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At least 811 records · Page 45

Generalized spin σ -SCF method

We introduce a generalization of the σ-SCF method to approximate noncollinear spin ground and excited single-reference electronic states by minimizing the Hamiltonian variance. The new method is based on the σ-SCF method, originally proposed by Ye et al. [J. Chem. Phys. 147, 214104 (2017)], and provides a prescription to determine ground and excited noncollinear spin states on an equal footing. Our implementation was carried out utilizing an initial simulated annealing stage followed by a mean-field iterative self-consistent approach to simplify the cumbersome search introduced by generalizing the spin degrees of freedom. The simulated annealing stage ensures a broad exploration of the Hilbert space spanned by the generalized spin single-reference states with random complex element-wise rotations of the generalized density matrix elements in the simulated annealing stage. The mean-field iterative self-consistent stage employs an effective Fockian derived from the variance, which is utilized to converge tightly to the solutions. This process helps us to easily find complex spin structures, avoiding manipulating the initial guess. As proof-of-concept tests, we present results for Hn (n = 3–7) planar rings and polyhedral clusters with geometrical spin frustration. We show that most of these systems have noncollinear spin excited states that can be interpreted in terms of geometric spin frustration. These states are not directly targeted by energy minimization methods, which are meant to converge to the ground state. This stresses the capability of the σ-SCF methodology to find approximate noncollinear spin structures as mean-field excited states.

Chemistry↗

A three-point velocity estimation method for two-dimensional coarse-grained imaging data

Time delay and velocity estimation methods have been widely studied subjects in the context of signal processing, with applications in many different fields of physics. The velocity of waves or coherent fluctuation structures is commonly estimated as the distance between two measurement points divided by the time lag that maximizes the cross correlation function between the measured signals, but this is demonstrated to result in erroneous estimates for two spatial dimensions. We present an improved method to accurately estimate both components of the velocity vector, relying on three non-aligned measurement points. We introduce a stochastic process describing the fluctuations as a superposition of uncorrelated pulses moving in two dimensions. Using this model, we show that the three-point velocity estimation method, using time delays calculated through cross correlations, yields the exact velocity components when all pulses have the same velocity. The two- and three-point methods are tested on synthetic data generated from realizations of such processes for which the underlying velocity components are known. The results reveal the superiority of the three-point technique. Finally, we demonstrate the applicability of the velocity estimation on gas puff imaging data of strongly intermittent plasma fluctuations due to the radial motion of coherent, blob-like structures at the boundary of the Alcator C-Mod tokamak.

Materials Science↗

A new method for solving the linearized 1D Vlasov–Poisson system yielding a new class of solutions

We describe a new method for solving the linearized 1D Vlasov–Poisson system by using properties of Cauchy-type integrals. Our method remedies critical flaws of the two standard methods, reveals a previously unrecognized Gaussian-in-time-like decay, and can also account for an externally applied electric field. The Landau approximation involves deforming the Bromwich contour around the poles closest to the real axis due to the analytically continued dielectric function, finding the long-time behavior for a stable system: Landau damping. Jackson's generalization encircles all poles while sending the contour to infinity, assuming its contribution vanishes, which is not true in general. This gives incorrect solutions for physically reasonable configurations and can exhibit pathological behavior, of which we show examples. The van Kampen method expresses the solution for a stable equilibrium as a continuous superposition of waves, resulting in an opaque integral. Case's generalization includes unstable systems and predicts a decaying discrete mode for each growing discrete mode, an apparent contradiction to both the Jackson solution and ours. We show, without imposing additional constraints, that the decaying modes are never present in the time evolution due to an exact cancellation with part of the continuum. Our solution is free of integral expressions, is obtained using algebra and Laurent series expansions, does not rely on analytic continuations, and results in a correct asymptotically convergent form in the case of infinite sums. The analysis used can be readily applied in higher-dimensional, electromagnetic systems and also provides a new technique for evaluating certain inverse Laplace transforms.

Physics↗

Dynamic response of 17-4 stainless steel as a function of manufacturing method and heat treatment

We present a series of plate-impact experiments on 17-4 stainless steel to study the effect of manufacturing method and heat treatment on the Hugoniot elastic limit (HEL), Hugoniot, phase transformation stress, and spallation strength. Two traditional manufacturing methods were considered, wrought processing and casting, as well as two additive manufacturing methods, laser powder-bed fusion (LPBF) and wire-fed electron beam (EBAM). For both LPBF and EBAM 17-4 stainless steel variants, two billets were printed, enabling the application of two unique heat treatments. The HEL stress depended heavily on the thermal history, with the HEL increasing after the formation of Cu-rich precipitates via heat treatment. The Hugoniot response both below and above the phase transition was unaffected by the manufacturing method or heat treatment. The phase transition stress depended heavily on the thermal history, with its variation being attributed to the presence of various microstructural features. This is supported by a marked increase in the phase transition stress after precipitation hardening. These results suggest that the notion of the phase transition stress being dictated by bulk composition is an oversimplification and the stress fields generated by the meso-scale structure are a dominant force. The spallation strength was lower in the cast material compared to all other 17-4 stainless steel variants due to the presence of brittle δ-ferrite inclusions. Additionally, a drop in the tensile strain-rate was observed in the spallation response above the phase transition stress, which was hypothesized to stem from the kinetics of the reversion to the low-pressure phase during spall.

Compressive stress↗

A novel method for thermal noise reduction, enabling measurements of broadband, low-amplitude electron temperature fluctuations using individual radiometer channels

A new analysis method has been developed for measurements of broadband, low-amplitude turbulent electron temperature fluctuations in fusion plasmas using individual radiometer channels of a correlation electron cyclotron emission diagnostic. This method takes advantage of differences in the correlation time of thermal noise compared to the correlation time of plasma fluctuations in fusion reactors. The validation of this single-channel method is demonstrated using comparisons with the standard dual-channel radiometer spectral decorrelation method for measurements of turbulent electron temperature fluctuations in the core and edge of low confinement (L), improved confinement (I), and high confinement (H)-mode plasmas at the ASDEX Upgrade tokamak.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

First-principles calculation of excited states of diatomic molecules: a benchmark for the Gutzwiller conjugate gradient minimisation method

We recently proposed the Gutzwiller conjugate gradient minimisation (GCGM) method for efficient and accurate calculation of the ground state total energy of molecular and bulk systems. The GCGM method is developed under the framework of Gutzwiller wave function but goes beyond the commonly adopted Gutzwiller approximation to improve the accuracy and flexibility in treating the correlation effects. In this conference proceeding, we benchmark the GCGM method with the calculation of excited state potential energy curves of three diatomic molecules, namely H 2 , N 2 , and O 2 . Our calculations demonstrate the flexibility and reasonable accuracy of the method.

74 ATOMIC AND MOLECULAR PHYSICS↗

Toward Exascale: Overview of Large Eddy Simulations and Direct Numerical Simulations of Nuclear Reactor Flows with the Spectral Element Method in Nek5000

At the beginning of the last decade, Petascale supercomputers (i.e., computers capable of more than 1 petaFLOP) emerged. Now, at the dawn of exascale supercomputing, we provide a review of recent landmark simulations of portions of reactor components with turbulence-resolving techniques that this computational power has made possible. In fact, these simulations have provided invaluable insight into flow dynamics, which is difficult or often impossible to obtain with experiments alone. We focus on simulations performed with the spectral element method, as this method has emerged as a powerful tool to deliver massively parallel calculations at high fidelity by using large eddy simulation or direct numerical simulation. We also limit this paper to constant-property incompressible flow of a Newtonian fluid in the absence of other body or external forces, although the method is by no means limited to this class of flows. We briefly review the fundamentals of the method and the reasons it is compelling for the simulation of nuclear engineering flows. We review in detail a series of Petascale simulations, including the simulations of helical coil steam generators, fuel assemblies, and pebble beds. Even with Petascale computing, however, limitations for nuclear modeling and simulation tools remain. In particular, the size and scope of turbulence-resolving simulations are still limited by computing power and resolution requirements, which scale with the Reynolds number. In the final part of this paper, we discuss the future of the field, including recent advancements in emerging architectures such as GPUbased supercomputers, which are expected to power the next generation of high-performance computers.

computational fluid dynamics↗

Improved Method for Evaluating and Specifying the Chromaticity of Light Sources

This article recommends a method for calculating and specifying light source chromaticity using the CIE 2015 10° color matching functions (CMFs), which, according to analysis of existing psychophysical experiment data, can reduce visual mismatch compared to specifications based on the traditional CIE 1931 2° CMFs. Specifically, this work evaluates, documents, and recommends for adoption a supporting system of measures to be used with the CIE 2015 10° CMFs: a new uniform chromaticity scale (UCS) diagram with coordinates (s, t), a measure of correlated color temperature (CCTst), and a measure of distance from the Planckian locus (Dst). It also presents options for updating nominal classification quadrangles. A complete method of this nature has not yet been standardized, which may be contributing to the slow uptake of the CIE 2015 CMFs. The proposed tools are analogous to u, v, CCT, Duv, and the ANSI C78.377 nominal classification quadrangles that are currently specified in the CIE 1960 UCS using the CIE 1931 2° CMFs. While conceptually equivalent, the differences between the current standard method and the new st system are important for reducing unintended mismatch in the chromaticity of light. Furthermore, the implications of changing chromaticity specification methods are identified by a comparison over a diverse set of real light source SPDs. Finally, as a step toward improving the design and specification of light sources for illumination purposes, we propose a process for implementing the recommendations.

42 ENGINEERING↗

Axisymmetric hydrodynamics in numerical relativity using a multipatch method

In this paper, we describe a method of implementing the axisymmetric evolution of general-relativistic hydrodynamics and magnetohydrodynamics through modification of a multipatch grid scheme. In order to ease the computational requirements required to evolve the post-merger phase of systems involving binary compact massive objects in numerical relativity, it is often beneficial to take advantage of these system's tendency to rapidly settle into states that are nearly axisymmetric, allowing for 2D evolution of secular timescales. We implement this scheme in the spectral Einstein code and show the results of application of this method to four test systems including viscosity, magnetic fields, and neutrino radiation transport. Our results show that this method can be used to quickly allow already existing 3D infrastructure that makes use of local coordinate system transformations to be made to run in axisymmetric 2D with the flexible grid creation capabilities of multipatch methods. Our code tests include a simple model of a binary neutron star postmerger remnant, for which we confirm the formation of a massive torus which is a promising source of post-merger ejecta.

79 ASTRONOMY AND ASTROPHYSICS↗

Review of nonflow estimation methods and uncertainties in relativistic heavy-ion collisions

Abstract Collective anisotropic flow, where particles are correlated over the entire event, is a prominent phenomenon in relativistic heavy-ion collisions and is sensitive to the properties of the matter created in those collisions. It is often measured by two- and multi-particle correlations and is therefore contaminated by nonflow, those genuine few-body correlations unrelated to the global event-wise correlations. Many methods have been devised to estimate nonflow contamination with various degrees of successes and difficulties. Here, we review those methods pedagogically, discussing the pros and cons of each method, and give examples of ballpark estimate of nonflow contamination and associated uncertainties in relativistic heavy-ion collisions. We hope such a review of the various nonflow estimation methods in a single place would prove helpful to future researches.

Feng, Yicheng (ORCID:0000000169010870)↗

Versatile recognition of graphene layers from optical images under controlled illumination through green channel correlation method

In this study, a simple yet versatile method is proposed for identifying the number of exfoliated graphene layers transferred on an oxide substrate from optical images, utilizing a limited number of input images for training, paired with a more traditional number of a few thousand well-published Github images for testing and predicting. Two thresholding approaches, namely the standard deviation-based approach and the linear regression-based approach, were employed in this study. The method specifically leverages the red, green, and blue color channels of image pixels and creates a correlation between the green channel of the background and the green channel of the various layers of graphene. This method proves to be a feasible alternative to deep learning-based graphene recognition and traditional microscopic analysis. The proposed methodology performs well under conditions where the effect of surrounding light on the graphene-on-oxide sample is minimum and allows rapid identification of the various graphene layers. Here, the study additionally addresses the functionality of the proposed methodology with nonhomogeneous lighting conditions, showcasing successful prediction of graphene layers from images that are lower in quality compared to typically published in literature. In all, the proposed methodology opens up the possibility for the non-destructive identification of graphene layers from optical images by utilizing a new and versatile method that is quick, inexpensive, and works well with fewer images that are not necessarily of high quality.

36 MATERIALS SCIENCE↗

Development of a tomographic reconstruction method for axisymmetric D α emission profiles in the ITER plasma boundary

A tomographic method for reconstructing the axially symmetric D α emission profile in the ITER scrape-off layer and divertor from D α intensity measurements in the fields of view (FoV) of Vis/IR TV and Divertor Impurity Monitor diagnostics is under development. The method takes into account the strong background signal due to stray light from divertor produced by reflections from the metal wall of the vacuum chamber. The method allows to filter out the reflections in D α signals measured in the main chamber. Here, the accuracy of this method is tested within the framework of a synthetic diagnostic, which uses the Raysect and Cherab numerical codes for ray-tracing simulations. The D α emission profiles, simulated with the SOLPS and OEDGE codes, are used as synthetic experimental data. Uncertainty in light reflection properties of the first wall (FW) is the major factor affecting the accuracy of the D α emission reconstruction. The dependence on the uncertainty in the FW surface roughness and on the ratio of diffusive to specular reflection of the error in recovering useful D α signals (the direct light without reflections) in the FoV of the ITER main chamber H-alpha and Visible Spectroscopy Diagnostic is obtained.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electric field determination in transient plasmas: in situ & non-invasive methods

Abstract One of the primary basic plasma parameters within transient nonequilibrium plasmas is the reduced electric field strength, roughly understood as the ratio of the electrical energy given to the charged species between two collisions. While physical probes have historically been used for electric field measurements, recent advances in high intensity lasers and sensitive detection methods have allowed for non-invasive optical electric field determination in nearly any discharge configuration with time-resolution up to the sub-nanosecond range and sub-millimeter spatial resolution. This topical review serves to highlight several non-invasive methods for in situ electric field strength determination in transient plasmas ranging from high vacuum environments to atmospheric pressure and above. We will discuss the advantages and proper implementation of (i) laser induced fluorescence dip spectroscopy for measurements in low pressure RF discharges, (ii) optical emission spectroscopy based methods for nitrogen, helium or hydrogen containing discharges, (iii) electric field induced coherent Raman scattering, and (iv) electric field induced second harmonic generation. The physical mechanism for each method will be described as well as basic implementation and highlighting recent results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A random-sampling method as an efficient alternative to variational Monte Carlo for solving Gutzwiller wavefunctions

Abstract We present a random-sampling (RS) method for evaluating expectation values of physical quantities using the variational approach. We demonstrate that the RS method is computationally more efficient than the variational Monte Carlo method using the Gutzwiller wavefunctions applied on single-band Hubbard models as an example. Non-local constraints can also been easily implemented in the current scheme that capture the essential physics in the limit of strong on-site repulsion. In addition, we extend the RS method to study the antiferromagnetic states with multiple variational parameters for 1D and 2D Hubbard models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Evaluating probabilistic deep learning methods for uncertainty quantification of temperature downscaling

Deep learning (DL) has emerged as a promising tool for downscaling coarse-resolution climate data to high-resolution outputs, enabling improved regional climate predictions. A critical aspect of DL-based downscaling is the incorporation of uncertainty quantification (UQ), which enhances the interpretability and reliability of predictions—key factors for climate risk assessment and decision-making. This study develops a DL model to downscale 2 m temperature across the contiguous United States using reanalysis datasets. We systematically evaluate three epistemic UQ methods—deep ensembles (DEns), Monte Carlo dropout (MCD), and Flipout—based on their probabilistic accuracy, downscaling performance, sensitivity to geographical features, and computational efficiency. Results indicate that MCD generally outperforms Flipout and DEns in terms of calibration and downscaling accuracy. However, DEns demonstrate lower calibration errors in coastal regions, indicating its higher confidence within these areas. Flipout, in contrast, is more sensitive to elevation gradients and exhibits higher calibration errors in mountainous regions. Hence, the choice of UQ method for this task depends on the specific requirements of the application. For applications that prioritize overall calibration, downscaling accuracy, and computational efficiency, MCD is a strong candidate. These findings highlight the importance of selecting UQ methods based on application-specific requirements, such as geographical context and computational constraints. By addressing the trade-offs between UQ methods, this study provides actionable insights for improving the reliability, scalability, and utility of DL-based downscaling in climate science.

Environmental sciences↗

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Electron tomography imaging methods with diffraction contrast for materials research

Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

36 MATERIALS SCIENCE↗

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗