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At least 433 records · Page 24

Magnetic ground states of a model for M Nb 3 S 6 ( M = Co, Fe, Ni)

The transition-metal-intercalated dichalcogenide CoNb 3 S 6 is a triangular antiferromagnet (AFM) that has recently been shown to exhibit a large anomalous Hall effect (AHE) below the Neel temperature, even though the response to an external field is very small. This suggests that there is an interesting magnetic structure that interacts with the electronic structure to yield the AHE, as collinear AFMs cannot exhibit a nonzero AHE. We propose a model for magnetic transition-metal-intercalated dichalcogenides and examine its ground state as a function of interaction parameters. The model exhibits transitions between planar spin spirals, nonplanar spin spirals, and a particular noncoplanar so-called 3q state. Finally, this latter state must exhibit a nonzero AHE, while the spin spirals do not.

36 MATERIALS SCIENCE↗

Role of water model on ion dissociation at ambient conditions

In this work, we study ion pair dissociation in water at ambient conditions using a combination of classical and ab initio approaches. The goal of this study is to disentangle the sources of discrepancy observed in computed potentials of mean force. In particular, we aim to understand why some models favor the stability of solvent-separated ion pairs vs contact ion pairs. We found that some observed differences can be explained by non-converged simulation parameters. However, we also unveil that for some models, small changes in the solution density can have significant effects on modifying the equilibrium balance between the two configurations. We conclude that the thermodynamic stability of contact and solvent-separated ion pairs is very sensitive to the dielectric properties of the underlying simulation model. In general, classical models are very robust in providing a similar estimation of the contact ion pair stability, while this is much more variable in density functional theory-based models. The barrier to transition from the solvent-separated to contact ion pair is fundamentally dependent on the balance between electrostatic potential energy and entropy. This reflects the importance of water intra- and inter-molecular polarizability in obtaining an accurate description of the screened ion–ion interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enriching Load Data Using Micro-PMUs and Smart Meters

In modern distribution systems, load uncertainty can be fully captured by micro-PMUs, which can record high-resolution data; however, in practice, micro-PMUs are installed at limited locations in distribution networks due to budgetary constraints. In contrast, smart meters are widely deployed but can only measure relatively low-resolution energy consumption, which cannot sufficiently reflect the actual instantaneous load volatility within each sampling interval. In this paper, we have proposed a novel approach for enriching load data for service transformers that only have low-resolution smart meters. The key to our approach is to statistically recover the high-resolution load data, which is masked by the low-resolution data, using trained probabilistic models of service transformers that have both high- and low-resolution data sources, i.e., micro-PMUs and smart meters. The overall framework consists of two steps: first, for the transformers with micro-PMUs, a Gaussian Process is leveraged to capture the relationship between the maximum/minimum load and average load within each low-resolution sampling interval of smart meters; a Markov chain model is employed to characterize the transition probability of known high-resolution load. Next, the trained models are used as teachers for the transformers with only smart meters to decompose known low-resolution load data into targeted high-resolution load data. The enriched data can recover instantaneous load uncertainty and significantly enhance distribution system observability and situational awareness. Here, we have verified the proposed approach using real high- and low-resolution load data.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Application of Machine Learning Techniques to an Agent-Based Model of Pantoea

Agent-based modeling (ABM) is a powerful simulation technique which describes a complex dynamic system based on its interacting constituent entities. While the flexibility of ABM enables broad application, the complexity of real-world models demands intensive computing resources and computational time; however, a metamodel may be constructed to gain insight at less computational expense. Here, we developed a model in NetLogo to describe the growth of a microbial population consisting of Pantoea . We applied 13 parameters that defined the model and actively changed seven of the parameters to modulate the evolution of the population curve in response to these changes. We efficiently performed more than 3,000 simulations using a Python wrapper, NL4Py . Upon evaluation of the correlation between the active parameters and outputs by random forest regression, we found that the parameters which define the depth of medium and glucose concentration affect the population curves significantly. Subsequently, we constructed a metamodel, a dense neural network, to predict the simulation outputs from the active parameters and found that it achieves high prediction accuracy, reaching an R 2 coefficient of determination value up to 0.92. Our approach of using a combination of ABM with random forest regression and neural network reduces the number of required ABM simulations. The simplified and refined metamodels may provide insights into the complex dynamic system before their transition to more sophisticated models that run on high-performance computing systems. The ultimate goal is to build a bridge between simulation and experiment, allowing model validation by comparing the simulated data to experimental data in microbiology.

59 BASIC BIOLOGICAL SCIENCES↗

Distributed Delay Differential Equation Representations of Cyclic Differential Equations

Compartmental ordinary differential equation (ODE) models are used extensively in mathematical biology. When transit between compartments occurs at a constant rate, the well-known linear chain trick can be used to show that the ODE model is equivalent to an Erlang distributed delay differential equation (DDE). Here, we demonstrate that compartmental models with nonlinear transit rates and possibly delayed arguments are also equivalent to a scalar distributed DDE. To illustrate the utility of these equivalences, we calculate the equilibria of the scalar DDE, and compute the characteristic function---without calculating a determinant. Further, we derive the equivalent scalar DDE for two examples of models in mathematical biology and use the DDE formulation to identify physiological processes that were otherwise hidden by the compartmental structure of the ODE model.

97 MATHEMATICS AND COMPUTING↗

Theoretical Studies of Polar Systems near Ferroelectrics Quantum Critical Points (Final Report)

The PI has studied emergent quantum phases near polar quantum critical points. A first challenge was to develop a theoretical description of the observation that many polar materials undergo classical first-order transitions while displaying quantum criticality. The possibility of novel metallic states near polar quantum critical points was then studied; identification and characterization of a non-Fermi liquid phase was made in a multiband system. In dilute quantum critical polar metals, electronic coupling to polar energy fluctuations was shown to result in attractive electron-electron interactions and to superconductivity. A spin-phonon resonance measurement in applied magnetic field was proposed to determine the magnitude of spin-orbit mediated electron-phonon coupling; furthermore in the polar phase new field-induced phonon collective modes were identified with specific signatures for experiment. In order to keep current, the PI has also worked on other types of strongly correlated problems. With experimental groups, she has developed phenomenologies to identify and explain observed dynamical critical behaviors. The PI has studied the interplay of topology, fractionalization and deconfinement in a minimalist spin model. An emergent phase transition in a 1 + 1 frustrated spin nanotube has also been identified and characterized. The PI has also begun exploring criticality out of equilibrium, characterizing rich dynamical phases associated with photoinduced polar transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Generative AI models for learning flow maps of stochastic dynamical systems in bounded domains

Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary interactions. Despite the success of machine learning-based methods in learning SDEs, existing learning methods are not applicable to SDEs in bounded domains because they cannot accurately capture the particle exit dynamics. We present a unified hybrid data-driven approach that combines a conditional diffusion model with an exit prediction neural network to capture both interior stochastic dynamics and boundary exit phenomena. Our ML model consists of two major components: a neural network that learns exit probabilities using binary cross-entropy loss with rigorous convergence guarantees, and a training-free diffusion model that generates state transitions for non-exiting particles using closed-form score functions. The two components are integrated through a probabilistic sampling algorithm that determines particle exit at each time step and generates appropriate state transitions. Here, the performance of the proposed approach is demonstrated via three test cases: a one-dimensional simplified problem for theoretical verification, a two-dimensional advection-diffusion problem in a bounded domain, and a three-dimensional problem of interest to magnetically confined fusion plasmas.

Bounded domains↗

A Deep Neural Network for Accurate and Robust Prediction of the Glass Transition Temperature of Polyhydroxyalkanoate Homo- and Copolymers

The purpose of this study was to develop a data-driven machine learning model to predict the performance properties of polyhydroxyalkanoates (PHAs), a group of biosourced polyesters featuring excellent performance, to guide future design and synthesis experiments. A deep neural network (DNN) machine learning model was built for predicting the glass transition temperature, Tg, of PHA homo- and copolymers. Molecular fingerprints were used to capture the structural and atomic information of PHA monomers. The other input variables included the molecular weight, the polydispersity index, and the percentage of each monomer in the homo- and copolymers. The results indicate that the DNN model achieves high accuracy in estimation of the glass transition temperature of PHAs. In addition, the symmetry of the DNN model is ensured by incorporating symmetry data in the training process. The DNN model achieved better performance than the support vector machine (SVD), a nonlinear ML model and least absolute shrinkage and selection operator (LASSO), a sparse linear regression model. The relative importance of factors affecting the DNN model prediction were analyzed. Sensitivity of the DNN model, including strategies to deal with missing data, were also investigated. Compared with commonly used machine learning models incorporating quantitative structure–property (QSPR) relationships, it does not require an explicit descriptor selection step but shows a comparable performance. The machine learning model framework can be readily extended to predict other properties.

quantitative structure–property relationship (QSPR↗

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.

Hsu, Darren J.↗

BETO 2021 Peer Review - WBS 4.1.2.32: Bioeconomy Scenario Analysis

The Bioeconomy Scenario Analysis project uses systems thinking and analysis to assess current and/or prospective techno-economics, research and development, deployment strategies, policy, and market conditions and their impact on the potential development trajectories of the bioenergy industry over time. Results from this project include identification of opportunities and constraints to industrial development, quantification of multiple metrics (energy, economic, environmental) and informing researchers, decision makers, and industry of the steps needed for a sustainable, nationwide biofuels industry. Analyses from this project enable the creation of a bioenergy industry by (1) inciting policy-makers to explore scenarios for nationwide biofuels production, identifying policy actions consistent with pathways for growth; (2) improving industry’s understanding of industry growth potential under different technology and investment conditions, better targeting their development efforts; and (3) providing universities and other interested stakeholders with tools and analyses that can be adapted to meet research and teaching objectives, connecting students with careers that build the industry. One of the many modeling tools used in this project, the Biomass Scenario Model (BSM) is a publicly-available, unique, validated, state-of-the-art, award-winning, fourth-generation model of the domestic biofuels supply chain which explicitly focuses on how and under what conditions biofuel technologies might be deployed to contribute to the U.S. transportation energy sector. We use models like the BSM to examine the implications of policies and incentives as well as their potential side-effects. The BSM uses a system-dynamics simulation to model dynamic interactions and transitions across the supply chain; it tracks the deployment of biofuels given industrial learning and the reaction of the investment community in the context of land availability, projected oil markets, consumer demand for biofuels, and government policies over time. Under expected market conditions, analyses using the BSM suggest that the biofuels industry may require significant external actions in the early years to thrive. Interventions that accelerate the industrial learning process (e.g. operation of pre-commercial and commercial facilities) have been identified as having strong influence in starting the growth of a commercial biofuel industry. Policies which are coordinated across the whole supply chain in BSM foster the growth of the biofuels industry and production of tens of billions of gallons of biofuels may occur under sufficiently favorable conditions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Quantification of High‐Temperature Transition Al 2 O 3 and Their Phase Transformations**

Abstract High‐temperature treatment of γ‐Al 2 O 3 can lead to a series of polymorphic transformations, including the formation of δ‐Al 2 O 3 and θ‐Al 2 O 3 . Quantification of the microstructure in the range where δ‐ and θ‐Al 2 O 3 are formed represents a formidable challenge, as both phases accommodate a high degree of structural disorder. In this work, we explore the use of an XRD recursive‐stacking formalism for the quantification of high‐temperature transition aluminas. We formulate the recursive‐stacking methodology for modelling of disorder in δ‐Al 2 O 3 and twinning in θ‐Al 2 O 3 and show that explicitly accounting for the disorder is necessary to reliably model the XRD patterns of high‐temperature transition alumina. We also use the recursive stacking approach to study phase transformation during high‐temperature (1050 °C) treatment. We show that the two different intergrowth modes of δ‐Al 2 O 3 have different transformation characteristics and that a significant portion of δ‐Al 2 O 3 is stabilized with θ‐Al 2 O 3 even after prolonged high‐temperature exposures.

Kovarik, Libor↗

Debunking common myths in coastal circulation modeling

Despite tremendous progress in algorithm development, computational efficiency and transition into operations over the past two decades, coastal modeling still lacks scientific rigor due to proliferation of many ‘gray’ areas related to various modeling choices made by modelers. Here, in this paper, we propose some guiding principles for the modeling community to improve performance, and we also debunk commonly held myths that make the coastal modeling lack rigor. Using our own experience in developing seamless cross-scale unstructured-grid based models for the past two decades, we describe in unprecedented detail the end-to-end modeling process (i.e., from digital elevation models (DEMs) to mesh generation to post analysis), and demonstrate that defensible modeling is within reach for any end user by following three guiding principles: (1) Bathymetry is a first order forcing in coastal domains and thus should be respected in all aspects of modeling; (2) Oceanographic processes are driven across multiple spatial scales and so models should enable appropriate resolution as needed; and (3) Model assessment should focus on physical processes. Through qualitative and quantitative model assessments, we demonstrate the fundamental role played by bathymetry/topography as embedded in DEMs in making the results defensible, which is unfortunately glossed over in many modeling studies. Focusing on process-based assessment simplifies the calibration process. A major conclusion of this work is that model developers and operators should maximize the scientific rigor for in silico oceanography by avoiding some common pitfalls that rely on error compensation at the expense of representation of physical system processes. We present some best practice procedures for defensive and trustworthy numerical modeling.

54 ENVIRONMENTAL SCIENCES↗

Ribbon Wrinkling Origin and Its Effect on Tape-Wound Core Shape

Improved understanding of advanced manufacturing techniques is needed to fabricate next- generation soft magnetic tape-wound cores. These utilize metal amorphous nano-composites (MANCs) in the form of long thin ribbons. MANCs exhibit attractive soft magnetic properties for use in high frequency and high power density magnetic components. Of particular interest here, the permeability and hysteresis of MANC ribbons can be tuned in a strain annealing process. An unexpected consequence is that wider ribbons develop longitudinal wrinkle patterns. This can substantially reduce the tape-wound core stacking factor. However, when winding a wrinkled ribbon into a toroidal core, the wrinkles can completely flatten, or crinkle. By this phenomenon, the stacking factor can be recovered. To understand the crinkling effect we have developed analytical and finite element analysis (FEA) models. Experiments with known boundary conditions demonstrate the transition from wrinkled to crinkled versus winding curvature. The models utilize an elastic modulus measured via ribbon tensile testing and a ribbon thickness value measurement made by profilometry. The analytical model provides insight into the crinkling effect but cannot explain the length of the transition region from wrinkling to crinkling. With FEA, we successfully predict the transition region and depending on wrinkling amplitude can determine when a ribbon will wind into a useable core. Such mechanics-based insight provides critical feedback for allowable processing parameters in the strain annealing process.

20 FOSSIL-FUELED POWER PLANTS↗

Coupling-dependent antiferromagnetic-ferromagnetic ordering in a pinwheel artificial spin ice

Nanopatterned magnetic thin films offer a platform for exploration of tailored magnetic properties such as emergent long-range order. A prominent example is artificial spin ice (ASI), where an arrangement of nanoscale magnetic elements, acting as macrospins, interact via their dipolar fields. In this study, we discuss the transition from antiferromagnetic (AFM) to ferromagnetic (FM) long-range order in a square lattice ASI as the magnetic elements are gradually rotated through 45⁢° to a “pinwheel” configuration. The AFM-FM transition is observed experimentally using synchrotron radiation x-ray spectromicroscopy and occurs for a certain rotation angle of the nanomagnets, dependent on the dipolar coupling strength determined by the separation of the magnets in the lattice. Large-scale magnetic dipole simulations show that the point-dipole approximation fails to capture the correct AFM-FM transition angle. However, excellent agreement with experimental data is obtained using a dumbbell-dipole model, which better reflects the actual dipolar fields of the magnets. This model also explains the coupling dependence of the transition angle, another feature not captured by the point-dipole model. Our findings resolve a discrepancy between measurement and theory in previous work on “pinwheel” ASIs and establish the coupling dependence of the AFM-FM transition. The revised dipole model, with a more accurate representation of the stray field, offers more precise control of magnetic order in artificial spin systems.

Artificial spin ice↗

Replica wormholes and the black hole interior

Recent work has shown how to obtain the Page curve of an evaporating black hole from holographic computations of entanglement entropy. We show how these computations can be justified using the replica trick, from geometries with a spacetime wormhole connecting the different replicas. In a simple model, we study the Page transition in detail by summing replica geometries with different topologies. We compute related quantities in less detail in more complicated models, including JT gravity coupled to conformal matter and the SYK model. Separately, we give a direct gravitational argument for entanglement wedge reconstruction using an explicit formula known as the Petz map; again, a spacetime wormhole plays an important role. We discuss an interpretation of the wormhole geometries as part of some ensemble average implicit in the gravity description.

2D gravity↗

Comparison Between the f-Electron and Conduction-Electron Density of States in the Falicov-Kimball Model at Low Temperature

The spinless Falicov-Kimball model is one of the simplest models of many-body physics. While the conduction-electron density of states is temperature independent in the normal state, the f -electron density of states is strongly temperature dependent—it has an orthogonality catastrophe singularity in the metallic phase and is gapped in the insulating phase. The question we address here is whether the spectral gap is the same for both electron species as T → 0. Finally, we find strong evidence to indicate that the answer is affirmative.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Calculating elements of matrix functions using divided differences

In this work, we introduce a method for calculating individual elements of matrix functions. Our technique makes use of a novel series expansion for the action of matrix functions on basis vectors that is memory efficient even for very large matrices. We showcase our approach by calculating the matrix elements of the exponential of a transverse-field Ising model and evaluating quantum transition amplitudes for large many-body Hamiltonians of sizes up to 2 64 x 2 64 on a single workstation. We also discuss the application of the method to matrix inverses. We relate and compare our method to the state-of-the-art and demonstrate its advantages. We also discuss practical applications of our method.

97 MATHEMATICS AND COMPUTING↗