]. These results stand in stark contrast to previously calculated barriers of 0.486 and 0.73 eV, which also used the single-mode formalism but were obtained by instead using ground-state-based finite-size corrections. Our reduced classical barrier for capture increases the temperature-dependent hole-capture coefficient of a C N (𝑞=−1) defect by more than two to four orders of magnitude for temperatures of 100–600 K, compared to the previous 0.486 eV results. While other defects may not be as dramatically affected as here, we suggest that incorporating proper finite-size corrections for the vertical-transition-like states embedded within CC diagrams is an essential, yet previously unrecognized, component of accurate modeling of carrier-capture when using the single-effective-mode formalism.

dielectric properties↗