Metal cation s lone-pairs increase octahedral tilting instabilities in halide perovskites
Lone-pair covalency can faciliate dynamic tilting of MBr 6 octahedra and increase dynamic structural instabilities.
36 MATERIALS SCIENCE↗
SEARCH · Engineering Papers
Results for “Structural dynamics”
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.
Traveling waves at the surface of active liquid crystals
The interface of an active liquid crystal can support travelling waves. We derive dispersion relations from a linear theory and compute the dynamical structure factor from continuum simulations.
Gulati, Paarth↗
High-pressure neutron powder diffraction study of an arsenolite deuterium inclusion compound: structure and formation kinetics
High-pressure variable-temperature neutron powder diffraction was employed to investigate the synthesis and structural properties of arsenolite (As 4 O 6 ), a cubic arsenic( III ) oxide polymorph, and its inclusion compound with deuterium. The compound forms with the stoichiometry As 4 O 6 ·2D 2 , consistent with earlier findings. At 295 K and 1.96(2) GPa, D 2 molecules occupy the 16c site (0, 0, 0) and are aligned along the <111> direction. The diffraction data suggest that the D 2 molecules at this site become rotationally disordered upon decompression to 0.78(2) GPa at 120 K, while no occupancy is observed at the 8a position (⅛, ⅛, ⅛) under any of the studied conditions. The kinetic data of the high-pressure inclusion compound synthesis at 1.56(2) and 1.96(2) GPa were analyzed using the Avrami model. The Avrami exponent, 0.135(16), remains invariant with pressure, demonstrating that the reaction topochemistry is unaffected by compression. Similarly, the reaction rates, 0.29(3) and 0.23(3) min −0.135 at 1.56(2) and 1.96(2) GPa, respectively, exhibit negligible pressure dependence and suggest a surprisingly low activation volume of 1.6 cm 3 mol −1 for the reaction. These results provide detailed insight into the structural dynamics and kinetics of deuterium inclusion in arsenolite under high pressure.
Guńka, Piotr A. [Warsaw University of Technology (↗
Turbulent-like flows in quasi two-dimensional dense suspensions of motile colloids
Dense bacterial suspensions exhibit turbulent-like flows at low Reynolds numbers, driven by the activity of the microswimmers. In this study, we develop a model system to examine these dynamics using motile colloids that mimic bacterial locomotion. The colloids are powered by the Quincke instability, which causes them to spontaneously roll in a random-walk pattern when exposed to a square-wave electric field. We experimentally investigate the flow dynamics in dense suspensions of these Quincke random walkers under quasi two-dimensional conditions, where the particle size is comparable to the gap between the electrodes. The results suggest a scaling regime in the energy spectrum ∼k −4 at high wavenumbers, observed consistently across activity levels and particle concentrations. We observe that velocity time correlations decay within a single period of the square-wave field, yet an anti-correlation appears between successive field applications, indicative of a dynamic structural memory of the ensemble.
Luo, Rui [Northwestern Univ., Evanston, IL (United↗
Analysis of the time-of-flight neutron scattering cross-section data for light water measured at the SEQUOIA spectrometer, Spallation Neutron Source (SNS)
Thermal neutron scattering cross-section data for light water available in the major nuclear data libraries observes significant differences especially at reactor operating temperatures. During the past few years there has been a renewed interest in reviewing the existing thermal scattering models and generating more accurate and reliable thermal scattering cross sections using existing experimental data and in some cases based on Molecular Dynamics (MD) simulations. There is a need for performing new time-of-flight experiments at high temperatures and pressures, to have a better understanding of the physics involved in the scattering process that could help improve the existing TSL data.Lack of experimental thermal scattering data for light water at high temperatures led to a new measurement campaign within the INSIDER project at the Institut de radioprotection et de sûreté nucléaire (IRSN). Double differential scattering cross section for light water have been measured at the SEQUOIA spectrometer based at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory, United States. Several measurements have been carried out at different temperatures and pressures corresponding to liquid light water. Measurements at five different incident neutron energies Ei (8, 60, 160, 280 and 800 meV) have been carried out to help exploring different regions of the frequency spectrum. This paper presents the analysis of the dynamic structure factor and the derived frequency spectrum of light water. The analysis of the experimental data would provide one with better confidence, the behavior of thermal scattering cross sections for light water at high temperatures, knowledge of which is very important for the design of novel reactors as well as existing pressurized water reactors.
Jaiswal, V↗
High energy electron diffraction instrument with tunable camera length
Ultrafast electron diffraction (UED) stands as a powerful technique for real-time observation of structural dynamics at the atomic level. In recent years, the use of MeV electrons from radio frequency guns has been widely adopted to take advantage of the relativistic suppression of the space charge effects that otherwise limit the temporal resolution of the technique. Nevertheless, there is not a clear choice for the optimal energy for a UED instrument. Scaling to beam energies higher than a few MeV does pose significant technical challenges, mainly related to the inherent increase in diffraction camera length associated with the smaller Bragg angles. In this study, we report a solution by using a compact post-sample magnetic optical system to magnify the diffraction pattern from a crystal Au sample illuminated by an 8.2 MeV electron beam. Our method employs, as one of the lenses of the optical system, a triplet of compact, high field gradients (>500 T/m), small-gap (3.5 mm) Halbach permanent magnet quadrupoles. Shifting the relative position of the quadrupoles, we demonstrate tuning the magnification by more than a factor of two, a 6× improvement in camera length, and reciprocal space resolution better than 0.1 Å –1 in agreement with beam transport simulations.
47 OTHER INSTRUMENTATION↗
Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions
In this paper, we describe the development of a reactive force field for C/O systems under extreme temperatures and pressures, based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model, which targets carbon condensation under thermodynamic conditions of 6500 K and 2.5 g cm –3 , affords a balance between model accuracy, complexity, and training set generation expense. We show that the model recovers much of the accuracy of density functional theory for the prediction of structure, dynamics, and chemistry when applied to dissociative condensed phase systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 104 increase in efficiency for the same system size (i.e., 128 atoms) and a linear system size scalability over standard quantum molecular dynamics methods, allowing the simulation of significantly larger systems than previously possible. We find that the model captures the condensed-phase reaction-coupled formation of carbon clusters implied by recent experiments, and that this process is susceptible to strong finite size effects. Overall, we find the present ChIMES model to be well suited for studying chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a broader high pressure–high temperature force-field for condensed phase chemistry in organic materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Active learning for robust, high-complexity reactive atomistic simulations
Machine learned reactive force fields based on polynomial expansions have been shown to be highly effective for describing simulations involving reactive materials. Nevertheless, the highly flexible nature of these models can give rise to a large number of candidate parameters for complicated systems. In these cases, reliable parameterization requires a well-formed training set, which can be difficult to achieve through standard iterative fitting methods. In this paper, we present an active learning approach based on cluster analysis and inspired by Shannon information theory to enable semi-automated generation of informative training sets and robust machine learned force fields. The use of this tool is demonstrated for development of a model based on linear combinations of Chebyshev polynomials explicitly describing up to four-body interactions, for a chemically and structurally diverse system of C/O under extreme conditions. We show that this flexible training database management approach enables development of models exhibiting excellent agreement with Kohn–Sham density functional theory in terms of structure, dynamics, and speciation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The ultrafast Kerr effect in anisotropic and dispersive media
The ultrafast optical Kerr effect (OKE) is widely used to investigate the structural dynamics and interactions of liquids, solutions, and solids by observing their intrinsic nonlinear temporal responses through nearly collinear four-wave mixing. Non-degenerate mixing schemes allow for background free detection and can provide information on the interplay between a material’s internal degrees of freedom. Here, we show a source of temporal dynamics in the OKE signal that is not reflective of the internal degrees of freedom but arises from a group index and momentum mismatch. It is observed in two-color experiments on condensed media with sizable spectral dispersion, a common property near an optical resonance. In particular, birefringence in crystalline solids is able to entirely change the character of the OKE signal via the off-diagonal tensor elements of the nonlinear susceptibility. We develop a detailed description of the phase-mismatched ultrafast OKE and show how to extract quantitative information on the spectrally resolved birefringence and group index from time-resolved experiments in one and two dimensions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Toward first principles-based simulations of dense hydrogen
Accurate knowledge of the properties of hydrogen at high compression is crucial for astrophysics (e.g., planetary and stellar interiors, brown dwarfs, atmosphere of compact stars) and laboratory experiments, including inertial confinement fusion. There exists experimental data for the equation of state, conductivity, and Thomson scattering spectra. However, the analysis of the measurements at extreme pressures and temperatures typically involves additional model assumptions, which makes it difficult to assess the accuracy of the experimental data rigorously. On the other hand, theory and modeling have produced extensive collections of data. They originate from a very large variety of models and simulations including path integral Monte Carlo (PIMC) simulations, density functional theory (DFT), chemical models, machine-learned models, and combinations thereof. At the same time, each of these methods has fundamental limitations (fermion sign problem in PIMC, approximate exchange–correlation functionals of DFT, inconsistent interaction energy contributions in chemical models, etc.), so for some parameter ranges accurate predictions are difficult. Recently, a number of breakthroughs in first principles PIMC as well as in DFT simulations were achieved which are discussed in this review. Here we use these results to benchmark different simulation methods. We present an update of the hydrogen phase diagram at high pressures, the expected phase transitions, and thermodynamic properties including the equation of state and momentum distribution. Furthermore, we discuss available dynamic results for warm dense hydrogen, including the conductivity, dynamic structure factor, plasmon dispersion, imaginary-time structure, and density response functions. We conclude by outlining strategies to combine different simulations to achieve accurate theoretical predictions that are based on first principles.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Combined molecular and spin dynamics simulation of BCC iron with vacancy defects
Utilizing an atomistic computational model, which handles both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to investigate the effect of vacancy defects on spin wave excitations in ferromagnetic iron. Fourier transforms of space- and time-displaced correlation functions yield the dynamic structure factor, providing characteristic frequencies and lifetimes of the spin wave modes. A comparison of the system with a 5% vacancy concentration with pure lattice data shows a decrease in frequency and a decrease in lifetime for all transverse spin wave excitations observed. In addition, the clearly defined transverse spin wave excitations are distorted with the introduction of vacancy defects, and we observe reduced excitation lifetimes due to increased magnon–magnon scattering. We observe further evidence of increased magnon–magnon scattering, as the peaks in the longitudinal spin wave spectrum become less distinct. Finally, similar impacts are observed in the vibrational subsystem, with a decrease in characteristic phonon frequency and flattening of lattice excitation signals due to vacancy defects.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Imaging transient molecular configurations in UV-excited diiodomethane
Femtosecond structural dynamics of diiodomethane (CH 2 I 2 ) triggered by ultraviolet (UV) photoabsorption at 290 and 330 nm are studied using time-resolved coincident Coulomb explosion imaging driven by a near-infrared probe pulse. Here, we map the dominant single-photon process, the cleavage of the carbon–iodine bond producing rotationally excited CH 2 I radical, identify the contributions of the three-body (CH 2 + I + I) dissociation and molecular iodine formation channels, which are primarily driven by the absorption of more than one UV photon, and demonstrate the existence of a weak reaction pathway involving the formation of short-lived transient species resembling iso-CH 2 I 2 -like geometries with a slightly shorter I–I separation compared to the ground-state CH 2 I 2 . These transient molecular configurations, which can be separated from the other channels by applying a set of conditions on the correlated momenta of three ionic fragments, are formed within ∼100 fs after the initial photoexcitation and decay within the next 100 fs.
Atomic and molecular processes↗
Effect of likelihood misspecification in Gaussian process-driven autonomous experimentation
In recent years, several groups have designed Autonomous Experiment (AE) models with the aim of using them as an alternative method for neutron scattering scanning. In an AE, Gaussian processes (GPs) are most frequently used due to their interpretability, their non-parametric nature, their universal approximation, and their closed-form predictive distribution. GPs have two key components, namely, the model for the likelihood of a neutron count knowing the underlying dynamic structure factor and the acquisition function. In this paper, we investigate the impact, on the quality of an AE, of the likelihood and acquisition function choices, in energy scans and (Q, ω) ones, with respect to the signal-over-noise ratio. While we hypothesized that the quality of GP predictions would decrease when the normal to Poisson likelihood approximation breaks down at low count rates, we found that the use of the correct Poisson likelihood does not improve the quality of the data collected, as well as yields very poor results in (Q, ω) scans at low count rates. In fact, the best results are obtained with a combination of normal likelihood, including the observation noise, and the change in variance acquisition function. In addition, we find that the performance, or quality of the predictive distribution, is a misleading measure of efficiency, that is, of the quality of the data collected.
Perryman, David Elliott [Inst. Laue-Langevin (ILL)↗
Spectral deconvolution without the deconvolution: Extracting temperature from x-ray Thomson scattering spectra without the source-and-instrument function
X-ray Thomson scattering (XRTS) probes the dynamic structure factor of the system, but the measured spectrum is broadened by the combined source-and-instrument function (SIF) of the setup. In order to extract properties such as temperature from an XRTS spectrum, the broadening by the SIF needs to be removed. Recent work [Dornheim et al. Nat. Commun. 13 , 7911 (2022)] has suggested that the SIF may be deconvolved using the two-sided Laplace transform. However, the extracted information can depend strongly on the shape of the input SIF, and the SIF is in practice challenging to measure accurately. Here, we propose an alternative approach: we demonstrate that considering ratios of Laplace-transformed XRTS spectra collected at different scattering angles is equivalent to performing the deconvolution, but without the need for explicit knowledge of the SIF. From these ratios, it is possible to directly extract the temperature from the scattering spectra, when the system is in thermal equilibrium. We find the method to be generally robust to spectral noise and physical differences between the spectrometers, and we explore situations in which the method breaks down. Furthermore, the fact that consistent temperatures can be extracted for systems in thermal equilibrium indicates that non-equilibrium effects could be identified by inconsistent temperatures of a few eV between the ratios of three or more scattering angles.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Evidence of a liquid–liquid transition in a glass-forming ionic liquid
A liquid–liquid transition (LLT) is a transformation from one liquid to another through a first-order transition. The LLT is fundamental to the understanding of the liquid state and has been reported in a few materials such as silicon, phosphorus, triphenyl phosphite, and water. Furthermore, it has been suggested that the unique properties of materials such as water, which is critical for life on the planet, are linked to the existence of the LLT. However, the experimental evidence for the existence of an LLT in many molecular liquids remains controversial, due to the prevalence and high propensity of the materials to crystallize. In this work, we show evidence of an LLT in a glass-forming trihexyltetradecylphosphonium borohydride ionic liquid that shows no tendency to crystallize under normal laboratory conditions. We observe a step-like increase in the static dielectric permittivity at the transition. Furthermore, the sizes of nonpolar local domains and ion-coordination numbers deduced from wide-angle X-ray scattering also change abruptly at the LLT. We independently corroborate these changes in local organization using Raman spectroscopy. The experimental access to the evolution of local order and structural dynamics across a liquid–liquid transition opens up unprecedented possibilities to understand the nature of the liquid state.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Topological signatures in nodal semimetals through neutron scattering
Abstract Topological nodal semimetals are known to host a variety of fascinating electronic properties due to the topological protection of the band-touching nodes. Neutron scattering, despite its power in probing elementary excitations, has not been routinely applied to topological semimetals, mainly due to the lack of an explicit connection between the neutron response and the signature of topology. In this work, we theoretically investigate the role that neutron scattering can play to unveil the topological nodal features: a large magnetic neutron response with spectral non-analyticity can be generated solely from the nodal bands. A new formula for the dynamical structure factor for generic topological nodal metals is derived. For Weyl semimetals, we show that the locations of Weyl nodes, the Fermi velocities and the signature of chiral anomaly can all leave hallmark neutron spectral responses. Our work offers a neutron-based avenue toward probing bulk topological materials.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans
Abstract Recent breakthroughs in structural biology have provided valuable new insights into enzymes involved in plant cell wall metabolism. More specifically, the molecular mechanism of synthesis of (1,3;1,4)-β-glucans, which are widespread in cell walls of commercially important cereals and grasses, has been the topic of debate and intense research activity for decades. However, an inability to purify these integral membrane enzymes or apply transgenic approaches without interpretative problems associated with pleiotropic effects has presented barriers to attempts to define their synthetic mechanisms. Following the demonstration that some members of the CslF sub-family of GT2 family enzymes mediate (1,3;1,4)-β-glucan synthesis, the expression of the corresponding genes in a heterologous system that is free of background complications has now been achieved. Biochemical analyses of the (1,3;1,4)-β-glucan synthesized in vitro, combined with 3-dimensional (3D) cryogenic-electron microscopy and AlphaFold protein structure predictions, have demonstrated how a single CslF6 enzyme, without exogenous primers, can incorporate both (1,3)- and (1,4)-β-linkages into the nascent polysaccharide chain. Similarly, 3D structures of xyloglucan endo-transglycosylases and (1,3;1,4)-β-glucan endo- and exohydrolases have allowed the mechanisms of (1,3;1,4)-β-glucan modification and degradation to be defined. X-ray crystallography and multi-scale modeling of a broad specificity GH3 β-glucan exohydrolase recently revealed a previously unknown and remarkable molecular mechanism with reactant trajectories through which a polysaccharide exohydrolase can act with a processive action pattern. The availability of high-quality protein 3D structural predictions should prove invaluable for defining structures, dynamics, and functions of other enzymes involved in plant cell wall metabolism in the immediate future.
59 BASIC BIOLOGICAL SCIENCES↗
An ascomycete H4 variant with an unknown function
Histone variants leading to altered nucleosome structure, dynamics and DNA accessibility occur frequently, albeit rarely for H4. We carried out a comprehensive in silico scrutiny of fungal genomes, which revealed the presence of a novel H4 variant (H4E) in the ascomycetes, throughout the Pezizomycotina, in basal species of the Taphrinomycotina and also in the Glomeromycota. The coding cognate genes show a specific intron/exon organization, different from H4 canonical genes. H4Es diverge from canonical H4s mainly in the N- and C-terminal extensions, showing marked differences in the distribution and number of Lys and Arg residues, which may result in novel post-translational modifications. In Aspergillus nidulans (Pezizomycotina, Eurotiomycetes) the H4E variant protein level is low in mycelia. However, the encoding gene is well expressed at 37°C under nitrogen starvation. H4E localizes to the nucleus and interacts with H3, but its absence or overexpression does not result in any detectable phenotype. Deletion of only one of the of the two canonical H4 genes results in a strikingly impaired growth phenotype, which indicates that H4E cannot replace this canonical histone. Thus, an H4 variant is present throughout a whole subphylum of the ascomycetes, but with hitherto no experimentally detectable function.
59 BASIC BIOLOGICAL SCIENCES↗