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At least 1,063 records · Page 59

Modeling Short-Range Order in Disordered Rocksalt Cathodes by Pair Distribution Function Analysis

Pair distribution function (PDF) analysis is a powerful technique for the characterization of short-range order (SRO) in disordered materials. Accurate interpretation of experimental PDF data is critically reliant on the development of structural models that can account for local variations in site occupancies and bond lengths. To this end, we outline an approach to model SRO using first-principles calculations based on the cluster-expansion formalism. These methods are validated on neutron scattering data from two disordered rocksalt oxyfluorides, Li 1.3 Mn 0.4 Ti 0.3 O 1.7 F 0.3 and Li 1.3 Mn 0.4 Nb 0.2 Ti 0.1 O 1.7 F 0.3 . For each composition, we demonstrate that an average structure without any SRO fails to reproduce several key features in the experimental PDF. To pinpoint the origin of the suspected SRO in these materials, configurational and displacive effects were separately investigated using two disparate models. Special quasi-random structures were relaxed using density functional theory to account for local changes in bond lengths while maintaining a near-random ionic configuration. This leads to slightly improved accuracy but still misrepresents asymmetry in the first few peaks of the PDF. Monte Carlo simulations were performed to model configurational SRO on a fixed lattice, which by itself is shown to have a minimal influence on the PDF. Instead, we find that it is the bond length relaxations within environments created by SRO which controls the details of the PDF, thereby highlighting the subtle but important coupling between configurational and displacive SRO in disordered materials.

36 MATERIALS SCIENCE↗

Combining Experimental and Theoretical Techniques to Gain an Atomic Level Understanding of the Defect Binding Mechanism in Hard Carbon Anodes for Sodium Ion Batteries

Sodium ion batteries (NIBs) are an attractive alternative to lithium–ion batteries in applications that require large–scale energy storage due to sodium's high natural abundance and low cost. Hard carbon (HC) is the most promising anode material for NIBs; however, there is a knowledge gap in the understanding of the sodium binding mechanism that prevents a rational design of HC. This study tunes sucrose–derived HC via synthesis temperature then evaluates the structural, physical, and electrochemical properties. Neutron total scattering is used to generate structural models by fitting pair distribution functions (PDF) with a combination of molecular dynamics and reverse Monte Carlo methods. From this model, the number and type of structural features are identified, quantified, and correlated to the galvanostatic charge/discharge. A method of PDF “fingerprinting” binding sites using Na probe atoms is developed and analyzing these PDFs reveals an atomistic view of ion binding sites responsible for “defect” storage mechanisms. Combining these techniques results in an atomic–level study that provides a big picture of the Na–binding mechanism in NIBs, which allows for more precise tuning of the structure–property relationships in the future. Finally, the methodologies developed will also enable new strategies for the analysis of amorphous functional materials.

25 ENERGY STORAGE↗

Machine-Learned Manifold-Based Models for Large Eddy Simulation of Turbulent Combustion

Reduced-order manifold combustion models are commonly used to lower the cost of reacting Large Eddy Simulations (LES) and may be derived either from physical principles as in flamelet models or from data-driven methods like Principal Component Analysis (PCA). In either case, neural networks are increasingly used as part of these models to provide a nonlinear mapping between a small set of pre-defined variables that parameterize the manifold and outputs of interest, such as reaction rates. In this work, we propose a new manifold-based modeling approach that combines the definition of the manifold-parameterizing variables (linear combinations of species), the nonlinear mapping to the outputs, and closure of filtered quantities for LES into the structure of a single neural network. This allows the process used to train the neural network to simultaneously optimize both the functional form of the model and the identities of the inputs to the model. The new approach can flexibly incorporate thermochemical data from any combustion system; if trained on data from 1D flames it can be interpreted as an optimized flamelet model, but it can also be used to learn models from data from more complex configurations. This work presents a priori evaluations of the new approach in both contexts. Evaluation using data from 1D premixed flames demonstrates the physical interpretability of the manifold variables generated by the new approach. Evaluation using data from direct numerical simulations of turbulent flames shows improved predictions relative to either flamelet or PCA-based models in a more complex configuration.

47 OTHER INSTRUMENTATION↗

Skyrme-Hartree-Fock-Bogoliubov mass models on a 3D mesh: III. From atomic nuclei to neutron stars

Here, we present BSkG3, the latest entry in the Brussels-Skyrme-on-a-grid series of large-scale models of nuclear structure based on an energy density functional. Compared to its predecessors, the new model offers a more realistic description of nucleonic matter at the extreme densities relevant to neutron stars. This achievement is made possible by incorporating a constraint on the infinite nuclear matter properties at high densities in the parameter adjustment, ensuring in this way that the predictions of BSkG3 for the nuclear Equation of State are compatible with the observational evidence for heavy pulsars with M > 2M ⊙ . Instead of the usual phenomenological pairing terms, we also employ a more microscopically founded treatment of nucleon pairing, resulting in extrapolations to high densities that are in line with the predictions of advanced many-body methods and are hence more suited to the study of superfluidity in neutron stars. By adopting an extended form of the Skyrme functional, we are able to reconcile the description of matter at high densities and at saturation density: the new model further refines the description of atomic nuclei offered by its predecessors. A qualitative improvement is our inclusion of ground state reflection asymmetry, in addition to the spontaneous breaking of rotational, axial, and time-reversal symmetry. Quantitatively, the model offers lowered root-mean-square deviations on 2457 masses (0.631 MeV), 810 charge radii (0.0237 fm) and an unmatched accuracy with respect to 45 primary fission barriers of actinide nuclei (0.33 MeV). Reconciling the complexity of neutron stars with those of atomic nuclei establishes BSkG3 as a tool of choice for applications to nuclear structure, the nuclear equation of state and nuclear astrophysics in general.

Physics↗

Physics-based reward driven image analysis in microscopy

The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated (Y, Dy)Ba 2 Cu 3 O 7–δ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.

47 OTHER INSTRUMENTATION↗

The symmetric quasi-classical model using on-the-fly time-dependent density functional theory within the Tamm–Dancoff approximation

The primary computational challenge when simulating nonadiabatic ab initio molecular dynamics is the unfavourable compute costs of electronic structure calculations with molecular size. Simple electronic structure theories, like time-dependent density functional theory within the Tamm–Dancoff approximation (TDDFT/TDA), alleviate this cost for moderately sized molecular systems simulated on realistic time scales. Although TDDFT/TDA does have some limitations in accuracy, an appealing feature is that, in addition to including electron correlation through the use of a density functional, the cost of calculating analytic nuclear gradients and nonadiabatic coupling vectors is often computationally feasible even for moderately sized basis sets. Here in this work, some of the benefits and limitations of TDDFT/TDA are discussed and analysed with regard to its applicability as a ‘back-end’ electronic structure method for the symmetric quasi-classical Meyer–Miller model (SQC/MM). In order to investigate the benefits and limitations of TDDFT/TDA, SQC/MM is employed to predict and analyse a prototypical example of excited-state hydrogen transfer in gas-phase malonaldehyde. Then, the ring-opening dynamics of selenophene are simulated, which highlight some of the deficiencies of TDDFT/TDA. Additionally, some new algorithms are proposed that speed up the calculation of analytic nuclear gradients and nonadiabatic coupling vectors for a set of excited electronic states.

molecular dynamics↗

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗

A priori analysis on deep learning of subgrid-scale parameterizations for Kraichnan turbulence

In the present study, we investigate different data-driven parameterizations for large eddy simulation of two-dimensional turbulence in the a priori settings. These models utilize resolved flow field variables on the coarser grid to estimate the subgrid-scale stresses. We use data-driven closure models based on localized learning that employs a multilayer feedforward artificial neural network with point-to-point mapping and neighboring stencil data mapping, and convolutional neural network fed by data snapshots of the whole domain. The performance of these data-driven closure models is measured through a probability density function and is compared with the dynamic Smagorinksy model (DSM). The quantitative performance is evaluated using the cross-correlation coefficient between the true and predicted stresses. We analyze different frameworks in terms of the amount of training data, selection of input and output features, their characteristics in modeling with accuracy, and training and deployment computational time. We also demonstrate computational gain that can be achieved using the intelligent eddy viscosity model that learns eddy viscosity computed by the DSM instead of subgrid-scale stresses. Here, we detail the hyperparameters optimization of these models using the grid search algorithm.

42 ENGINEERING↗

A Theoretical Benchmark of the Geometric and Optical Properties for 3d Transition Metal Nanoclusters via Density Functional Theory

Understanding structure–property relationships in atomically precise metal nanoclusters is vital in finding selective and tunable catalysts. Here, in this study, density functional theory (DFT) was used to benchmark seven exchange correlation functionals at different basis sets for 17 atomically precise nanoclusters against experimentally determined geometries, band gaps, and optical gaps. The set contains both monometallic and bimetallic clusters that possess at least two types of 3d transition metals (specifically, Cu, Ni, Fe, or Co). The benchmark highlights that PBE0 is a good functional to use regardless of the basis set, and Minnesota functionals do well with respect to specific metals. Further, while long-range corrected functionals overestimate band and optical gaps, they model absorption features better than the other considered functionals. The study additionally looks at the photoinduced hydrogen evolution reaction (HER) and the CO 2 reduction mechanism on nanoclusters reported from the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ground Heat Flux Reconstruction Using Bayesian Uncertainty Quantification Machinery and Surrogate Modeling

Ground heat flux (G 0 ) is a key component of the land-surface energy balance of high-latitude regions. Despite its crucial role in controlling permafrost degradation due to global warming, G 0 is sparsely measured and not well represented in the outputs of global scale model simulation. In this study, an analytical heat transfer model is tested to reconstruct G 0 across seasons using soil temperature series from field measurements, Global Climate Model, and climate reanalysis outputs. The probability density functions of ground heat flux and of model parameters are inferred using available G 0 data (measured or modeled) for snow-free period as a reference. When observed G 0 is not available, a numerical model is applied using estimates of surface heat flux (dependent on parameters) as the top boundary condition. These estimates (and thus the corresponding parameters) are verified by comparing the distributions of simulated and measured soil temperature at several depths. Aided by state-of-the-art uncertainty quantification methods, the developed G 0 reconstruction approach provides novel means for assessing the probabilistic structure of the ground heat flux for regional permafrost change studies.

54 ENVIRONMENTAL SCIENCES↗

Redshift evolution of the underlying type Ia supernova stretch distribution

The detailed nature of type Ia supernovae (SNe Ia) remains uncertain, and as survey statistics increase, the question of astrophysical systematic uncertainties arises, notably that of the evolution of SN Ia populations. We study the dependence on redshift of the SN Ia SALT2.4 light-curve stretch, which is a purely intrinsic SN property, to probe its potential redshift drift. The SN stretch has been shown to be strongly correlated with the SN environment, notably with stellar age tracers. We modeled the underlying stretch distribution as a function of redshift, using the evolution of the fraction of young and old SNe Ia as predicted using the SNfactory dataset, and assuming a constant underlying stretch distribution for each age population consisting of Gaussian mixtures. We tested our prediction against published samples that were cut to have marginal magnitude selection effects, so that any observed change is indeed astrophysical and not observational in origin. In this first study, there are indications that the underlying SN Ia stretch distribution evolves as a function of redshift, and that the age drifting model is a better description of the data than any time-constant model, including the sample-based asymmetric distributions that are often used to correct Malmquist bias at a significance higher than 5σ. The favored underlying stretch model is a bimodal one, composed of a high-stretch mode shared by both young and old environments, and a low-stretch mode that is exclusive to old environments. The precise effect of the redshift evolution of the intrinsic properties of a SN Ia population on cosmology remains to be studied. The astrophysical drift of the SN stretch distribution does affect current Malmquist bias corrections, however, and thereby the distances that are derived based on SN that are affected by observational selection effects. We highlight that this bias will increase with surveys covering increasingly larger redshift ranges, which is particularly important for the Large Synoptic Survey Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗

Asymptotic Freedom at the Berezinskii-Kosterlitz-Thouless Transition without Fine-Tuning Using a Qubit Regularization

We propose a two-dimensional hard-core loop-gas model as a way to regularize the asymptotically free massive continuum quantum field theory that emerges at the Berezinskii-Kosterlitz-Thouless transition. Without fine-tuning, our model can reproduce the universal step-scaling function of the classical lattice X Y model in the massive phase as we approach the phase transition. This is achieved by lowering the fugacity of Fock-vacuum sites in the loop-gas configuration space to zero in the thermodynamic limit. Some of the universal quantities at the Berezinskii-Kosterlitz-Thouless transition show smaller finite size effects in our model as compared to the traditional X Y model. Our model is a prime example of qubit regularization of an asymptotically free massive quantum field theory in Euclidean space-time and helps understand how asymptotic freedom can arise as a relevant perturbation at a decoupled fixed point without fine-tuning. Published by the American Physical Society 2024

Physics↗

Search for an Anomalous Production of Charged-Current 𝜈 𝑒 Interactions without Visible Pions across Multiple Kinematic Observables in MicroBooNE

This Letter presents an investigation of low-energy electron-neutrino interactions in the Fermilab Booster Neutrino Beam by the MicroBooNE experiment, motivated by the excess of electron-neutrino-like events observed by the MiniBooNE experiment. This is the first measurement to use data from all five years of operation of the MicroBooNE experiment, corresponding to an exposure of 1.11 × 10 21 protons on target, a 70% increase on past results. Two samples of electron neutrino interactions without visible pions are used, one with visible protons and one without any visible protons. The MicroBooNE data show reasonable agreement with the nominal prediction, with 𝑝 values ≥26.7% when the two 𝜈 𝑒 samples are combined, though the prediction exceeds the data in limited regions of phase space. The data are further compared to two empirical models that modify the predicted rate of electron-neutrino interactions in different variables in the simulation to match the unfolded MiniBooNE low energy excess. In the first model, this unfolding is performed as a function of electron neutrino energy, while the second model aims to match the observed shower energy and angle distributions of the MiniBooNE excess. This measurement excludes an electronlike interpretation of the MiniBooNE excess based on these models at >99% CLs in all kinematic variables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tracking and Rejection of Biased Sinusoidal Signals Using Generalized Predictive Controller

Some novel applications require the tracking/rejection of biased sinusoidal reference/distur-bances. According to the internal model principle (IMP), a controller must embed the model of a biased sinusoidal signal to track references and also reject perturbations modeled through the aforementioned signal. However, the design of that kind of controller is not straightforward, especially when they are implemented in digital processors. This paper presents a controller, based on generalized predictive control (GPC), designed for tracking/rejection of biased sinusoidal signals. In general, GPC is based on the prediction of the plant responses through an augmented prediction model. The proposed approach develops an augmented model that predicts the future errors. The prediction model and the control law used in the proposed approach embed the discrete-time model of a biased sinusoidal signal. Thus, the proposed controller can track/reject biased sinusoidal references/disturbances. The predicted errors and the future inputs of the proposed augmented model are used to define the cost function that measures the control performance. An optimization technique was applied to obtain the solution of the cost function, which is the optimal sequence of future model inputs that allows defining the control law. Experimental tests prove that the proposed controller can asymptotically track and reject biased sinusoidal signals.

42 ENGINEERING↗

Process-based balance of system cost modeling for offshore wind power plants in the United States

This paper describes the development of a process-based and open-source balance of system cost model that provides the capability to evaluate both existing and novel offshore wind technologies. Individual design and installation steps are represented with bottom-up engineering models that compute times and costs associated with the process; furthermore, operational constraints are assigned to each process so that delays caused by weather and presence of marine mammals may be accounted for in the overall project timeline. The model structure, assumptions, inputs, and results are vetted with industry partners and compared against actual projects for validation. Installation times show reasonable agreement with real data. Project cost sensitivities are investigated to compute the system-level impact of different design choices. First, individual vessel efficiencies are computed for varying numbers of installation vessels and weather time series to show the diminishing returns of more than two feeder barges. Then, array cable capital costs and installation times are determined for a representative project with different turbine sizes. These values quantify the cost-benefit tradeoffs and show a net-cost savings of decreasing numbers of turbines, increased turbine spacing, and fewer turbine terminations. These results demonstrate that the balance of system model features the accuracy, functionality, and accessibility to serve as the foundation for a wide range of analyses to identify cost reduction potentials for offshore wind energy in the United States.

17 WIND ENERGY↗

Institute for Catalysis in Energy Processes (ICEP) (Final Report)

The Institute for Catalysis in Energy Processes (ICEP) was a multi-PI program located at the Northwestern University Center for Catalysis and Surface Science from 2006-2024. Over several renewal cycles and several organizing themes, ICEP addressed fundamental questions in catalysis science. In turn, the scientific questions addressed were directly relevant to the efficient use of the nation’s resources to produce fuels and commodity chemicals, harness alternate energy sources for chemical reactions such as light or electricity, reduce emissions and waste, and minimize the impact of our use of plastics. Selective oxidation, (oxidative) dehydrogenation, deNOx, CO 2 reduction, hydrogen release, polymer decomposition / depolymerization, and many other reactions of intense interest to the US Department of Energy were studied in the center. Major ICEP strengths were in catalyst synthesis, in measurements that elucidated catalyst properties, in reaction mechanisms and kinetics, and in predictive theory and modeling. ICEP researchers were often the inventors or developers of materials and methods that were brought to bear on the Institute’s catalytic systems. Key characterization tools advanced through this project included resonance Raman and related techniques, sum frequency generation, and X-ray standing wave spectroscopy. Center members relied extensively on computational tools such as density functional theory and microkinetic modeling to fully investigate catalyst structures and catalytic mechanisms. ICEP researchers were early developers of atomic layer deposition (ALD) for catalyst synthesis and were early pioneers of metal organic frameworks for catalysis. ICEP innovations are found in areas of intense research such as single-atom catalysts, catalytic deconstruction of plastics, and catalytic MOFs, to name a few. Research areas initiated by ICEP indirectly led to DOE EFRCs, startup companies, and other achievements. Over its 18 years of existence, ICEP involved two different PIs (Stair and Notestein) and 24 senior investigators across several academic disciplines at Northwestern University. There were tight collaborations with Argonne National Laboratory, including specialized equipment and experiments permanently located there. The center supported ~400 person-years of effort by graduate students and postdocs, either directly through DOE support or indirectly by leveraging independent support provided to the trainees, e.g. through the NSF GRFP or internal fellowships. The project resulted in 328 manuscripts and numerous conference presentations.

36 MATERIALS SCIENCE↗

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗

Energy Dependence Analysis of Neutrino-Nucleus Interactions in Scintillator for MINERvA

This thesis is on the intrinsic energy dependence in neutrino-nucleus interaction models, especially quasielastic scattering and 2p2h process, and the implications for understanding data from MINERvA, NOvA, and DUNE. Neutrino-nucleus interactions are modeled using fve structure functions, W1, W2, W3, W4 and W5, and each structure function contributes diferently to the energy dependence once it enters the cross-section calculations. The energy independent term in the calculations contains only W2 and the next lower order term (of the order 1/E) contains W3 also. In this thesis, we show that W2 is good enough to describe MINERvA data and energy dependence coming from the cross-section directly is small. However, W3 will be signifcant for lower energy experiments such as NOvA and DUNE (especially at and below the oscillation maximum). We have also developed a method to extract structure functions directly from MINERvA data though we find that systematic uncertainties present in the data are too big to successfully determine 1/E Term. In addition to this, we have applied muon angle cuts on MINERvA data and MC, which have their own energy dependent effects. An apparent energy dependent discrepancy comes from known shortcomings especially in the pion production model. Finally, because the energy dependence analysis has similarities to the low-$\nu$ method, we have evaluated discrepancies between the data and MC in light of diferent fux constraint techniques. The results suggest including MINERvA s low-$\nu$ method constraint is an improvement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗