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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗
DOE OSTI2023

Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics

Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. Here we show that existing force fields that place all non-Coulomb forces on the Drude core and none on the shell inadvertently couple the dipole to non-Coulombic forces. This introduces errors where interactions with neutral particles can erroneously induce atomic polarization, leading to spurious polarizations in the absence of an electric field, exacerbating violations of equipartition in the employed Carr–Parinello scheme. A suitable symmetrization of the interaction potential that correctly splits the force between the Drude core and shell can correct this shortcoming, improving the stability and numerical performance of Drude oscillator-based simulations. The symmetrization procedure is straightforward and only requires the rescaling of a few force field parameters.

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

Three-dimensional atomic packing in amorphous solids with liquid-like structure

Liquids and solids are two fundamental states of matter. However, our understanding of their three-dimensional atomic structure is mostly based on physical models. Here we use atomic electron tomography to experimentally determine the three-dimensional atomic positions of monatomic amorphous solids, namely a Ta thin film and two Pd nanoparticles. We observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Instead of forming icosahedra, the majority of pentagonal bipyramids arrange into pentagonal bipyramid networks with medium-range order. Molecular dynamics simulations further reveal that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. Furthermore, these results expand our understanding of the atomic structures of amorphous solids and will encourage future studies on amorphous–crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Fermionic quantum processing with programmable neutral atom arrays

Simulating the properties of many-body fermionic systems is an outstanding computational challenge relevant to material science, quantum chemistry, and particle physics.-5.4pc]Please note that the spelling of the following author names in the manuscript differs from the spelling provided in the article metadata: D. González-Cuadra, D. Bluvstein, M. Kalinowski, R. Kaubruegger, N. Maskara, P. Naldesi, T. V. Zache, A. M. Kaufman, M. D. Lukin, H. Pichler, B. Vermersch, Jun Ye, and P. Zoller. The spelling provided in the manuscript has been retained; please confirm. Although qubit-based quantum computers can potentially tackle this problem more efficiently than classical devices, encoding nonlocal fermionic statistics introduces an overhead in the required resources, limiting their applicability on near-term architectures. In this work, we present a fermionic quantum processor, where fermionic models are locally encoded in a fermionic register and simulated in a hardware-efficient manner using fermionic gates. We consider in particular fermionic atoms in programmable tweezer arrays and develop different protocols to implement nonlocal gates, guaranteeing Fermi statistics at the hardware level. We use this gate set, together with Rydberg-mediated interaction gates, to find efficient circuit decompositions for digital and variational quantum simulation algorithms, illustrated here for molecular energy estimation. Finally, we consider a combined fermion-qubit architecture, where both the motional and internal degrees of freedom of the atoms are harnessed to efficiently implement quantum phase estimation as well as to simulate lattice gauge theory dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

The Debye-Waller factor of disordered solids: The case for amorphous silicon

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (α-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in α-Si networks. It has been observed that the MSDs associated with tetrahedrally bonded Si atoms are considerably lower than their dangling-bond counterparts—originating from isolated and vacancy-induced clustered defects—and those on the surface of microvoids, leading to an asymmetric non-Gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in α-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of α-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of α-Si at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Ab initio studies of the impact of the Debye-Waller factor on the structural and dynamical properties of amorphous semiconductors: The case of a-Si

This paper presents a first-principles study of the Debye-Waller factor and the Debye temperature for amorphous silicon (a-Si) from lattice-dynamical calculations and direct molecular-dynamics simulations using density-functional theory (DFT). The effects of temperature and structural disorder on the intensity of the diffraction maxima and the vibrational mean-square displacement (MSD) of Si atoms are studied in the harmonic approximation, with particular emphasis on the bond-length disorder, the presence of coordination defects, and microvoids in a-Si networks. It has been observed that the MSDs associated with tetrahedrally-bonded Si atoms are considerably lower than their dangling-bond counterparts – originating from isolated and vacancy-induced clustered defects – and those on the surface of microvoids, leading to an asymmetric non-gaussian tail in the distribution of atomic displacements. An examination of the effect of anharmonicity on the MSD at high temperatures using direct ab initio molecular-dynamics simulations (without the harmonic approximation) suggests that the vibrational motion in a-Si is practically unaffected by anharmonic effects at temperatures below 400 K, as far as the present DFT calculations are concerned. The Debye temperature of a-Si is found to be in the range of 488–541 K from specific-heat and MSD calculations using first-principles lattice-dynamical calculations in the harmonic approximation, which matches closely with the experimental value of 487–528 K obtained from specific-heat measurements of a-Si at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2026

An Atom-Precise Approach to Damp First-Order Phase Transitions and Its Implications for Neuromorphic Signal Processing

Neuromorphic computing inspired by mammalian intelligence aims to emulate the nonlinear dynamics of biological neurons and synapses to achieve fast, low-energy, and highly efficient information processing. Brain-inspired computing relies on the design and discovery of materials exhibiting nonlinear current–voltage profiles, frequently underpinned by electronic state transitions, to achieve spiking neurons and dynamically tunable synapses. A signature challenge in the design of artificial neurons is controlling the steepness of first-order transitions in active elements, as abrupt transitions are at risk of driving unstable voltage and temperature oscillations, which result in catastrophic device failure. A critical knowledge gap is the lack of structure–function correlations mapping the composition and atomistic structure of crystalline solids to nonlinear dynamical response characteristics. Here, we address the key question of how modification of atomistic structure correlates with alteration of neuron-like functionality. Constructing oscillator circuits from millimeter-scale single crystals enables high-resolution atomic structure solutions, which we use to demonstrate that the selective positioning of Pb cations modifies charge ordering along a one-dimensional CuxV2O5 framework even at low insertion stoichiometries, thereby providing an atom-precise design parameter for damping first-order transitions. We use temperature-variant X-ray diffraction and X-ray spectroscopy to elucidate the suppression of Cu-ion shuttling based on the precise positioning of Pb ions in seven-coordinated tunnel interstitial sites as the mechanistic basis for transition broadening, thus bridging a critical gap between statistical mechanics and quantum chemical descriptions of phase transitions. Such mechanistic understanding thus paves the way to site-selective modification strategies for modulating the sharpness of first-order transitions, with an exemplary demonstration here in tuning neuronal signal processing.

Crystal structure↗
DOE OSTI2023

Role of three-body dynamics in nucleon-deuteron correlation functions

Correlation functions of hadrons can be accessed in high-energy collisions of atomic nuclei, revealing information about the underlying interaction. This work complements experimental efforts to study nucleon-deuteron Nd—with N=p (proton) or N=n (neutron)—correlations with theory evaluations using different techniques. The correlation functions C nd and C pd are calculated based on a scattering wave function, extending previous benchmarks for the Nd scattering matrix to this new observable. We use hyperspherical harmonics and Faddeev techniques with one of the widely used nucleon-nucleon (NN) interactions, the Argonne v18 potential. Moreover, in the low-energy region we perform additional calculations in the framework of pionless effective field theory. The pd correlation function is computed in the large-energy region to make contact with a recent measurement by the ALICE Collaboration. We show that the scattering wave function has the proper dynamical input to describe an initial rise and subsequent oscillations of C pd as a function of the energy. Effects on the observables using different NN and three-nucleon potentials are evaluated with the conclusion that variations of around 2% are observed. Although these effects are small, future measurements can go beyond this accuracy, allowing for new detailed studies of strong interaction in light nuclear systems. Furthermore, the present study supports the current efforts devoted to the measurement of correlation functions in systems dominated by the strong interactions, such as pd, ppp, Λd, and ppΛ.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Towards a multiscale approach for understanding irradiation induced swelling and creep in 316 stainless steels - A coupled cluster dynamics and crystal plasticity approach

Structural materials undergo mechanical degradation, in part due to irradiation-induced swelling and creep, under nuclear reactor conditions. While swelling results from the migration and clustering of irradiation-induced atomic-scale mobile defects, the interaction of mesoscale dislocations with these defects causes creep deformation. A coupled crystal plasticity (CP) and mean-field cluster dynamics (CD) approach is presented to investigate the effect of irradiation on the long-term mechanical behavior of 316 stainless steel, which are under consideration for use in nuclear reactors. The temporal evolution of Frenkel pairs and extended defect population, under a chosen irradiation flux and temperature, is predicted using the CD model. The impact of the irradiation defects on the stress state, and the resulting dislocation-mediated inelastic deformation, is modeled concurrently with the CP model. The inelastic deformation is irradiation flux dependent, and early-stage defect evolution determines the later-stage mechanical behavior in 316 stainless steel.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Evaluation of δ-Phase ZrH1.4 to ZrH1.7 Thermal Neutron Scattering Laws Using Ab Initio Molecular Dynamics Simulations

Zirconium hydride is commonly used for next-generation reactor designs due to its excellent hydrogen retention capacity at temperatures below 1000 K. These types of reactors operate at thermal neutron energies and require accurate representation of thermal scattering laws (TSLs) to optimize moderator performance and evaluate the safety indicators for reactor design. In this work, we present an atomic-scale representation of sub-stoichiometric ZrH2−x(0.3≤x≤0.6), which relies on ab initio molecular dynamics (AIMD) in tandem with velocity auto-correlation (VAC) analysis to generate phonon density of states (DOS) for TSL development. The novel NJOY+NCrystal tool, developed by the European Spallation Source community, was utilized to generate the TSL formulations in the A Compact ENDF (ACE) format for its utility in neutron transport software. First, stoichiometric zirconium hydride cross sections were benchmarked with experiments. Then sub-stoichiometric zirconium hydride TSLs were developed. Significant deviations were observed between the new δ-phase ZrH2−x TSLs and the TSLs in the current ENDF release. It was also observed that varying the hydrogen vacancy defect concentration and sites did not cause as significant a change in the TSLs (e.g., ZrH1.4 vs. ZrH1.7) as was caused by the lattice transformation from ϵ- to δ-phase.

42 ENGINEERING↗
DOE OSTI2021

Single-Atom Metal Oxide Sites as Traps for Charge Separation in the Zirconium-Based Metal–Organic Framework NDC–NU-1000

Solvothermal deposition in metal–organic frameworks (MOFs) can be utilized to mount single-metal-atom catalytic species at chemically reactive sites on hexa-Zr(IV)-oxy(oxo,hydroxo,aqua) nodes in nanoscale crystallites of the MOF NDC-NU-1000 in a self-limiting fashion. Upon photoexcitation of the 1,3,6,8-tetrakis( p -benzoato)pyrene chromophores of the parent framework, charge transfer may occur between the chromophores and the installed heterometal sites. Extended X-ray absorption fine structure studies revealed the single-atom nature of the installed species. A combination of steady-state and ultrafast optical spectroscopy was utilized to uncover evidence of a charge-separated (CS) state arising in the metalated samples. The relevant dynamics were characterized with transient photoluminescence and femtosecond transient absorption spectroscopy. Here, we find that a titanium-oxy single atom site gives rise to the longest-lived CS species compared to cobalt and nickel in a similar arrangement. This study provides guidance in designing MOF-based catalytic systems for photocatalysis and solar-fuel production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.

Lin, Jiusheng [University of Nebraska, Lincoln, NE↗
DOE OSTI2020

Precipitation of calcium–alumino–silicate–hydrate gels: The role of the internal stress

Concrete gains its strength from the precipitation of a calcium–alumino–silicate–hydrate (C–A–S–H) colloidal gel, which acts as its binding phase. However, despite concrete’s ubiquity in the building environment, the atomic-scale mechanism of C–A–S–H precipitation is still unclear. Here, we use reactive molecular dynamics simulations to model the early-age precipitation of a C–A–S–H gel. We find that, upon gelation, silicate and aluminate precursors condensate and polymerize to form an aluminosilicate gel network. Notably, we demonstrate that the gelation reaction is driven by the existence of a mismatch of atomic-level internal stress between Si and Al polytopes, which are initially experiencing some local tension and compression, respectively. The polymerization of Si and Al polytopes enables the release of these competitive stresses.

Zhao, Cheng↗
DOE OSTI2022

Kuramoto synchronization of quantum tunneling polarons for describing the dynamic structure in cuprate superconductors

A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by extended x-ray absorption fine structure (EXAFS) experiments, anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here, in this paper, we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant 6-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization transition between coupled internal quantum tunneling of polarons associated with the two-site distribution of the copper–apical oxygen (Cu-O ap ) pair in the dynamic structure. The transition is driven by the anharmonicity of the lattice vibrations and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide plane. Simultaneously, a finite projection of the internal quantum tunneling polaron extends to the copper–planar oxygen (Cu-O pl ) pair. All these findings allow an interpretation based on an effective quantum-mechanical triple-well potential associated with the oxygen sites of the 6-atom cluster, which accurately represents the phase synchronization of apical oxygens and lattice-assisted charge transfer to the CuO 2 plane.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Energy-efficient pathway for selectively exciting solute molecules to high vibrational states via solvent vibration-polariton pumping

Abstract Selectively exciting target molecules to high vibrational states is inefficient in the liquid phase, which restricts the use of IR pumping to catalyze ground-state chemical reactions. Here, we demonstrate that this inefficiency can sometimes be solved by confining the liquid to an optical cavity under vibrational strong coupling conditions. For a liquid solution of 13 CO 2 solute in a 12 CO 2 solvent, cavity molecular dynamics simulations show that exciting a polariton (hybrid light-matter state) of the solvent with an intense laser pulse, under suitable resonant conditions, may lead to a very strong (>3 quanta) and ultrafast (<1 ps) excitation of the solute, even though the solvent ends up being barely excited. By contrast, outside a cavity the same input pulse fluence can excite the solute by only half a vibrational quantum and the selectivity of excitation is low. Our finding is robust under different cavity volumes, which may lead to observable cavity enhancement on IR photochemical reactions in Fabry–Pérot cavities.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Thermally frustrated phase transition at high pressure in B 2-ordered FeV

X-ray diffraction measurements of equiatomic B2-ordered FeV were performed in a diamond-anvil cell at room temperature at several pressure points up to 80 GPa that showed the cubic phase to be stable with no indication of structural phase transitions. Density functional theory at 0 K predicts Fermi surface nesting, an electronic topological transition, and a phonon dynamical instability within the experimentally investigated pressure range. Nevertheless, the instability is absent in phonon dispersion curves extracted from ab initio molecular dynamics simulations below the critical volume at temperatures as low as 10 K, indicating that thermal atomic displacements can frustrate the phase transition by renormalizing the phonon dispersion curves. Ferrimagnetism is critical for the stability of the cubic phase at low temperature, but thermal atomic displacements are enough to support the structure at and above the Néel temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Cavity molecular dynamics simulations of liquid water under vibrational ultrastrong coupling

We simulate vibrational strong coupling (VSC) and vibrational ultrastrong coupling (V-USC) for liquid water with classical molecular dynamics simulations. When the cavity modes are resonantly coupled to the O–H stretch mode of liquid water, the infrared spectrum shows asymmetric Rabi splitting. The lower polariton (LP) may be suppressed or enhanced relative to the upper polariton (UP) depending on the frequency of the cavity mode. Furthermore, although the static properties and the translational diffusion of water are not changed under VSC or V-USC, we do find the modification of the orientational autocorrelation function of H 2 O molecules especially under V-USC, which could play a role in ground-state chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Phase Synergy Enables Low‐Power Ferroelectric Switching in HfO 2 Epitaxial Films

HfO 2 -based ferroelectric materials have emerged as leading candidates for next-generation non-volatile memory technologies, owing to their nanoscale robust ferroelectricity and complementary metal–oxide–semiconductor (CMOS) compatibility. However, challenges and debates persist in advancing and comprehensively understanding their ferroelectric behavior. In particular, conventional approaches typically regard non-ferroelectric phases as detrimental and primarily focus on suppressing their formation, yet overlooking their potentially synergistic contributions—particularly those of the tetragonal (T) phase. Here, we unambiguously clarify the beneficial role of the T-phase and introduce a phase-boundary engineering strategy that deliberately harnesses it to enhance ferroelectricity in HfO 2 films. By stabilizing optimal coherent boundaries between ferroelectric orthorhombic (O) and T phases in epitaxial La-doped HfO 2 films, we achieve significant improvements in ferroelectric properties—doubling the remanent polarization (P r ∼ 30 µC/cm 2 ) and substantially reducing the coercive field (E c ∼ 3 MV/cm) by 30% compared to low-La doped samples without such boundaries. Atomic-scale electron microscopy reveals the structural nature of the atomically sharp, coherent O–T boundaries. Combined with deep-learning enhanced molecular dynamics simulations, our results unravel that these boundaries facilitate intermediate polarization states that lower the switching energy barrier. Consequently, phase coexistence shifts from an inherent drawback to a tunable design element, offering a broadly applicable route to ultra-low-power HfO 2 -based nanoelectronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗