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At least 793 records · Page 44

Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules

A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field integrals (the X2CAMF scheme) is reported. Furthermore, the present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. The CD-based implementation extends the applicability of X2CAMF-CC and EOMCC methods to medium-sized molecules with the correlation of around 1000 spinors. Benchmark calculations for uranium-containing small molecules have been performed to assess the dependence of CC results with respect to the Cholesky threshold. A Cholesky threshold of 10 –4 is shown to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond dissociation energy of the uranium hexafluoride molecule, UF 6 , with up to quadruple-zeta basis sets and the lowest excitation energy in solvated uranyl ion [UO 2 2+ (H 2 O) 12 ].

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sample Preparation Methods for Targeted Single-Cell Proteomics

We compared three cell isolation and two proteomic sample preparation methods for single-cell and near-single-cell analysis. Whole blood was used to quantify hemoglobin (Hb) and glycated-Hb (gly-Hb) in erythrocytes using targeted mass spectrometry and stable isotope-labeled standard peptides. Each method differed in cell isolation and sample preparation as follows: 1) FACS and automated preparation in one-pot for trace samples (autoPOTS); 2) limited dilution via microscopy and a novel rapid one-pot sample preparation method that circumvented the need for the solid-phase extraction, low-volume liquid handling instrumentation and humidified incubation chamber; and 3) CellenONE-based cell isolation and the same one-pot sample preparation method used for limited dilution. Only the CellenONE device routinely isolated single-cells from which Hb was measured to be 540–660 amol per red blood cell (RBC), which was comparable to the calculated SI reference range for mean corpuscular hemoglobin (390–540 amol/RBC). FACSAria sorter and limited dilution could routinely isolate single-digit cell numbers, to reliably quantify CMV-Hb heterogeneity. Finally, we observed that repeated measures, using 5–25 RBCs obtained from N = 10 blood donors, could be used as an alternative and more efficient strategy than single RBC analysis to measure protein heterogeneity, which revealed multimodal distribution, unique for each individual.

59 BASIC BIOLOGICAL SCIENCES↗

A Versatile Method for Creating Ultrathin Films of Polyzwitterions with Antifouling Properties

Protein repellent (i.e., antifouling) properties of ultrathin polymeric films have been ascribed to the formation of a dense layer of adsorbed polymers, which causes steric hindrance to protein adsorption on underlying substrates. The antifouling properties of the films are hypothesized to be independent of polymer hydrophilicity based on previous studies involving uncharged polymers. Here, to test the hypothesis and extend it to the realm of charged polymers, we have developed a grafting method for creating ultrathin layers of polyzwitterions on solid surfaces. To demonstrate the efficacy of this method, poly[1-(3-sulfopropyl-1)-2-vinylpyridinium betaine] (P2VPPS) was synthesized via free-radical polymerization and immobilized onto surfaces by using a photoreactive benzophenone derivative as the cross-linker, which was covalently bonded to either quartz or Si/SiOx substrates through a silane anchor. We found that ultrathin films with thicknesses of less than 10 nm can be obtained in dry states using 365 nm ultraviolet (UV) cured/cross-linked surface coatings. These films were found to be hydrophilic and undergo structural rearrangements in the presence of water. The antifouling performance of the films was evaluated using Pseudomonas aeruginosa strain PAO1 bacterium as the fouling agent and exhibited antifouling properties with a kinetic control via the coating method (i.e., spin-coating and drop-casting). In particular, the surface area coverages due to the PAO1 cell attachment on the quartz substrates coated with P2VPPS were found to be ∼5% and ∼0% for the spin-coated and drop-casted films, respectively, after 4 h. These results show that the grafting method can be used to generate surfaces with antifouling properties based on ultrathin films of polyzwitterions.

Pseudomonas aeruginosa↗

A Scalable Method for Thickness and Lateral Engineering of 2D Materials

The physical properties of two-dimensional (2D) materials depend strongly on the number of layers. Hence, methods for controlling their thickness with atomic layer precision are highly desirable, yet still too rare, and demonstrated for only a limited number of 2D materials. Here we present a simple and scalable method for the continuous layer-by-layer thinning that works for a large class of 2D materials, notably layered germanium pnictides and chalcogenides. It is based on a simple oxidation/etching process, which selectively occurs on the topmost layers. Through a combination of atomic force microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy and X-ray diffraction experiments we demonstrate the thinning method on germanium arsenide (GeAs), germanium sulfide (GeS) and germanium disulfide (GeS 2 ). We use first-principles simulation to provide insights into the oxidation mechanism. Our strategy, which could be applied to other classes of 2D materials upon proper choice of the oxidation/etching reagent, could pave the way for the realization of 2D material-based devices, such as electronic or optoelectronic ones, where a precise control over the number of layers (hence over the material’s physical properties) is needed. We also show that when used in combination with lithography, our method can be used to make precise patterns in the 2D materials.

2D materials↗

Advanced Newton methods for geodynamical models of Stokes flow with viscoplastic rheologies

Strain localization and resulting plasticity and failure play an important role in the evolution of the lithosphere. These phenomena are commonly modeled by Stokes flows with viscoplastic rheologies. The nonlinearities of these rheologies make the numerical solution of the resulting systems challenging, and iterative methods often converge slowly or not at all. Yet accurate solutions are critical for representing the physics. Moreover, for some rheology laws, aspects of solvability are still unknown. We study a basic but representative viscoplastic rheology law. The law involves a yield stress that is independent of the dynamic pressure, referred to as von Mises yield criterion. Two commonly used variants, perfect/ideal and composite viscoplasticity, are compared. We derive both variants from energy minimization principles, and we use this perspective to argue when solutions are unique. We propose a new stress-velocity Newton solution algorithm that treats the stress as an independent variable during the Newton linearization but requires solution only of Stokes systems that are of the usual velocity-pressure form. To study different solution algorithms, we implement 2-D and 3-D finite element discretizations, and we generate Stokes problems with up to 7 orders of magnitude viscosity contrasts, in which compression or tension results in significant nonlinear localization effects. Comparing the performance of the proposed Newton method with the standard Newton method and the Picard fixed-point method, we observe a significant reduction in the number of iterations and improved stability with respect to problem nonlinearity, mesh refinement, and the polynomial order of the discretization.

Rudi, Johann↗

A Drift‐Kinetic Method for Obtaining Gradients in Plasma Properties From Single‐Point Distribution Function Data

Abstract In this paper, we derive a new drift‐kinetic method for estimating gradients in the plasma properties through a velocity space distribution at a single point. The gradients are intrinsically related to agyrotropic features of the distribution function. This method predicts the gradients in the magnetized distribution function and can predict gradients of arbitrary moments of the gyrotropic background distribution function. The method allows for estimates on density and pressure gradients on the scale of a Larmor radius, proving to resolve smaller scales than any method currently available to spacecraft. The model is verified with a set of fully kinetic VPIC particle‐in‐cell simulations.

Wetherton, B. A.↗

Analysis of Narrow Bipolar Events Using Mode Decomposition Methods

Multi-resolution analysis methods can reveal the underlying physical dynamics of nonstationary signals, such as those from lightning. In this paper we demonstrate the application of two multi-resolution analysis methods: Ensemble Empirical Mode Decomposition (EEMD) and Variational Mode Decomposition (VMD) in a comparative way in the analysis of electric field change waveforms from lightning. EEMD and VMD decompose signals into a set of Intrinsic Mode Functions (IMFs). The IMFs can be combined using distance and divergence metrics to obtain noise reduction or to obtain new waveforms that isolate the physical processes of interest while removing irrelevant components of the original signal. We apply the EEMD and VMD methods to the observations of three close Narrow Bipolar Events (NBEs) that were reported by Rison et al. The ΔE observations reveal the occurrence of complex oscillatory processes after the main NBE sferic. We show that both EEMD and VMD are able to isolate the oscillations from the main NBE, with VMD being more effective of the two methods since it requires the least user supervision. The oscillations are found to begin at the end of the NBEs' downward fast positive breakdown and appear to be produced by a half-wavelength standing wave within a weakly-conducting resonant ionization cavity left behind in the wake of the streamer-based NBE event. In conclusion, additional analysis shows that one of the NBEs was likely initiated by an energetic cosmic ray shower, and also corrects a misinterpretation in the literature that fast breakdown is an artifact of NBE-like events in interferometer observations.

54 ENVIRONMENTAL SCIENCES↗

A New Post‐Hoc Method to Reduce the Energy Imbalance in Eddy Covariance Measurements

Abstract Latent and sensible heat flux observations are essential for understanding land–atmosphere interactions. Measurements from the eddy covariance technique are widely used but suffer from systematic energy imbalance problems, partly due to missing large eddies from sub‐mesoscale transport. Because available energy drives the development of large eddies, we propose an available energy based correction method for turbulent flux measurements. We apply our method to 172 flux tower sites and show that we can reduce the energy imbalance from −14.99 to −0.65 W m −2 on average, together with improved consistency between turbulent fluxes and available energy and associated increases inr 2 at individual sites and across networks. Our results suggest that our method is conceptually and empirically preferable over the method implemented in the ONEFlux processing. This can contribute to the efforts in understanding and addressing the energy imbalance issue, which is crucial for the evaluation and calibration of land surface models.

Geology↗

Prediction of the SYM-H Index Using a Bayesian Deep Learning Method With Uncertainty Quantification

We propose a novel deep learning framework, named SYMHnet, which employs a graph neural network and a bidirectional long short-term memory network to cooperatively learn patterns from solar wind and interplanetary magnetic field parameters for short-term forecasts of the SYM-H index based on 1- and 5-min resolution data. SYMHnet takes, as input, the time series of the parameters' values provided by NASA's Space Science Data Coordinated Archive and predicts, as output, the SYM-H index value at time point t + w hours for a given time point t where w is 1 or 2. By incorporating Bayesian inference into the learning framework, SYMHnet can quantify both aleatoric (data) uncertainty and epistemic (model) uncertainty when predicting future SYM-H indices. Experimental results show that SYMHnet works well at quiet time and storm time, for both 1- and 5-min resolution data. The results also show that SYMHnet generally performs better than related machine learning methods. For example, SYMHnet achieves a forecast skill score (FSS) of 0.343 compared to the FSS of 0.074 of a recent gradient boosting machine (GBM) method when predicting SYM-H indices (1 hr in advance) in a large storm (SYM-H = -393 nT) using 5-min resolution data. When predicting the SYM-H indices (2 hr in advance) in the large storm, SYMHnet achieves an FSS of 0.553 compared to the FSS of 0.087 of the GBM method. In addition, SYMHnet can provide results for both data and model uncertainty quantification, whereas the related methods cannot.

79 ASTRONOMY AND ASTROPHYSICS↗

Analytical Identification Method of Generalized Short‐Circuit Ratio Using Phasor Measurement Units

This paper introduces a novel analytical approach for the identification of the admittance matrix and the generalized short-circuit ratio (gSCR) in power systems integrated with renewable energy sources. The proposed method leverages voltage and current measurements from phasor measurement units (PMUs) to construct a least squares objective function, which is then solved using matrix calculus and partial derivatives. Unlike conventional optimization algorithms, this approach provides an analytical solution that substantially reduces data requirements, enabling the efficient and accurate identification of the gSCR with smaller datasets. Additionally, its fixed computational complexity allows for real-time updates as new data are collected, ensuring continuous refinement of the system of equations and enabling rapid, precise gSCR calculations. The method also exhibits strong robustness against measurement noise, making it well-suited for practical applications in dynamic power systems. The combination of reduced data requirements, real-time adaptability, noise robustness and fixed computational load establishes this method as a highly efficient and reliable tool for real-time power system stability analysis. Case studies on an EPRI 36-bus system demonstrate the method's effectiveness, highlighting its accuracy in closely matching true gSCR values, even under diverse disturbances and noisy conditions.

Han, Zelei [Hohai University, Nanjing (China)] (OR↗

A Unified Analytical Method to Quantify Three Types of Fast Frequency Response from Inverter-Based Resources

With more inverter-based resources (IBRs), our power systems have lower frequency nadirs following N-1 contingencies, and undesired under-frequency load shedding (UFLS) can occur. To address this challenge, IBRs can be programmed to provide at least three types of fast frequency response (FFR), e.g., step response, proportional response (P/f droop response), and derivative response (synthetic inertia). However, these heterogeneous FFR challenge the study of power system frequency dynamics. Thus, this paper develops an analytical frequency nadir prediction method that allows for the consideration of all three potential forms of FFR provided by IBRs. The proposed method provides fast and accurate frequency nadir estimation after N-1 generation tripping contingencies. Our method is grounded on the closed-form solution for the frequency nadir, which is solved from the second-order system frequency response model considering the governor dynamics and three types of FFR. The simulation results in the IEEE 39-bus system with different types of FFR demonstrate that the proposed method provides an accurate and fast prediction of the frequency nadir under various disturbances.

fast frequency response↗

Employing Technology to Enable Remote Research Charrettes as a Method for Engaging Industry and Uncovering Best Practices: A Novel Approach for a Post-COVID-19 World

Methods to collect data in construction engineering and management (CEM) research are evolving, informed by recent technological advancements. One such method is research charrettes that allow effective interactions and knowledge sharing between expert industry practitioners and academic researchers, all colocated in a single venue, enabling rich data collection and live communication. A pivot point in technological evolution occurred with the COVID-19 pandemic, forcing a global shift to remote work. Hence, planned in-person research charrettes had to shift to remote sessions, relying on virtual conferencing platforms and online data collection mechanisms. Technology-enabled charrettes have allowed the authors to collect significantly richer data sets and ensure a more diverse representation of participants, while saving tremendous amounts of time. With the continuing emergence of technological applications, the world might not go back to functioning fully in person. The authors believe remote research charrettes (RRCs) will still be used in a post-COVID-19 world because of their superior performance. This paper builds on a previous publication that described traditional research charrettes as a method to enhance CEM research a decade ago; it offers a significantly updated and improved RRC method based on the knowledge gained from transitioning a dozen in-person charrettes into RRCs. It also presents performance comparisons between RRCs and traditional charrettes by quantifying metrics indicating how RRCs are more time-efficient and cost-saving, harness more participants from more diverse locations, and enable the collection of richer data sets and four times more industry comments and expert feedback. This paper also provides guidance on the integration of technology with traditional research charrettes, hence contributing to the CEM body of knowledge.

42 ENGINEERING↗

Collective mode Brownian dynamics: A method for fast relaxation of statistical ensembles

Sampling equilibrium configurations of correlated systems of particles with long relaxation times (e.g., polymeric solutions) using conventional molecular dynamics and Monte Carlo methods can be challenging. This is especially true for systems with complicated, extended bond network topologies and other interactions that make the use and design of specialized relaxation protocols infeasible. We introduce a method based on Brownian dynamics simulations that can reduce the computational time it takes to reach equilibrium and draw decorrelated samples. Importantly, the method is completely agnostic to the particle configuration and the specifics of interparticle forces. In particular, we develop a mobility matrix that excites non-local, collective motion of N particles and can be computed efficiently in $\mathcal{O}(N)$ time. Particle motion in this scheme is computed by integrating the overdamped Langevin equation with an Euler–Maruyama scheme, in which Brownian displacements are drawn efficiently using a low-rank representation of the mobility matrix in position and wave space. We demonstrate the efficacy of the method with various examples from the realm of soft condensed matter and release a massively parallel implementation of the code as a plugin for the open-source package HOOMD-blue [J. A. Anderson et al., J. Comput. Phys. 227, 5342 (2008) and J. Glaser et al., Comput. Phys. Commun. 192, 97 (2015)] which runs on graphics processing units

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental methods for laboratory measurements of helium spectral line broadening in white dwarf photospheres

White Dwarf (WD) stars are the most common stellar remnant in the universe. WDs usually have a hydrogen or helium atmosphere, and helium WD (called DB) spectra can be used to solve outstanding problems in stellar and galactic evolution. DB origins, which are still a mystery, must be known to solve these problems. DB masses are crucial for discriminating between different proposed DB evolutionary hypotheses. Current DB mass determination methods deliver conflicting results. The spectroscopic mass determination method relies on line broadening models that have not been validated at DB atmosphere conditions. We performed helium benchmark experiments using the White Dwarf Photosphere Experiment (WDPE) platform at Sandia National Laboratories' Z-machine that aims to study He line broadening at DB conditions. Using hydrogen/helium mixture plasmas allows investigating the importance of He Stark and van der Waals broadening simultaneously. Accurate experimental data reduction methods are essential to test these line-broadening theories. In this paper, we present data calibration methods for these benchmark He line shape experiments. We give a detailed account of data processing, spectral power calibrations, and instrument broadening measurements. Uncertainties for each data calibration step are also derived. We demonstrate that our experiments meet all benchmark experiment accuracy requirements: WDPE wavelength uncertainties are <1 Å, spectral powers can be determined to within 15%, densities are accurate at the 20% level, and instrumental broadening can be measured with 20% accuracy. Fulfilling these stringent requirements enables WDPE experimental data to provide physically meaningful conclusions about line broadening at DB conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

Machine learning methods for probabilistic locked-mode predictors in tokamak plasmas

A rotating tokamak plasma can interact resonantly with the external helical magnetic perturbations, also known as error fields. This can lead to locking and then to disruptions. We leverage machine learning (ML) methods to predict the locking events. We use a coupled third-order nonlinear ordinary differential equation model to represent the interaction of the magnetic perturbation and the plasma rotation with the error field. This model is sufficient to describe qualitatively the locking and unlocking bifurcations. Here, we explore using ML algorithms with the simulation data and experimental data, focusing on the methods that can be used with sparse datasets. These methods lead to the possibility of the avoidance of locking in real-time operations. We describe the operational space in terms of two control parameters: the magnitude of the error field and the rotation frequency associated with the momentum source that maintains the plasma rotation. The outcomes are quan- tified by order parameters that completely characterize the state, whether locked or unlocked. We use unsupervised ML methods to classify locked/unlocked states and note the usefulness of a certain normalization of the order parameters. Three supervised ML classifiers are used in suite to estimate the probability of locking in the region of control parameter space with hysteresis, i.e., the set of control parameters for which both locked and unlocked states can exist. The results show that a neural network gives the best estimate of the locking probability. An analogy of the present locking model with the van der Waals equation of state is also provided.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Chiral propulsion: The method of effective boundary conditions

We propose to apply an “effective boundary condition” method to the problem of chiral propulsion. For the case of a rotating helix moving through a fluid at a low Reynolds number, the method amounts to replacing the original helix (in the limit of small pitch) by a cylinder, but with a special kind of partial slip boundary conditions replacing the non-slip boundary conditions on the original helix. These boundary conditions are constructed to reproduce far-field velocities of the original problem and are defined by a few parameters (slipping lengths) that can be extracted from a problem in planar rather than cylindrical geometry. We derive the chiral propulsion coefficients for spirals, helicoids, helically modulated cylinders and some of their generalizations using the introduced method. In the case of spirals, we compare our results with the ones derived by Lighthill and find a very good agreement. Here, the proposed method is general and can be applied to any helical shape in the limit of a small pitch. Furthermore, we have established that for a broad class of helical surfaces the dependence of the chiral propulsion on the helical angle θ is universal, x ~ cos θ sin 2θ with the maximal propulsion achieved at the universal angle θ m = tan –1 (1/√2) ≈ 35.26°.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A discussion on various experimental methods of impact ionization coefficient measurement in GaN

Impact ionization coefficients play a critical role in semiconductors. In addition to silicon, silicon carbide and gallium nitride are important semiconductors that are being seen more as mainstream semiconductor technologies. As a reflection of the maturity of these semiconductors, predictive modeling has become essential to device and circuit designers, and impact ionization coefficients play a key role here. Recently, several studies have measured impact ionization coefficients. We dedicated the first part of our study to comparing three experimental methods to estimate impact ionization coefficients in GaN, which are all based on photomultiplication but feature characteristic differences. The first method inserts an InGaN hole-injection layer, the accuracy of which is challenged by the dominance of ionization in InGaN, leading to possible overestimation of the coefficients. The second method utilizes the Franz–Keldysh effect for hole injection but not for electrons, where the mixed injection of induced carriers would require a margin of error. The third method uses complementary p–n and n–p structures that have been at the basis of this estimation in Si and SiC and leans on the assumption of a constant electric field, and any deviation would require a margin of error. In the second part of our study, we evaluated the models using recent experimental data from diodes demonstrating avalanche breakdown.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A method to predict texture effect on ion beam channeling analysis of polycrystals and the application to study the mosaic spreading effect in highly oriented pyrolytic graphite

We propose a method to convert the channeling Rutherford backscattering spectrum yield map of a single crystal to a polycrystal through a matrix rotation technique. The rotation matrix is determined by the deviation of the crystal axial direction from the original z axis. The final yield map is created after averaging the rotated yields using the texture function as the weight factor. For highly oriented pyrolytic graphite (HOPG) exhibiting mosaic spread, the method leads to a Gaussian kernel averaging of the map obtained from a single crystal. The yield map of a single crystal is obtained by a simulation of ion trajectories in a potential field described by Moliere screened Coulomb potentials. Yield maps are calculated under various σ values (standard deviations of mosaic spread). The simulated results are compared with experimental results obtained using 1.2 MeV alpha particle. σ is extracted through the best fitting, demonstrating that the method can be used to obtain texture details. The effects of mosaic spread on minimum yield χ min and the half-width at half maximum of angular scans ψ ½ are systematically modeled and compared with previous theoretical equations. The study also shows that previous theoretical equations are valid only at small σ values. The proposed method can be applied to any type of polycrystal and is not limited to HOPG. It provides near-surface mosaic spread and crystallography information with a longitudinal depth resolution of tens of nanometers and is not influenced by grain shapes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗