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At least 361 records · Page 20

The difference between molecules and materials: Reassessing the role of exact conditions in density functional theory

Exact conditions have long been used to guide the construction of density functional approximations. However, hundreds of empirical-based approximations tailored for chemistry are in use, of which many neglect these conditions in their design. We analyze well-known conditions and revive several obscure ones. Two crucial distinctions are drawn: that between necessary and sufficient conditions and that between all electronic densities and the subset of realistic Coulombic ground states. Simple search algorithms find that many empirical approximations satisfy many exact conditions for realistic densities and non-empirical approximations satisfy even more conditions than those enforced in their construction. The role of exact conditions in developing approximations is revisited.

Chemistry↗

Method for estimating optimal spectral and energy parameters of laser irradiation in photodynamic therapy of biological tissue

We have solved the problem of layer-by-layer laser-light dosimetry in biological tissues and of selecting an individual therapeutic dose in laser therapy. A method is proposed for real-time monitoring of the radiation density in tissue layers in vivo, concentrations of its endogenous (natural) and exogenous (specially administered) chromophores, as well as in-depth distributions of the spectrum of light action on these chromophores. As the background information use is made of the spectrum of diffuse light reflected from a patient's tissue, measured by a fibre-optic spectrophotometer. The measured spectrum is quantitatively analysed by the method of approximating functions for fluxes of light multiply scattered in tissue and by a semi-analytical method for calculating the in-depth distribution of the light flux in a multi-layered medium. We have shown the possibility of employing the developed method for monitoring photosensitizer and oxyhaemoglobin concentrations in tissue, light power absorbed by chromophores in tissue layers at different depths and laser-induced changes in the tissue morphology (vascular volume content and ratios of various forms of haemoglobin) during photodynamic therapy. (biophotonics)

60 APPLIED LIFE SCIENCES↗

Atomic ionization: sd energy imbalance and Perdew–Zunger self-interaction correction energy penalty in 3d atoms

To accurately describe the energetics of transition metal systems, density functional approximations (DFAs) must provide a balanced description of s- and d- electrons. One measure of this is the sd transfer error, which has previously been defined as E ( 3 d n − 1 4 s 1 ) − E ( 3 d n − 2 4 s 2 ) . Theoretical concerns have been raised about this definition due to its evaluation of excited-state energies using ground-state DFAs. A more serious concern appears to be strong correlation in the 4s 2 configuration. Here, we define a ground-state measure of the sd energy imbalance, based on the errors of s- and d-electron second ionization energies of the 3d atoms, that effectively circumvents the aforementioned problems. We find an improved performance as we move from the local spin density approximation (LSDA) to the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) to the regularized and restored Strongly Constrained and Appropriately Normed (r 2 SCAN) meta-GGA for first-row transition metal atoms. However, we find large (∼2 eV) ground-state sd energy imbalances when applying a Perdew–Zunger 1981 self-interaction correction. This is attributed to an “energy penalty” associated with the noded 3d orbitals. A local scaling of the self-interaction correction to LSDA results in a balance of s- and d-errors.

Science & Technology - Other Topics↗

Expanded capabilities of the CarMa code in modeling resistive wall mode dynamics with 3-D conductors

In this work, an improved version of the CarMa code is presented, called CarMa-D, for the analysis of resistive wall modes (RWMs) in fusion devices, simultaneously considering the effects of volumetric three-dimensional conducting structures, plasma dynamics, toroidal rotation or drift-kinetic damping. Unlike static CarMa, CarMa-D does not rely on the simplifying assumptions such as neglecting the plasma mass, toroidal rotation and kinetic damping. The new coupling strategy is based on matrix-based Padé rational functions approximation of plasma a response. The arising mathematical model is formally equivalent to the original CarMa model, but with a higher number of degrees of freedom to model the dynamics of the plasma. CarMa-D overcomes the main limitations of the original CarMa, in particular: (i) the massless assumption for the plasma is removed, allowing modeling of global modes growing both on ideal kink time scales and in the typical RWM growth rate regime, with a suitable treatment of the model; (ii) the effects of toroidal plasma flow and drift kinetic damping can be included into the new model, providing a powerful tool to study macroscopic phenomena where both plasma dynamics and 3-D conducting structures play important roles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Ab Initio Bulk Free Energy Surface of Proper Ferroelectrics

We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core of our approach is the metadynamics algorithm that extracts the polarization dependence of the FES from all-atom molecular dynamics simulations without an a priori ansatz. The rest of the FES is derived from the metadynamics trajectories that span the relevant phase space. We demonstrate our approach in the case of lead titanate. The errors across the phase transition, due to DFT numerics, all-atom molecular dynamics, and free energy evaluation by enhanced sampling, can be systematically controlled and are of the order of 1 meV/atom. The accuracy of the resulting ab initio FES is only limited by the adopted functional approximation of DFT.

Xie, Pinchen [Lawrence Berkeley National Laborator↗

First principles study of the Fermi surface topology of CeCu 2 ⁢Si 2

Since the discovery of heavy-fermion superconductivity in CeCu 2 ⁢Si 2 , the material has attracted great interest, particularly with regard to the nature of the superconducting pairing and its mechanism. Consequently, it is essential to better understand the electronic Fermi surface topology and its role in strong antiferromagnetic fluctuations. The standard density functional theory method is insufficient to model the interplay of strong on-site Coulomb repulsion in localized 4⁢𝑓 electrons and their hybridization with itinerant ligand-orbital electrons. We have performed electronic ground-state calculations on CeCu 2 ⁢Si 2 using the Gutzwiller wave function approximation. The Gutzwiller approximation captures the quasiparticle band renormalization from the strong on-site Coulomb repulsion. We have performed an analysis of this effect on the electronic structure and the Fermi surface topology by varying the interaction strength and taking into account the crystal-field splitting. Using the de Haas-van Alphen effect, the extremal Fermi surface cross-sectional areas were calculated to quantify the effects of quasiparticle mass renormalization on the Fermi surface. Our results confirm the presence of two Fermi surface sheets corresponding to the heavy (488⁢𝑚 𝑒 ) and light (4.35⁢𝑚 𝑒 ) quasiparticles when the crystal-field splitting is accounted for on equal footing with the electronic correlations. This method gives the best agreement with experimental measurements as well as the renormalized band method.

36 MATERIALS SCIENCE↗

Probing the state of hydrogen in δ − AlOOH at mantle conditions with machine learning potential

Hydrous and nominally anhydrous minerals are a fundamental class of solids of enormous significance to geophysics. They are the water carriers in the deep geological water cycle and impact structural, elastic, plastic, and thermodynamic properties and phase relations in Earth's forming aggregates (rocks). They play a critical role in the geochemical and geophysical processes that shape the planet. Their complexity has prevented predictive calculations of their properties, but progress in materials simulations ushered by machine-learning potentials is transforming this state of affairs. Here, we adopt a hybrid approach that combines deep learning potentials (DPs) with the strongly constrained and appropriately normed meta-generalized gradient approximation functional to simulate a prototypical hydrous system. We illustrate the success of this approach to simulate δ − AlOOH ( δ ) , a phase capable of transporting water down to near the core-mantle boundary of the Earth ( ∼ 2900 km depth and ∼ 135 GPa ) in subducting slabs. A high-throughput sampling of phase space using molecular dynamics simulations with DPs sheds light on the hydrogen-bond behavior and proton diffusion at geophysical conditions. These simulations provide a pathway for a deeper understanding of these crucial components that shape Earth's internal state. Published by the American Physical Society 2024

Luo, Chenxing (ORCID:0000000341166851)↗

Report on the sixth blind test of organic crystal structure prediction methods

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z ' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

Chemistry↗

Compressive Neural Representations of Volumetric Scalar Fields

Here, we present an approach for compressing volumetric scalar fields using implicit neural representations. Our approach represents a scalar field as a learned function, wherein a neural network maps a point in the domain to an output scalar value. By setting the number of weights of the neural network to be smaller than the input size, we achieve compressed representations of scalar fields, thus framing compression as a type of function approximation. Combined with carefully quantizing network weights, we show that this approach yields highly compact representations that outperform state-of-the-art volume compression approaches. The conceptual simplicity of our approach enables a number of benefits, such as support for time-varying scalar fields, optimizing to preserve spatial gradients, and random-access field evaluation. We study the impact of network design choices on compression performance, highlighting how simple network architectures are effective for a broad range of volumes.

97 MATHEMATICS AND COMPUTING↗

Carriers confinement study of GaNAsBi/GaAs QWs emitting at 1.3 and 1.55 μm

Band structures of GaN{sub 0.58y}As{sub 1–1.58y}Bi{sub y}/GaAs quantum wells (QWs) were studied using the band anticrossing model and the envelope function approximation. The confined states energies and the oscillator strengths of interband transitions were determined for well widths L{sub W} and Bi composition y varying in the range of 4–10 nm and 0–0.07 respectively. The emissions 1.3 and 1.55 μm were reached for specific couples (L{sub W}, y). The band anticrossing effect on the in-plane carriers effective mass has been investigated at k = 0. The absorbance spectra were calculated for QWs operating at 1.3 and 1.55 μm.

36 MATERIALS SCIENCE↗

Characteristics of the Schottky barriers of two-terminal thin-film Al/nano-Si film/ITO structures

The temperature dependence of the Schottky-barrier height and series resistance of two-terminal thin-film Al/nano-Si film/ITO structures are determined from the current—voltage (I–V) characteristics in the temperature range of 20–150°C. It is found that the form of the I–V characteristic at all investigated temperatures can be described by a model of two Schottky diodes connected back-to-back. For these diodes, the general formula is obtained, which allows the construction of functions approximating experimental curves with high accuracy. Based on this formula, a computational model is built, which generalizes the theoretical data obtained by S.K. Cheung and N.W. Cheung widely used for analyzing the I–V characteristics of single Schottky diodes. A technique is developed for calculating the Schottky-barrier heights in a system of two Schottky diodes connected back-to-back, their ideality factors, and the series resistance of the system. It is established that the barrier heights in the investigated temperature range are ~1 eV. According to the temperature dependence of the barrier height, such large values result from the presence of a SiO{sub x} (0 ≤ x ≤ 2) oxide layer at the nanoparticle boundaries. Charge carriers can overcome this layer by means of thermal excitation or tunneling. It is established that the intrinsic Schottky-barrier height of the Al/nc-Si film and nc-Si film/ITO junctions is ~0.1 eV. The activation dependences of the series resistance of the Al/nc-Si film/ITO structures and impedance spectra show that combined electric-charge transport related to ionic and electronic conductivity takes place in the structures under study. It is shown that the contribution of the electronic conductivity to the total transport process increases as the sample temperature is raised.

36 MATERIALS SCIENCE↗

A Least-Squares-Based Weak Galerkin Finite Element Method for Second Order Elliptic Equations

Here, in this article, we introduce a least-squares-based weak Galerkin finite element method for the second order elliptic equation. This new method is shown to provide very accurate numerical approximations for both the primal and the flux variables. In contrast to other existing least-squares finite element methods, this new method allows us to use discontinuous approximating functions on finite element partitions consisting of arbitrary polygon/polyhedron shapes. We also develop a Schur complement algorithm for the resulting discretization problem by eliminating all the unknowns that represent the solution information in the interior of each element. Optimal order error estimates for both the primal and the flux variables are established. An extensive set of numerical experiments are conducted to demonstrate the robustness, reliability, flexibility, and accuracy of the least-squares-based weak Galerkin finite element method. Finally, the numerical examples cover a wide range of applied problems, including singularly perturbed reaction-diffusion equations and the flow of fluid in porous media with strong anisotropy and heterogeneity.

nite element methods↗

nmrfit

Nmrfit reads the output from a nuclear magnetic resonance (NMR) experiment and, through a number of intuitive API calls, produces a least-squares fit of Voigt-function approximations via particle swarm optimization.

Source record↗

LBC (Learning Building Control)

LBC encompasses the source code and data to reproduce and extend results for a manuscript that compares demand responsive control schemes for multi-zone buildings. It includes examples of model predictive control (MPC), value function approximation via CVXPYLAYERS, and differentiable predictive control (DPC). The goal of the study is to evaluate state-of-the-art controllers and establish the efficacy (if any) of learning-based approaches that leverage deep neural networks in one way or another.

Zhang, Xiangyu↗

Comparing machine learning and interpolation methods for loop-level calculations

The need to approximate functions is ubiquitous in science, either due to empirical constraints or high computational cost of accessing the function. In high-energy physics, the precise computation of the scattering cross-section of a process requires the evaluation of computationally intensive integrals. A wide variety of methods in machine learning have been used to tackle this problem, but often the motivation of using one method over another is lacking. Comparing these methods is typically highly dependent on the problem at hand, so we specify to the case where we can evaluate the function a large number of times, after which quick and accurate evaluation can take place. We consider four interpolation and three machine learning techniques and compare their performance on three toy functions, the four-point scalar Passarino-Veltman D_0 D 0 function, and the two-loop self-energy master integral M. We find that in low dimensions (d = 3), traditional interpolation techniques like the Radial Basis Function perform very well, but in higher dimensions (d=5, 6, 9) we find that multi-layer perceptrons (a.k.a neural networks) do not suffer as much from the curse of dimensionality and provide the fastest and most accurate predictions.

97 MATHEMATICS AND COMPUTING↗

Model-form Error Correction using Universal Differential Equations for an Agent-Based Model of Infectious Disease

This report demonstrates universal differential equations (UDEs) as an approach to bridge the gap between ordinary differential equations (ODE) models and agent-based models (ABMs). Using UDE models as surrogates for ABMs allows us to preserve the foundational ODE that represents global disease dynamics while coupling it with a neural network model to approximate functions for the local behaviors of the ABM.

59 BASIC BIOLOGICAL SCIENCES↗

Properties of Dislocation Drag from Phonon Wind at Ambient Conditions

It is well known that, under plastic deformation, dislocations are not only created but also move through the crystal, and their mobility is impeded by their interaction with the crystal structure. At high stress and temperature, this “drag” is dominated by phonon wind, i.e., phonons scattering off dislocations. Employing the semi-isotropic approach discussed in detail in a previous paper (J. Phys. Chem. Solids 2019, 124, 24–35), we discuss here the approximate functional dependence of dislocation drag B on dislocation velocity in various regimes between a few percent of transverse sound speed c T and c T (where c T is the effective average transverse sound speed of the polycrystal). In doing so, we find an effective functional form for dislocation drag B ( v ) for different slip systems and dislocation characters at fixed (room) temperature and low pressure.

36 MATERIALS SCIENCE↗