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At least 1,279 records · Page 71

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗

The structural information filtered features (SIFF) potential: Maximizing information stored in machine-learning descriptors for materials prediction

Machine learning inspired potentials continue to improve the ability for predicting structures of materials. However, many challenges still exist, particularly when calculating structures of disordered systems. These challenges are primarily due to the rapidly increasing dimensionality of the feature-vector space which in most machine-learning algorithms is dependent on the size of the structure. In this article, we present a feature-engineered approach that establishes a set of principles for representing potentials of physical structures (crystals, molecules, and clusters) in a feature space rather than a physically motivated space. Our goal in this work is to define guiding principles that optimize information storage of the physical parameters within the feature representations. In this manner, we focus on keeping the dimensionality of the feature space independent of the number of atoms in the structure. Our Structural Information Filtered Features (SIFF) potential represents structures by utilizing a feature vector of low-correlated descriptors, which correspondingly maximizes information within the descriptor. We present results of our SIFF potential on datasets composed of disordered (carbon and carbon–oxygen) clusters, molecules with C 7 O 2 H 2 stoichiometry in the GDB9-14B dataset, and crystal structures of the form (Al x Ga y In z ) 2 O 3 as proposed in the NOMAD Kaggle competition. Our potential's performance is at least comparable, sometimes significantly more accurate, and often more efficient than other well-known machine-learning potentials for structure prediction. However, primarily, we offer a different perspective on how researchers should consider opportunities in maximizing information storage for features.

36 MATERIALS SCIENCE↗

Dynamics of poly[n]catenane melts

Inspired by advances in the chemical synthesis of interlocking polymer architectures, extensive molecular dynamics simulations have been conducted to study the dynamical properties of poly[n]catenanes-polymers composed entirely of interlocking rings-in the melt state. Both the degree of polymerization (number of links) and the number of beads per ring are systematically varied, and the results are compared to linear and ring polymers. Herein, a simple Rouse-like model is presented, and its analytical solution suggests a decomposition of the dynamics into "ring-like" and "linear-like" regimes at short and long times, respectively. In agreement with this picture, multiple sub-diffusive regimes are observed in the monomer mean-squared-displacements even though interchain entanglement is not prevalent in the system. However, the Rouse-type model does not account for the topological effects of the mechanical bonds, which significantly alter the dynamics at intermediate length scales both within the rings and at the chain segment scales. The stress relaxation in the system is extremely rapid and may be conveniently separated into ring-like and linear-like contributions, again in agreement with the Rouse picture. However, the viscosity has a non-monotonic dependence on the ring size for long chains, which disagrees strongly with theoretical predictions. This unexpected observation cannot be explained in terms of chain disentanglement and is inconsistent with other measures of polymer relaxation. Possible mechanisms for this behavior are proposed and implications for materials design are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting molecular dipole moments by combining atomic partial charges and atomic dipoles

The molecular dipole moment ( μ ) is a central quantity in chemistry. It is essential in predicting infrared and sum-frequency generation spectra as well as induction and long-range electrostatic interactions. Furthermore, it can be extracted directly—via the ground state electron density—from high-level quantum mechanical calculations, making it an ideal target for machine learning (ML). Here, we choose to represent this quantity with a physically inspired ML model that captures two distinct physical effects: local atomic polarization is captured within the symmetry-adapted Gaussian process regression framework which assigns a (vector) dipole moment to each atom, while the movement of charge across the entire molecule is captured by assigning a partial (scalar) charge to each atom. The resulting “MuML” models are fitted together to reproduce molecular μ computed using high-level coupled-cluster theory and density functional theory (DFT) on the QM7b dataset, achieving more accurate results due to the physics-based combination of these complementary terms. The combined model shows excellent transferability when applied to a showcase dataset of larger and more complex molecules, approaching the accuracy of DFT at a small fraction of the computational cost. We also demonstrate that the uncertainty in the predictions can be estimated reliably using a calibrated committee model. The ultimate performance of the models—and the optimal weighting of their combination—depends, however, on the details of the system at hand, with the scalar model being clearly superior when describing large molecules whose dipole is almost entirely generated by charge separation. These observations point to the importance of simultaneously accounting for the local and non-local effects that contribute to μ ; furthermore, they define a challenging task to benchmark future models, particularly those aimed at the description of condensed phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations

State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted due to the risk of "variational collapse" down to the ground state. We employ the recently developed square gradient minimization algorithm to reliably avoid variational collapse and study the effectiveness of orbital optimized density functional theory (DFT) at predicting second period element 1s core-level spectra of open-shell systems. Several density functionals (including SCAN, B3LYP, and ωB97X-D3) are found to predict excitation energies from the core to singly occupied levels with high accuracy (≤0.3 eV RMS error) against available experimental data. Higher excited states are, however, more challenging by virtue of being intrinsically multiconfigurational. We thus present a configuration interaction inspired route to self-consistently recouple single determinant mixed configurations obtained from DFT, in order to obtain approximate doublet states. This recoupling scheme is used to predict the C K-edge spectra of the allyl radical, the O K-edge spectra of CO + , and the N K-edge of NO 2 with high accuracy relative to experiment, indicating substantial promise in using this approach for the computation of core-level spectra for doublet species [vs more traditional time dependent DFT, equation of motion coupled cluster singles and doubles (EOM-CCSD), or using unrecoupled mixed configurations]. Finally, we also present general guidelines for computing core-excited states from orbital optimized DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biomimetic composite architecture achieves ultrahigh rate capability and cycling life of sodium ion battery cathodes

Sodium ion batteries are an emerging candidate to replace lithium ion batteries in large-scale electrical energy storage systems due to the abundance and widespread distribution of sodium. Despite the growing interest, the development of high-performance sodium cathode materials remains a challenge. In particular, polyanionic compounds are considered as a strong cathode candidate owing to their better cycling stability, a flatter voltage profile, and stronger thermal stability compared to other cathode materials. Here, we report the rational design of a biomimetic bone-inspired polyanionic Na3V2(PO4)3-reduced graphene oxide composite (BI-NVP) cathode that achieves ultrahigh rate charging and ultralong cycling life in a sodium ion battery. At a charging rate of 1 C, BI-NVP delivers 97% of its theoretical capacity and is able to retain a voltage plateau even at the ultra-high rate of 200 C. It also shows long cycling life with capacity retention of 91% after 10 000 cycles at 50 C. The sodium ion battery cells with a BI-NVP cathode and Na metal anode were able to deliver a maximum specific energy of 350 W h kg−1 and maximum specific power of 154 kW kg−1. In situ and postmortem analyses of cycled BI-NVP (including by Raman and XRD spectra) HRTEM, and STEM-EELS, indicate highly reversible dilation–contraction, negligible electrode pulverization, and a stable NVP-reduced graphene oxide layer interface. The results presented here provide a rational and biomimetic material design for the electrode architecture for ultrahigh power and ultralong cyclability of the sodium ion battery full cells when paired with a sodium metal anode.

25 ENERGY STORAGE↗

Two-dimensional electronic Stark spectroscopy of a photosynthetic dimer

Stark spectroscopy, which measures changes in the linear absorption of a sample in the presence of an external DC electric field, is a powerful experimental tool for probing the existence of charge-transfer (CT) states in photosynthetic systems. CT states often have small transition dipole moments, making them insensitive to other spectroscopic methods, but are particularly sensitive to Stark spectroscopy due to their large permanent dipole moment. In a previous study, we demonstrated a new experimental method, two- dimensional electronic Stark spectroscopy (2DESS), which combines two-dimensional electronic spectroscopy (2DES) and Stark spec- troscopy. In order to understand how the presence of CT states manifest in 2DESS, here, we perform computational modeling and calculations of 2DESS as well as 2DES and Stark spectra, studying a photosynthetic dimer inspired by the photosystem II reaction center. Here, we identify specific cases where qualitatively different sets of system parameters produce similar Stark and 2DES spectra but significantly different 2DESS spectra, showing the potential for 2DESS to aid in identifying CT states and their coupling to excitonic states.

14 SOLAR ENERGY↗

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↗

A cautionary tale: Problems in the valence-CASSCF description of the ground state (X1Σ+) of BF

In the full optimized reaction space and valence-complete active space self-consistent field (vCAS) methods, a set of active orbitals is defined as the union of the valence orbitals on the atoms, all possible configurations involving the active orbitals are generated, and the orbitals and configuration coefficients are self-consistently optimized. Such wave functions have tremendous flexibility, which makes these methods incredibly powerful but can also lead to inconsistencies in the description of the electronic structure of molecules. In this paper, the problems that can arise in vCAS calculations are illustrated by calculations on the BH and BF molecules. BH is well described by the full vCAS wave function, which accounts for molecular dissociation and 2s–2p near-degeneracy in the boron atom. The same is not true for the full vCAS wave function for BF. There is mixing of core and active orbitals at short internuclear distances and swapping of core and active orbitals at large internuclear distances. In addition, the virtual 2π orbitals, which were included in the active space to account for the 2s–2p near degeneracy effect, are used instead to describe radial correlation of the electrons in the F2pπ-like pairs. Although the above changes lead to lower vCAS energies, they lead to higher vCAS+1+2 energies as well as irregularities and/or discontinuities in the potential energy curves. All of the above problems can be addressed by using the spin-coupled generalized valence bond-inspired vCAS wave function for BF, which includes only a subset of the atomic valence orbitals in the active space.

Xu, Lu T. (ORCID:0000000182064902)↗

Ultrasonic oscillatory two-phase flow in microchannels

Experimental and numerical investigations are performed to provide an assessment of the transport behavior of an ultrasonic oscillatory two-phase flow in a microchannel. The work is inspired by the flow observed in an innovative ultrasonic fabric drying device using a piezoelectric bimorph transducer with microchannels, where a water-air two-phase flow is transported by harmonically oscillating microchannels. The flow exhibits highly unsteady behavior as the water and air interact with each other during the vibration cycles, making it significantly different from the well-studied steady flow in microchannels. Here, the computational fluid dynamics (CFD) modeling is realized by combing the turbulence Reynolds-averaged Navier-Stokes (RANS) k – ω model with the phase-field method to resolve the dynamics of the two-phase flow. The numerical results are qualitatively validated by the experiment. Through parametric studies, we specifically examined the effects of vibration conditions (i.e., frequency and amplitude), microchannel taper angle, and wall surface contact angle (i.e., wettability) on the flow rate through the microchannel. The results will advance the potential applications where oscillatory or general unsteady microchannel two-phase flows may be present.

42 ENGINEERING↗

A domain wall-magnetic tunnel junction artificial synapse with notched geometry for accurate and efficient training of deep neural networks

Inspired by the parallelism and efficiency of the brain, several candidates for artificial synapse devices have been developed for neuromorphic computing, yet a nonlinear and asymmetric synaptic response curve precludes their use for backpropagation, the foundation of modern supervised learning. Spintronic devices—which benefit from high endurance, low power consumption, low latency, and CMOS compatibility—are a promising technology for memory, and domain-wall magnetic tunnel junction (DW-MTJ) devices have been shown to implement synaptic functions such as long-term potentiation and spike-timing dependent plasticity. In this work, we propose a notched DW-MTJ synapse as a candidate for supervised learning. Using micromagnetic simulations at room temperature, we show that notched synapses ensure the non-volatility of the synaptic weight and allow for highly linear, symmetric, and reproducible weight updates using either spin transfer torque (STT) or spin–orbit torque (SOT) mechanisms of DW propagation. We use lookup tables constructed from micromagnetics simulations to model the training of neural networks built with DW-MTJ synapses on both the MNIST and Fashion-MNIST image classification tasks. Accounting for thermal noise and realistic process variations, the DW-MTJ devices achieve classification accuracy close to ideal floating-point updates using both STT and SOT devices at room temperature and at 400 K. Our work establishes the basis for a magnetic artificial synapse that can eventually lead to hardware neural networks with fully spintronic matrix operations implementing machine learning.

42 ENGINEERING↗

Advances in coherent coupling between magnons and acoustic phonons

The interaction between magnetic and acoustic excitations have recently inspired many interdisciplinary studies ranging from fundamental physics to circuit implementation. Specifically, the exploration of their coherent interconversion enabled via the magnetoelastic coupling opens a new playground combining straintronics and spintronics, and provides a unique platform for building up on-chip coherent information processing networks with miniaturized magnonic and acoustic devices. In this Perspective, we will focus on the recent progress of magnon-phonon coupled dynamic systems, including materials, circuits, imaging and new physics. In particular, we highlight the unique features such as nonreciprocal acoustic wave propagation and strong coupling between magnons and phonons in magnetic thin-film systems, which provides a unique platform for their coherent manipulation and transduction. We will also review the frontier of surface acoustic wave resonators in coherent quantum transduction and discuss how the novel acoustic circuit design can be applied in microwave spintronics.

36 MATERIALS SCIENCE↗

Multi-junction solar cells paving the way for super high-efficiency

In order to realize a clean energy society by using renewable energies, high-performance solar cells are a very attractive proposition. The development of high-performance solar cells offers a promising pathway toward achieving high power per unit cost for many applications. As state-of-the-art of single-junction solar cells are approaching the Shockley–Queisser limit of 32%–33%, an important strategy to raise the efficiency of solar cells further is stacking solar cell materials with different bandgaps to absorb different colors of the solar spectrum. The III–V semiconductor materials provide a relatively convenient system for fabricating multi-junction solar cells providing semiconductor materials that effectively span the solar spectrum as demonstrated by world record efficiencies (39.2% under one-sun and 47.1% under concentration) for six-junction solar cells. This success has inspired attempts to achieve the same with other materials like perovskites for which lower manufacturing costs may be achieved. Recently, Si multi-junction solar cells such as III–V/Si, II–VI/Si, chalcopyrite/Si, and perovskite/Si have become popular and are getting closer to economic competitiveness. Here, we discuss the perspectives of multi-junction solar cells from the viewpoint of efficiency and low-cost potential based on scientific and technological arguments and possible market applications. In addition, this article provides a brief overview of recent developments with respect to III–V multi-junction solar cells, III–V/Si, II–VI/Si, perovskite/Si tandem solar cells, and some new ideas including so-called 3rd generation concepts.

14 SOLAR ENERGY↗

Quadrupole-mediated dielectric response and the charge-asymmetric solvation of ions in water

Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of the solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for basic length and energy scales of ion solvation, computer simulations indicate not only its quantitative inaccuracies but also its inability to capture some basic and important aspects of microscopic polarization response. Here, we consider one such shortcoming, a failure to distinguish the solvation thermodynamics of cations from that of otherwise-identical anions, and we pursue a simple, physically inspired modification of the dielectric continuum model to address it. The adaptation is motivated by analyzing the orientational response of an isolated water molecule whose dipole is rigidly constrained. Its free energy suggests a Hamiltonian for dipole fluctuations that accounts implicitly for the influence of higher-order multipole moments while respecting constraints of molecular geometry. Finally, we propose a field theory with the suggested form, whose nonlinear response breaks the charge symmetry of ion solvation. An approximate variational solution of this theory, with a single adjustable parameter, yields solvation free energies that agree closely with simulation results over a considerable range of solute size and charge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of particle loading and phase coupling on gas–solid flow dynamics: A case study of a two-phase, gas–solid flow in an annular pipe

The present study is devoted to a two-phase, gas–solid flow in an annular pipe (hollow cylinder) at an elevated pressure of 15 bars and moderate Reynolds number of circa 6000. The influence of the particle loading, the interaction between the phases, and turbulence dispersion on the flow dynamics is systematically studied by means of computational fluid dynamics simulations, employing the Ansys FLUENT commercial package. The cases with a particle volumetric fraction of 1.2% are referred to as “high particle loading,” and those with 0.13% are denoted as “low particle loading.” The following cases are investigated: (1) pure gas flow; (2) low particle loading two-phase flow with one-way coupling and with turbulence dispersion; (3) low particle loading two-phase flow with two-way coupling but without turbulence dispersion; (4) low particle loading two-phase flow with two-way coupling and with turbulence dispersion; (5) high particle loading two-phase flow with one-way coupling and with turbulence dispersion; (6) high particle loading two-phase flow with two-way coupling but without turbulence dispersion; and (7) high particle loading two-phase flow with two-way coupling and with turbulence dispersion. Additionally, the boundary layer is found to grow without fluctuations of the turbulent kinetic energy (TKE) for cases 1, 2, and 5. For case 4, the TKE fluctuations have been identified, although they appear to be less substantial than those in cases 6 and 7. The authors attribute the semi-chaotic nature of the TKE fluctuations to the particle loading and two-way coupling. In addition, the onset and development of the flow instability have been observed at a random axial distance in cases 4, 6, and 7. Such instability is also attributed to the two-way coupling with turbulence dispersion in the flow. It is concluded that the particle loading, one-way, or two-way coupling between the phases, and the turbulence dispersion models significantly influence the development of the flow dynamics with the same inlet and boundary conditions. Consequently, it is not a trivial question, which result a user should trust. The present computational results inspire to perform verification as well as experimental validation of the simulations, so the simulation results can subsequently be used with confidence for design analysis.

42 ENGINEERING↗

On closures for reduced order models - A spectrum of first-principle to machine-learned avenues

For over a century, reduced order models (ROMs) have been a fundamental discipline of theoretical fluid mechanics. Early examples include Galerkin models inspired by the Orr–Sommerfeld stability equation and numerous vortex models, of which the von Karman vortex street is one of the most prominent. Subsequent ROMs typically relied on first principles, like mathematical Galerkin models, weakly nonlinear stability theory, and two- and three-dimensional vortex models pioneered the data-driven proper orthogonal decomposition (POD) modeling. In early POD modeling, available data were used to build an optimal basis, which was then utilized in a classical Galerkin procedure to construct the ROM, but data have made a profound impact on ROMs beyond the Galerkin expansion. In this paper, we take a modest step and illustrate the impact of data-driven modeling on one significant ROM area. Specifically, we focus on ROM closures, which are correction terms that are added to the classical ROMs in order to model the effect of the discarded ROM modes in under-resolved simulations. Through simple examples, we illustrate the main modeling principles used to construct the classical ROMs, motivate and introduce modern ROM closures, and show how data-driven modeling, artificial intelligence, and machine learning have changed the standard ROM methodology over the last two decades. Finally, we outline our vision on how the state-of-the-art data-driven modeling can continue to reshape the field of reduced order modeling.

42 ENGINEERING↗

High-level coupled-cluster energetics by merging moment expansions with selected configuration interaction

Inspired by our earlier semi-stochastic work aimed at converging high-level coupled-cluster (CC) energetics, we propose a novel form of the CC(P; Q) theory in which the stochastic Quantum Monte Carlo propagations, used to identify dominant higher-than-doubly excited determinants, are replaced by the selected configuration interaction (CI) approach using the perturbative selection made iteratively (CIPSI) algorithm. The advantages of the resulting CIPSI-driven CC(P; Q) methodology are illustrated by a few molecular examples, including the dissociation of F 2 and the automerization of cyclobutadiene, where we recover the electronic energies corresponding to the CC calculations with a full treatment of singles, doubles, and triples based on the information extracted from compact CI wave functions originating from relatively inexpensive Hamiltonian diagonalizations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗