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At least 55 records · Page 3

Substitution of Aromatic Residues with Polar Residues in the Active Site Pocket of epi -Isozizaene Synthase Leads to the Generation of New Cyclic Sesquiterpenes

The sesquiterpene cyclase epi-isozizaene synthase (EIZS) catalyzes the cyclization of farnesyl diphosphate to form the tricyclic hydrocarbon precursor of the antibiotic albaflavenone. The hydrophobic active site pocket of EIZS serves as a template as it binds and chaperones the flexible substrate and carbocation intermediates through the conformations required for a multistep reaction sequence. We previously demonstrated that the substitution of hydrophobic residues with other hydrophobic residues remolds the template and expands product chemodiversity. Here, we show that the substitution of hydrophobic residues—specifically, Y69, F95, F96, and W203—with polar side chains also yields functional enzyme catalysts that expand product chemodiversity. Fourteen new EIZS mutants are reported that generate product arrays in which eight new sesquiterpene products have been identified. Of note, some mutants generate acyclic and cyclic hydroxylated products, suggesting that the introduction of polarity in the hydrophobic pocket facilitates the binding of water capable of quenching carbocation intermediates. Furthermore, the substitution of polar residues for F96 yields high-fidelity sesquisabinene synthases. Crystal structures of selected mutants reveal that residues defining the three-dimensional contour of the hydrophobic pocket can be substituted without triggering significant structural changes elsewhere in the active site. Finally, more radical nonpolar–polar amino acid substitutions should be considered when terpenoid cyclase active sites are remolded by mutagenesis with the goal of exploring and expanding product chemodiversity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonequilibrium information entropy approach to ternary fission of actinides

Ternary fission of actinides probes the state of the nucleus at scission. Light clusters are produced in space and time very close to the scission point. Within the nonequilibrium statistical operator method, a generalized Gibbs distribution is constructed from the information given by the observed yields of isotopes. Using this relevant statistical operator, yields are calculated taking excited states and continuum correlations into account, in accordance with the virial expansion of the equation of state. Furthermore, clusters with mass number A≤10 are well described using the nonequilibrium generalizations of temperature and chemical potentials. Improving the virial expansion, in-medium effects may become of importance in determining the contribution of weakly bound states and continuum correlations to the intrinsic partition function. Yields of larger clusters, which fail to reach this quasiequilibrium form of the relevant distribution, are described by nucleation kinetics, and a saddle-to-scission relaxation time of about 7000 fm/c is inferred. Light-charged particle emission, described by reaction kinetics and virial expansions, may therefore be regarded as a very important tool to probe the nonequilibrium time evolution of actinide nuclei during fission.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Uncertainty propagation in feed-forward neural network models

We develop new uncertainty propagation methods for feed-forward neural network architectures with leaky ReLU activation functions subject to random perturbations in the input vectors. In particular, we derive analytical expressions for the probability density function (PDF) of the neural network output and its statistical moments as a function of the input uncertainty and the parameters of the network, i.e., weights and biases. A key finding is that an appropriate linearization of the leaky ReLU activation function yields accurate statistical results even for large perturbations in the input vectors. This can be attributed to the way information propagates through the network. We also propose new analytically tractable Gaussian copula surrogate models to approximate the full joint PDF of the neural network output. To validate our theoretical results, we conduct Monte Carlo simulations and a thorough error analysis on a multi-layer neural network representing a nonlinear integro-differential operator between two polynomial function spaces. Our findings demonstrate excellent agreement between the theoretical predictions and Monte Carlo simulations.

MLP networks↗

Spin currents of charged Dirac particles in rotating coordinates

The semiclassical Boltzmann transport equation of charged, massive fermions in a rotating frame of reference, in the presence of external electromagnetic fields is solved in the relaxation time approach to establish the distribution function up to linear order in the electric field in rotating coordinates, centrifugal force and the derivatives. The spin and spin current densities are calculated by means of this distribution function at zero temperature up to the first order. It is shown that the nonequilibrium part of the distribution function yields the spin Hall effect for fermions constrained to move in a plane perpendicular to the angular velocity and magnetic field. Moreover it yields an analogue of Ohm’s law for spin currents whose resistivity depends on the external magnetic field and the angular velocity of the rotating frame. Spin current densities in three-dimensional systems are also established.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Extreme sparsification of physics-augmented neural networks for interpretable model discovery in mechanics

Data-driven constitutive modeling with neural networks has received increased interest in recent years due to its ability to easily incorporate physical and mechanistic constraints and to overcome the challenging and time-consuming task of formulating phenomenological constitutive laws that can accurately capture the observed material response. However, even though neural network-based constitutive laws have been shown to generalize proficiently, the generated representations are not easily interpretable due to their high number of trainable parameters. Sparse regression approaches exist that allow for obtaining interpretable expressions, but the user is tasked with creating a library of model forms which by construction limits their expressiveness to the functional forms provided in the libraries. Here, in this work, we propose to train regularized physics-augmented neural network-based constitutive models utilizing a smoothed version of $L^0$-regularization. This aims to maintain the trustworthiness inherited by the physical constraints, but also enables interpretability which has not been possible thus far on any type of machine learning-based constitutive model where model forms were not assumed a priori but were actually discovered. During the training process, the network simultaneously fits the training data and penalizes the number of active parameters, while also ensuring constitutive constraints such as thermodynamic consistency. We show that the method can reliably obtain interpretable and trustworthy constitutive models for compressible and incompressible hyperelasticity, yield functions, and hardening models for elastoplasticity, using synthetic and experimental data. This work aims to set a new paradigm for interpretable machine learning models in the broad area of solid mechanics where low and limited data is available along with prior knowledge of physical constraints that the learned maps need to obey. This paradigm can potentially be extended to a broader spectrum of scientific exploration.

Data-driven constitutive models↗

Bridging the gap between simulated and experimental ionic conductivities in lithium superionic conductors

Lithium superionic conductors (LSCs) are of major importance as solid electrolytes for next-generation all-solid-state lithium-ion batteries. While ab initio molecular dynamics have been extensively applied to study these materials, there are often large discrepancies between predicted and experimentally measured ionic conductivities and activation energies due to the high temperatures and short time scales of such simulations. Here, we present a strategy to bridge this gap using moment tensor potentials (MTPs). We show that MTPs trained on energies and forces computed using the van der Waals optB88 functional yield much more accurate lattice parameters, which in turn leads to accurate prediction of ionic conductivities and activation energies for the Li 0·33 La 0·56 TiO 3 , Li 3 YCl 6 and Li 7 P 3 S 11 LSCs. NPT MD simulations using the optB88 MTPs also reveal that all three LSCs undergo a transition between two quasi-linear Arrhenius regimes at relatively low temperatures. This transition can be traced to an increase in the number and diversity of diffusion pathways, in some cases with a change in the dimensionality of diffusion. Furthermore, this work presents not only an approach to develop high accuracy MTPs, but also outlines the diffusion characteristics for LSCs which is otherwise inaccessible through ab initio computation.

25 ENERGY STORAGE↗

Experimental study of compaction localization in carbonate rock and constitutive modeling of mechanical anisotropy

Abstract Sedimentary rocks are inherently anisotropic and prone to strain localization. While the influence of rock anisotropy on the brittle/dilative regime has been studied extensively, its influence on the ductile/compactive regime is much less explored. This paper discusses the anisotropic behavior of a high‐porosity carbonate rock from central Europe (the Maastricht Tuffeau). A set of triaxial tests with concurrent x‐ray tomography has been performed at different confining pressures. The anisotropic characteristics of this rock have been investigated by testing samples cored at different inclinations of the bedding, thus revealing non‐negligible effects of the coring direction on yielding and compaction behavior. Specifically, samples cored perpendicular to bedding display higher strength and longer stages of post‐yielding deformation before manifesting re‐hardening. Despite such alterations of the inelastic response, Digital Image Correlation has revealed that the strain localization mode is independent of the coring direction, thus being primarily affected by the confinement level. To capture the observed interaction between material anisotropy and compaction behavior at the continuum‐scale, an elastoplastic constitutive law has been proposed. For this purpose, a set of tensorial bases has been introduced to replicate how the oriented rock fabric modulates the yielding and plastic flow characteristics of the material. The analyses show that the impact of the coring direction on yield function and plastic flow rule is fundamentally different, thus requiring the use of distinct projection strategies (a strategy here defined heterotopic mapping). The performance of the model, studied through parametric analyses and by calibrating the experimental results, illustrates the improved capability of the proposed constitutive approach when applied to strongly anisotropic porous rocks.

Shahin, Ghassan↗

A micromorphically regularized Cam-clay model for capturing size-dependent anisotropy of geomaterials

Here we introduce a regularized anisotropic modified Cam-clay (MCC) model which captures the size-dependent anisotropic elastoplastic responses for clay, mudstone, shales, and sedimentary rock. By homogenizing the multiscale anisotropic effects induced by clay particle aggregate, clusters, peds, micro-fabric, and mineral contact across length scales, we introduce two distinctive anisotropic mechanisms for the MCC model at the material point and mesoscale levels. We first employ a mapping that links the anisotropic stress state to a fictitious isotropic principal stress-space to introduce anisotropy at the material point scale. Then, the mesoscale anisotropy is introduced via an anisotropic regularization mechanism. This anisotropic regularization mechanism is triggered by introducing gradient-dependence of the internal variables through a penalty method such that the resultant gradient-enhanced plastic flow may exhibit anisotropic responses non-coaxial to the stress gradient of the yield function. The influence of the size-dependent anisotropy on the formation of the shear band and the macroscopic responses of the effective media are analyzed in 2D and 3D numerical examples.

42 ENGINEERING↗

Connections between collinear and transverse-momentum-dependent polarized observables within the Collins–Soper–Sterman formalism

We extend the improved Collins–Soper–Sterman (iCSS) W+Y construction recently presented in [1] to the case of polarized observables, where we focus in particular on the Sivers effect in semi-inclusive deep-inelastic scattering. We further show how one recovers the expected leading-order collinear twist-3 result from a (weighted) q T -integral of the differential cross section. We are also able to demonstrate the validity of the well-known relation between the (TMD) Sivers function and the (collinear twist-3) Qiu–Sterman function within the iCSS framework. This relation allows for their interpretation as functions yielding the average transverse momentum of unpolarized quarks in a transversely polarized spin-$\frac{1}{2}$ target. We further outline how this study can be generalized to other polarized quantities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accuracy of Density Functional Theory Methods for the Calculation of Magnetic Exchange Couplings in Binuclear Iron(III) Complexes

We assess the performance of popular hybrid density functional approximations for the prediction of magnetic exchange couplings (J) in FeIII complexes. To this end, eleven dinuclear oxo-bridged iron(III) complexes with accurately determined J values were chosen to cover cases of weak and strong antiferromagnetic couplings ranging from -6 cm -1 to -132 cm -1 . Six representative exchange-correlation functionals ranging from the hybrids PBE and B3LYP to meta hybrids (M06, M062X), range separated functionals (HSE, LC-!PBE), and LSDA with 30 % of HF exchange were used for this assessment. These functionals have been suggested as good performers for this particular property in transition metal complexes and hence this assessment aims to narrow the interval of con dence for the particular case of Fe complexes. In addition, we examined the performance of an alternative method based on di erential local spin rotations to calculate magnetic exchange coupling parameters in these complexes. Our results show that, although some of these functionals perform on par, the M06 and HSE functionals yields magnetic exchange couplings in closer agreement with experimental data, with a mean absolute percentage errors of 8.6 and 9.2 %, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

M11plus: A Range-Separated Hybrid Meta Functional with Both Local and Rung-3.5 Correlation Terms and High Across-the-Board Accuracy for Chemical Applications

The way to improve Kohn–Sham density functional theory is to improve the exchange–correlation functionals, and functionals have been successively improved by adding new ingredients, especially local spin density gradients, nonlocal Hartree–Fock exchange, and local meta terms based on kinetic energy density. Here, we present a new kind of functional obtained by adding rung-3.5 terms to a functional including local gradients, local meta terms, and range-separated Hartree–Fock exchange. A rung-3.5 term has short-range nonlocality designed to account for nondynamic correlation; we add two kinds of rung-3.5 terms, one kind modeled on position-dependent Hartree–Fock exchange and another modeled on the spin density at a point interacting with the opposite-spin exchange hole at the same point. Here, optimization of the functional yields broad accuracy for both ground states and excited states with especially significant improvement for systems with strong correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Determining Gyration Tensor of Orienting Macromolecules through Their Scattering Signature

A method is presented for quantitatively evaluating the shape and size of deformed particles in dispersion from their two-dimensional anisotropic spectra by small-angle scattering. By means of real spherical harmonic expansion, we derive analytical expressions of the gyration tensor R in terms of experimentally measured anisotropic scattering functions, yielding a tensorial extension of the Guinier law. We demonstrate the usefulness of this approach by a model study of an affinely deformed Gaussian chain. We further show that radius of gyration R g is the source term of intraparticle structure factor at the mean-field limit, and from this perspective, we address the connection between R and conformation asphericity. As a result, the developed method not only facilitates quantitative scattering studies of deforming materials, but also provides insightful information regarding their deformation behavior at the molecular level based on the symmetric properties of real spherical harmonics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First Analysis of Earth's Stratospheric γ ‐Ray Emission in Geographical Coordinates With Fermi LAT

Abstract From low‐Earth orbit, the Earth is an extremely bright γ ‐ray source compared to distant astrophysical objects. The high‐energy γ ‐ray emission, from the Earth's upper atmosphere, is produced by the interactions between cosmic rays (CRs) and air molecules. As CRs are predominantly charged particles, the geomagnetic field acts as a spectrometer, forbidding CRs below a certain energy to arrive and interact with the atmosphere at a given geomagnetic location from a given direction. We use photon data between 0.2 and 20 GeV as observed by the Fermi Large Area Telescope (LAT) to create, for the first time, stratospheric γ ‐ray emission maps of the Earth in the geographical coordinate system, for different viewing directions from LAT altitude. These maps confirm a strong association between measured γ ‐ray fluxes and geomagnetic cutoffs for CRs. We also report the spectrum of the Earth's stratospheric γ ‐ray emission in cardinal directions and use the geomagnetic spectrometer effect to infer the atmosphere's yield function of γ rays per incoming CR proton as a function of CR rigidity at the altitude of the Fermi spacecraft. This work is relevant to the study of near‐Earth radiation exposure for astronauts and spacecraft, modeling the geomagnetic field, and CR‐air interactions.

Madlee, S.↗

Quantum optical microcombs

We present that a key challenge for quantum science and technology is to realize large-scale, precisely controllable, practical systems for non-classical secured communications, metrology and, ultimately, meaningful quantum simulation and computation. Optical frequency combs represent a powerful approach towards this goal, as they provide a very high number of temporal and frequency modes that can result in large-scale quantum systems. The generation and control of quantum optical frequency combs will enable a unique, practical and scalable framework for quantum signal and information processing. Here, we review recent progress on the realization of energy–time entangled optical frequency combs and discuss how photonic integration and the use of fibre-optic telecommunications components can enable quantum state control with new functionalities, yielding unprecedented capability.

42 ENGINEERING↗

Demonstration of nearly pinhole-free epitaxial aluminum thin films by sputter beam epitaxy

Superconducting resonators with high quality factors have been fabricated from aluminum films, suggesting potential applications in quantum computing. Improvement of thin film crystal quality and removal of void and pinhole defects will improve quality factor and functional yield. Epitaxial aluminum films with superb crystallinity, high surface smoothness, and interface sharpness were successfully grown on the c-plane of sapphire using sputter beam epitaxy. This study assesses the effects of varying substrate preparation conditions and growth and prebake temperatures on crystallinity and smoothness. X-ray diffraction and reflectivity measurements yield extensive Laue oscillations and Kiessig thickness fringes for films grown at 200 °C under 15 mTorr Ar, indicating excellent crystallinity and surface smoothness; moreover, an additional substrate preparation procedure which involves (1) a modified substrate cleaning procedure and (2) prebake at 700 °C in 20 mTorr O 2 is shown by atomic force microscopy to yield nearly pinhole-free film growth while maintaining epitaxy and high crystal quality. The modified cleaning procedure is environmentally friendly and eliminates the acid etch steps common to conventional sapphire preparation, suggesting potential industrial application both on standard epitaxial and patterned surface sapphire substrates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On the geometric dependence of the molecular dipole polarizability in water: A benchmark study of higher-order electron correlation, basis set incompleteness error, core electron effects, and zero-point vibrational contributions

In this work, we investigate how geometric changes influence the static dipole polarizability ($α$) of a water molecule by explicitly computing the corresponding dipole polarizability surface (DPS) across 3125 total (1625 symmetry-unique) geometries using linear response coupled cluster theory including single, double, and triple excitations (LR-CCSDT) and the doubly augmented triple-$ζ$ basis set (d-aug-cc-pVTZ). Analytical formulae based on power series expansions of this $ab initio$ surface are generated using linear least-squares analysis and provide highly accurate estimates of this quantity as a function of molecular geometry (i.e., bond and angle variations) in a computationally tractable manner. An additional database, which consists of 25 representative molecular geometries and incorporates a more thorough treatment of both basis sets and core electron effects, is provided as a current benchmark for this quantity and the corresponding leading-order $C_6$ dispersion coefficient. This database has been utilized to assess the importance of these effects as well as the relative accuracy that can be obtained using several quantum chemical methods and a library of density functional approximations. In addition to high-level electron correlation methods (like CCSD) and our analytical least-squares formulae, we find that the SCAN0, PBE0, MN15, and B97-2 hybrid functionals yield the most accurate descriptions of the molecular polarizability tensor in H 2 O. Using first-order perturbation theory, we compute the zero-point vibrational correction to $α$ at the CCSDT/d-aug-cc-pVTZ level and find that this correction contributes approximately 3% to the isotropic ($α$ iso ) and nearly 50% to the anisotropic ($α$ aniso ) polarizability values. In doing so, we find that $α$ iso = 9.8307 bohr 3 , which is in excellent agreement with the experimental value of 9.83 ± 0.02 bohr 3 provided by Russell and Spackman. The DPS reported herein provides a benchmark-quality quantum mechanical estimate of this fundamental quantity of interest and should find extensive use in the development (and assessment) of next-generation force fields and machine-learning based approaches for modeling water in complex condensed-phase environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites

Quantum dot (QD) biological imaging and sensing applications often require surface modification with single-stranded deoxyribonucleic acid (ssDNA) oligonucleotides. Furthermore, ssDNA conjugation can be leveraged for precision QD templating via higher-order DNA nanostructures to exploit emergent behaviors in photonic applications. Use of ssDNA-QDs across these platforms requires compact, controlled conjugation that engenders QD stability over a wide pH range and in solutions of high ionic strength. However, cur-rent ssDNA-QD conjugation approaches suffer from limitations, such as the requirement for thick coatings, low control over ssDNA labeling density, requirement of large amounts of ssDNA, or low colloidal or photostability, restraining implementation in many applications. Here, we combine thin, multidentate, phytochelatin-3 (PC3) QD passivation techniques with strain-promoted copper-free alkyne-azide click chemistry to yield functional ssDNA-QDs with high stability. This process was broadly applicable across QD sizes (i.e.,λ em = 540, 560, 600 nm), ssDNA lengths (i.e., 10–16 base pairs, bps), and sequences (poly thymine, mixed bps). The resulting compacts sDNA-QDs displayed a fluorescence quenching efficiency of up to 89% by hybridization with complementary ssDNA-AuNPs. Further-more, ssDNA-QDs were successfully incorporated with higher-order DNA origami nanostructure templates. Finally, this approach, combining PC3 passivation with click chemistry, generates ssDNA-PC3-QDs that enable emergent QD properties in DNA-based devices and applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

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↗