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Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Toward Accurate Spin–Orbit Splittings from Relativistic Multireference Electronic Structure Theory

Most nonrelativistic electron correlation methods can be adapted to account for relativistic effects, as long as the relativistic molecular spinor integrals are available, from either a four-, two-, or one-component mean-field calculation. Furthermore, relativistic multireference correlation methods remain a relatively unexplored area, with mixed evidence regarding the improvements brought by perturbative treatments. We report, for the first time, the implementation of state-averaged four-component relativistic multireference perturbation theories to second and third order based on the driven similarity renormalization group (DSRG). With our methods, named 4c-SA-DSRG-MRPT2 and 3, we find that the dynamical correlation included on top of 4c-CASSCF references can significantly improve the spin-orbit splittings in p-block elements and potential energy surfaces when compared to 4c-CASSCF and 4c-CASPT2 results. We further show that 4c-DSRG-MRPT2 and 3 are applicable to these systems over a wide range of the flow parameter, with systematic improvement from second to third order in terms of both improved error statistics and reduced sensitivity with respect to the flow parameter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Efficient sparse state preparation via quantum walks

Continuous-time quantum walks (CTQWs) on dynamic graphs, referred to as dynamic CTQWs, are a recently introduced universal model of computation that offers a new paradigm in which to envision quantum algorithms. In this work, we develop an algorithm that converts single-edge and self-loop dynamic CTQWs to the gate model of computation. We use this mapping to introduce an efficient sparse quantum state preparation framework based on dynamic CTQWs. Our approach utilizes combinatorics techniques such as minimal hitting sets, minimum spanning trees, and shortest Hamiltonian paths to reduce the number of controlled gates required to prepare sparse states. We show that our framework encompasses the current state of the art ancilla-free sparse state preparation method by reformulating this method as a CTQW. This CTQW-based framework offers an alternative to the uniformly controlled rotation method used by Qiskit by requiring fewer CX gates when the target state has a polynomial number of non-zero amplitudes.

dynamic continuous time quantum walks

Establishing In-House Titration Capabilities: Part I. Hydroxyl Group Titration through Acetic Anhydride Acetylation

This lessons learned document provides a detailed analysis of the hydroxy termination titration methods employed for determining hydroxyl group content in various chemical samples. The primary focus is on the evaluation of techniques such as ASTM E222 and their practical applications in laboratory settings. Through examination of method selection, sample preparation, and titration execution, key insights have been identified that enhance the accuracy and reliability of results. Notable findings include the advantages of using pressure bottle methods for improved heating uniformity and reduced solvent loss, as well as the challenges associated with endpoint detection in dark-colored solutions. Recommendations for alternative sampling and titration techniques are proposed to address these challenges. This document serves as a valuable resource for enhancing the effectiveness and efficiency of hydroxy termination titration methods in chemical analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

ExtremeMETA: High-speed Lightweight Image Segmentation Model by Remodeling Multi-channel Metamaterial Imagers

Deep neural networks (DNNs) have heavily relied on traditional computational units, such as CPUs and GPUs. However, this conventional approach brings significant computational burden, latency issues, and high power consumption, limiting their effectiveness. This has sparked the need for lightweight networks such as ExtremeC3Net. Meanwhile, there have been notable advancements in optical computational units, particularly with metamaterials, offering the exciting prospect of energy-efficient neural networks operating at the speed of light. Yet, the digital design of metamaterial neural networks (MNNs) faces precision, noise, and bandwidth challenges, limiting their application to intuitive tasks and low-resolution images. In this study, we proposed a large kernel lightweight segmentation model, ExtremeMETA. Based on ExtremeC3Net, our proposed model, ExtremeMETA maximized the ability of the first convolution layer by exploring a larger convolution kernel and multiple processing paths. With the large kernel convolution model, we extended the optic neural network application boundary to the segmentation task. To further lighten the computation burden of the digital processing part, a set of model compression methods was applied to improve model efficiency in the inference stage. The experimental results on three publicly available datasets demonstrated that the optimized efficient design improved segmentation performance from 92.45 to 95.97 on mIoU while reducing computational FLOPs from 461.07 MMacs to 166.03 MMacs. The large kernel lightweight model ExtremeMETA showcased the hybrid design’s ability on complex tasks.

large convolution kernel

Physics-informed latent neural operator for real-time predictions of time-dependent parametric PDEs

Deep operator network (DeepONet) has shown significant promise as surrogate models for systems governed by partial differential equations (PDEs), enabling accurate mappings between infinite-dimensional function spaces. However, when applied to systems with high-dimensional input-output mappings arising from large numbers of spatial and temporal collocation points, these models often require heavily overparameterized networks, leading to long training times. Latent DeepONet addresses some of these challenges by introducing a two-step approach: first learning a reduced latent space using a separate model, followed by operator learning within this latent space. While efficient, this method is inherently data-driven and lacks mechanisms for incorporating physical laws, limiting its robustness and generalizability in data-scarce settings. Here, in this work, we propose PI-Latent-NO, a physics-informed latent neural operator framework that integrates governing physics directly into the learning process. Our architecture features two coupled DeepONets trained end-to-end: a Latent-DeepONet that learns a low-dimensional representation of the solution, and a Reconstruction-DeepONet that maps this latent representation back to the physical space. By embedding PDE constraints into the training via automatic differentiation, our method eliminates the need for labeled training data and ensures physics-consistent predictions. The proposed framework is both memory and compute-efficient, exhibiting near-constant scaling with problem size and demonstrating significant speedups over traditional physics-informed operator models. We validate our approach on a range of parametric PDEs, showcasing its accuracy, scalability, and suitability for real-time prediction in complex physical systems.

Latent representations

Viability of Additively Manufactured Electrodes for Lithium-Ion Batteries

As the global economy becomes increasingly electrified, the demand for batteries and energy storage is expected to rise significantly, particularly in the transportation and electricity sectors. Lithium-ion batteries (LIBs) are currently the most advanced and widely used technology in this field. Traditionally, LIBs are manufactured using simple 2D planar geometries to maximize production efficiency and minimize costs. However, this approach limits energy density due to the restricted design flexibility of the electrodes. Additive manufacturing (AM) offers a promising solution to enhance the energy density and efficiency of LIBs by enabling the design of architectures that reduce diffusive losses and allow for a greater amount of active material to be incorporated within the same device footprint, thereby minimizing the use of inactive materials. Different AM techniques come with their own set of limitations, including printing speed, material compatibility, and scale, which must be considered when designing electrodes. Scalable and cost-effective methods are particularly important for electric vehicle batteries, while achieving higher energy densities in microbatteries is crucial for the miniaturization of wearable electronics and medical devices. Here, in this study, we simulate various 3D porous electrode designs for LIBs using graphite and nickel manganese cobalt oxide (NMC) electrodes. These designs are selected to represent structures that could be produced using different AM techniques, such as direct ink writing, fused deposition modeling, and stereolithography. Our results indicate that at higher charging rates and increased areal mass loading, 3D structures can outperform traditional 2D electrodes, although the benefits may diminish with more complex designs that are harder to manufacture. The observed gains in energy density are attributed to improved electrode utilization and reduced diffusive energy losses. This comprehensive analysis of structure–performance relationships will provide valuable insights to guide future research on 3D designs, material selection, and AM techniques for additively manufactured battery electrodes.

25 ENERGY STORAGE

Neural network denoising of x-ray images from high-energy-density experiments

Noise is a consistent problem for x-ray transmission images of High-Energy-Density (HED) experiments because it can significantly affect the accuracy of inferring quantitative physical properties from these images. We consider experiments that use x-ray area backlighting to image a thin layer of opaque material within a physics package to observe its hydrodynamic evolution. The spatial variance of the x-ray transmission across the system due to changing opacity serves as an analog for measuring density in this evolving layer. The noise in these images adds nonphysical variations in measured intensity, which can significantly reduce the accuracy of our inferred densities, particularly at small spatial scales. Denoising these images is thus necessary to improve our quantitative analysis, but any denoising method also affects the underlying information in the image. In this paper, we present a method for denoising HED x-ray images via a deep convolutional neural network model with a modified DenseNet architecture. In our denoising framework, we estimate the noise present in the real (data) images of interest and apply the inferred noise distribution to a set of natural images. These synthetic noisy images are then used to train a neural network model to recognize and remove noise of that character. We show that our trained denoiser network significantly reduces the noise in our experimental images while retaining important physical features.

47 OTHER INSTRUMENTATION

Multiple Changepoint Detection for Non‐Gaussian Time Series

ABSTRACT This article combines methods from existing techniques to identify multiple changepoints in non‐Gaussian autocorrelated time series. A transformation is used to convert a Gaussian series into a non‐Gaussian series, enabling penalized likelihood methods to handle non‐Gaussian scenarios. When the marginal distribution of the data is continuous, the methods essentially reduce to the change of variables formula for probability densities. When the marginal distribution is count‐oriented, Hermite expansions and particle filtering techniques are used to quantify the scenario. Simulations demonstrating the efficacy of the methods are given and two data sets are analyzed: 1) the proportion of home runs hit by Major League Baseball batters from 1920 to 2023 and 2) a six‐dimensional series of tropical cyclone counts from the Earth's basins of generation from 1980 to 2023. In the first series, beta marginal distributions are used to describe the proportions; in the second, Poisson marginal distributions seem appropriate.

Lund, Robert [Department of Statistics University

Simulation of gas mixture dynamics in a pipeline network using explicit staggered-grid discretization

Here we develop an explicit staggered finite difference discretization scheme for simulating the transport of highly heterogeneous gas mixtures through pipeline networks. This study is motivated by the proposed blending of hydrogen into natural gas pipelines to reduce end use carbon emissions while using existing pipeline systems throughout their planned lifetimes. Our computational method accommodates an arbitrary number of constituent gases with very different physical properties that may be injected into a network with significant spatiotemporal variation. In this setting, the gas flow physics are highly location- and time- dependent, so that local composition and nodal mixing must be accounted for. The resulting conservation laws are formulated in terms of pressure, partial densities and flows, and volumetric and mass fractions of the constituents. We include non-ideal equations of state that employ linear approximations of gas compressibility factors, so that the pressure dynamics propagate locally according to a variable wave speed that depends on mixture composition and density. We derive compatibility relationships for network edge boundary values that are more complex than for a homogeneous gas. The simulation method is evaluated on initial boundary value problems for a single pipe and a small network, is cross-validated with a lumped element simulation, and used to demonstrate a local monitoring and control policy for maintaining allowable concentration levels.

97 MATHEMATICS AND COMPUTING

Advanced Method Optimization for Sampling and Analysis Instrumentation

This work presents a generalized approach for analytical method optimization that branches the gap between techniques historically employed and accurate modern optimization techniques suitable for various applications. The novelty of the described strategy is the utilization of multivariate, multiobjective optimization with Karush-Kuhn-Tucker conditions to bound the optimization space to solutions within the physical limitations of instrumentation. Briefly, the basic steps outlined in this paper are to (1) determine the objective(s) that should be maximized or minimized based on the goals of the analytical application, (2) conduct a screening experiment, (3) perform ANOVA to determine the parameters which have a statistically significant effect on the objective, (4) conduct an experiment (e.g., Box-Behnken design) to collect data for fitting the objective equation, and (5) determine the physical constraints of the parameters and solve the Lagrangian to determine the optimal method parameters. A broad approach to optimization target selection allows for robust method tuning to develop improved data sets amenable for chemometrics and machine learning algorithm development. Gas chromatography-mass spectrometry was selected as a use case due to its broad use across scientific fields and time-consuming method development involving numerous parameters. In conclusion, this strategy can reduce the cost of research, improve data quality, and enable the rapid development of new analytical technique.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Adaptive immersed isogeometric level-set topology optimization

Here, this paper presents for the first time an adaptive immersed approach for level-set topology optimization using higher-order truncated hierarchical B-spline discretizations for design and state variable fields. Boundaries and interfaces are represented implicitly by the iso-contour of one or multiple level-set functions. An immersed finite element method, the eXtended IsoGeometric Analysis, is used to predict the physical response. The proposed optimization framework affords different adaptively refined higher-order B-spline discretizations for individual design and state variable fields. The increased continuity of higher-order B-spline discretizations together with local refinement enables direct control over the accuracy of the representation of each field while simultaneously reducing computational cost compared to uniformly refined discretizations. A flexible mesh adaptation strategy enables local refinement based on geometric measures or physics-based error indicators. These adaptive discretization and analysis approaches are integrated into gradient-based optimization schemes, evaluating the design sensitivities using the adjoint method. Numerical studies illustrate the features of the proposed framework with static, linear elastic, multi-material, two- and three-dimensional problems. The examples provide insight into the effect of refining the design variable field on the optimization result and the convergence rate of the optimization process. Using coarse higher-order B-spline discretizations for level-set fields promotes the development of smooth designs and suppresses the emergence of small features. Moreover, adaptive mesh refinement for state variable fields results in a reduction of overall computational cost. Higher-order B-spline discretizations are especially interesting when evaluating gradients of state variable fields due to their higher inter-element continuity.

36 MATERIALS SCIENCE

Scale effects on core design, fuel costs, and spent fuel volume of pressurized water reactors

The desire to improve the economic competitiveness and deployment pace of nuclear energy through modularization, manufacturing, and series production had led to the development of smaller size reactors. As the standard 17x17 fuel technology is mainly maintained in the pressurized water reactors (PWRs) category, this translates into a lower number of fuel assemblies in the core and sometimes a reduced fuel height. To assess the impact of such scale change in core design on fuel cycle cost and spent fuel volume, a scoping analysis tool is developed based on infinite lattice calculations, leakage, fuel management reduced models, and levelized unit cost of electricity (LCOE) estimate. As such, cost dynamics driven by fuel specific power, burnup, core leakage, feed, cycle length, fuel assembly height as well as uranium market data are captured with consistent set of assumptions and analysis methods. A selection of 5 reactor designs representative of leading PWR developers is assessed and compared. Pursuing higher specific powers and optimal burnups are highlighted as the main fuel cost reduction drivers, nevertheless, practical limitations and opportunities must be evaluated to establish the feasibility of such enhanced fuel operation. In consequence, a detailed core design is performed using SIMULATE3 code for 5 PWR variations including natural and forced coolant circulation modes, two reactor scales, power densities of 73, 112, and 123 kW/l and higher discharge burnups. Design and optimization are performed at the lattice level, for the reflector, and at the core loading level. Satisfactory steady-state operation including power distribution, coolant operating limits, and reactivity requirements are analyzed and reported in this paper. The fuel economics of the detailed core designs confirm the scoping analysis findings. Despite the unlocked power uprates in small PWRs, the achievable burnup for a given fuel specific power requires more enrichment and shorter fuel height results in higher fabrication costs per mass of fuel, which makes scaling down core size a more expensive endeavor on the fuel cycle front. Spent fuel volumes are reported for the PWRs designed in this paper. Furthermore, these volumes are driven by the core average discharge burnup regardless of the scale in consideration. Additional cost and core performance aspects related to heavy reflector gains, fuel-reflector substitution, and disposal cost policy in the U.S. are examined.

42 ENGINEERING

Perspectives on Systematic Cloud Microphysics Scheme Development With Machine Learning

Cloud microphysics—the collection of processes that govern the small‐scale formation, evolution, and interactions of liquid droplets and ice crystals in clouds and precipitation—remains a major source of uncertainty in weather and climate models. Although too small in scale to be explicitly resolved in any large‐eddy simulation, weather, or climate model, the representation of cloud microphysical processes has significant impact at the climate scale. Current microphysical schemes are limited by both parametric uncertainty, linked to uncertainty in physical parameter values, and structural uncertainty, arising from incomplete physical understanding of the processes at play or approximations made for computational efficiency. Recent advances in the application of machine learning (ML) to the physical sciences show significant potential for minimizing these limitations by leveraging high‐fidelity simulations and observations. Here we outline the challenges that must be addressed to apply ML toward cloud microphysics scheme development. This perspectives paper synthesizes recent progress in using data‐driven methods, including ML, to improve cloud microphysics parameterizations and highlights opportunities to address key uncertainties. We discuss the roles of aleatoric (irreducible, or statistical) and epistemic (reducible, or systematic) errors in contributing to microphysics parameterization uncertainty. ML can leverage observations to improve microphysical schemes via bottom‐up and top‐down constraints. Methods such as differentiable programming and ML‐enhanced sampling strategies and the creation of large scale benchmark data sets promise to bridge the gap between observations and models and to improve the consistency of cloud microphysical representation across temporal and spatial scales.

Lamb, Kara D. [Columbia Univ., New York, NY (Unite

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING

Integrated Metrics for County-Level Resilience Ranking Using Entropy and TOPSIS

In the face of atypical weather events, power infrastructure failures, and limited resources for resilience investment, energy decision-makers need data-driven metrics to allocate resilience investments and maximize the reduction of power outage impacts. For state-level planning, for instance, ranking the resilience of each county is key to ensuring effective distribution of resources. In such cases, resilience for each spatial unit is multifaceted and is captured by a set of indicators (i.e., metrics) that can be combined into an overall score that reduces the complexity of power outage dynamics to a single decision metric. However, weighting of these indicators is often addressed by simplifying assumptions (i.e., equal weights) or semi-subjective methods that rely on user-defined weights that can introduce biases (e.g., weighted average score). Within the disaster risk reduction and resilience engineering community, a recurring challenge in multicriteria decision-making is the objective weighting of indicators for composite indices. To address this issue, we have leveraged a Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) combined with an entropy-based weighting approach to calculated the integrated scores. This method objectively determines the importance of each metric, better discerns between spatial units (i.e., counties), and offers a more reliable ranking of counties according to their relative resilience attributes. By improving methods for integrating resilience indicators, our approach helps planners and decision-makers prioritize resources more effectively for more efficient resilience investments.

Bhusal, Narayan [Oak Ridge National Laboratory (OR

ML-based Dimension Reduction Strategies

Deep learning (DL)--based surrogate models have achieved success in various applications in carbon capture and storage (CCS). However, the model training on high-dimensional spaces is computationally expensive and impractical for large-scale and complex geological models, because the models usually contain hundreds of thousands to millions of grid cells, each with a set of parameters. Furthermore, the high cost of generating training data with sufficient variation is another limitation of model training on high-dimensional spaces, which may result in overfitting and reduce the model efficiency and prediction performance. We proposed the workflow incorporating dimension reduction methods and deep learning models, which aim to extract the latent variables of input parameters and output state variables, and then build the mapping function at the latent spaces. The proposed workflow can significantly reduce the computational complexity in solving both forward and inverse problems compared to models trained on high-dimensional spaces. Dimensionality reduction models showed great potential in workflows for fast reservoir simulation, history matching, prior model generation, visualization, and more, ultimately enhancing DL model performance in related SMART Work Packages.

Hosseini, Seyyed

Harnessing Machine Learning to Predict MoS 2 Solid Lubricant Performance

Physical vapor deposited (PVD) molybdenum disulfide (MoS 2 ) solid lubricant coatings are an exemplar material system for machine learning methods due to small changes in process variables often causing large variations in microstructure and mechanical/tribological properties. Here, in this work, a gradient boosted regression tree machine learning method is applied to an existing experimental data set containing process, microstructure, and property information to create deeper insights into the process-structure–property relationships for molybdenum disulfide (MoS 2 ) solid lubricant coatings. The optimized and cross-validated models show good predictive capabilities for density, reduced modulus, hardness, wear rate, and initial coefficients of friction. The contribution of individual deposition variables (i.e., argon pressure, deposition power, target conditioning) on coating properties is highlighted through feature importance. The process-property relationships established herein show linear and non-linear relationships and highlight the influence of uncontrolled deposition variables (i.e., target conditioning) on the tribological performance.

MoS2