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At least 325 records · Page 18

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗

Online State Estimation for Time-Varying Systems

The paper investigates the problem of estimating the state of a time-varying system with a linear measurement model; in particular, the paper considers the case where the number of measurements available can be smaller than the number of states. In lieu of a batch linear least-squares (LS) approach well-suited for static networks, where a sufficient number of measurements could be collected to obtain a full-rank design matrix the paper proposes an online algorithm to estimate the possibly time-varying state by processing measurements as and when available. The design of the algorithm hinges on a generalized LS cost augmented with a proximal-point-type regularization. With the solution of the regularized LS problem available in closed-form, the online algorithm is written as a linear dynamical system where the state is updated based on the previous estimate and based on the new available measurements. Conditions under which the algorithmic steps are in fact a contractive mapping are shown, and bounds on the estimation error are derived for different noise models. Numerical simulations are provided to corroborate the analytical findings.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Closed-Form Approximation of the Total Variation Proximal Operator

Total variation (TV) is a widely used function for regularizing imaging inverse problems that is particularly appropriate for images whose underlying structure is piecewise constant. TV regularized optimization problems are typically solved using proximal methods, but the way in which they are applied is constrained by the absence of a closed-form expression for the proximal operator of the TV function. A closed-form approximation of the TV proximal operator has previously been proposed, but its accuracy was not theoretically explored in detail. Here, we address this gap by making several new theoretical contributions, proving that the approximation leads to a proximal operator of some convex function, it is equivalent to a gradient descent step on a smoothed version of TV, and that its error can be fully characterized and controlled with its scaling parameter. We experimentally validate our theoretical results on image denoising and sparse-view computed tomography (CT) image reconstruction.

97 MATHEMATICS AND COMPUTING↗

Power System Event Identification Based on Deep Neural Network With Information Loading

Online power system event identification and classification are crucial to enhancing the reliability of transmission systems. In this study, we develop a deep neural network (DNN) based approach to identify and classify power system events by leveraging real-world measurements from hundreds of phasor measurement units (PMUs) and labels from thousands of events. Two innovative designs are embedded into the baseline model built on convolutional neural networks (CNNs) to improve the event classification accuracy. First, we propose a graph signal processing based PMU sorting algorithm to improve the learning efficiency of CNNs. Second, we deploy information loading based regularization to strike the right balance between memorization and generalization for the DNN. Numerical results based on real-world dataset from the Eastern Interconnection of the U.S power transmission grid show that the combination of PMU based sorting and the information loading based regularization techniques help the proposed DNN approach achieve highly accurate event identification and classification results.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Make the Fastest Faster: Importance Mask Synthesis for Interactive Volume Visualization using Reconstruction Neural Networks

Visualizing a large-scale volumetric dataset with high resolution is challenging due to the substantial computational time and space complexity. Recent deep learning-based image inpainting methods significantly improve rendering latency by reconstructing a high-resolution image for visualization in constant time on GPU from a partially rendered image where only a portion of pixels go through the expensive rendering pipeline. However, existing solutions need to render every pixel of either a predefined regular sampling pattern or an irregular sample pattern predicted from a low-resolution image rendering. Both methods require a significant amount of expensive pixel-level rendering. In this work, we provide Importance Mask Learning (IML) and Synthesis (IMS) networks, which are the first attempts to directly synthesize important regions of the regular sampling pattern from the user’s view parameters, to further minimize the number of pixels to render by jointly considering the dataset, user behavior, and the downstream reconstruction neural network. Our solution is a unified framework to handle various types of inpainting methods through the proposed differentiable compaction/decompaction layers. Experiments show our method can further improve the overall rendering latency of state-of-the-art volume visualization methods using reconstruction neural network for free when rendering scientific volumetric datasets. Our method can also directly optimize the off-the-shelf pre-trained reconstruction neural networks without elongated retraining.

Large-scale data↗

3D Deep Learning Joint Inversion of Active Seismic Full Waveform and Passive Seismic Traveltime Data for Reservoir Imaging and Uncertainty Quantification

Here, we present deep learning (DL) networks for three-dimensional (3D) joint inversion of active seismic full waveform and passive seismic traveltime data to image reservoirs and their properties and quantify imaging uncertainties. Active seismic full-waveform data can provide high-resolution monitoring images but are collected only intermittently because of their high acquisition cost. In contrast, passive seismic data can be gathered at relatively low cost between regular active surveys, although their imaging quality can be compromised by factors such as low signal-to-noise ratios and limited ray coverage of the target. Although these datasets are routinely acquired together at CO 2 storage sites, their combined inversion within a 3D DL framework has not been previously demonstrated. To our knowledge, this is the first study to address this gap, combining the strength of both data types. For efficient data storage and DL training with large 3D seismic datasets, we use a 3D data matrix in which a random number of passive seismic traveltime data are stored as parabolic envelopes using one-hot encoding and a 3D full-waveform data matrix in which multiple shot gathers are summed. Two network architectures are evaluated: a single-encoder U-Net for single-data type inversion and a dual-encoder U-Net for joint inversion of active and passive seismic data. We also evaluate the single-encoder U-Net for joint inversion by concatenating full-waveform data and traveltime data. We propose a systematic approach for selecting an optimal dropout rate that balances regularization during training and Monte Carlo dropout-based uncertainty quantification during prediction by examining the correlation coefficient between standard deviation and prediction error, along with the training misfit, across a range of dropout rates. 3D DL inversion experiments include five different network configurations, with evaluations under ideal, noisy and dropout-enabled conditions. Both model and data uncertainties are assessed, as well as their combined effects. Across all conditions, the networks consistently predict accurate CO 2 saturation models with low prediction errors, such as a structural similarity index of 0.993 and CO 2 difference of 1.1%. Uncertainty estimates show strong spatial correlation with prediction errors, confirming the effectiveness of the proposed dropout selection approach. The results demonstrate that our DL approach, utilizing compact data representations and appropriate uncertainty quantification, yields accurate subsurface images under various inversion conditions and provides valuable insights into the reliability of predictions.

Um, Evan Schankee [Lawrence Berkeley National Labo↗

A Hybrid Lagrangian/Eulerian Collocated Velocity Advection and Projection Method for Fluid Simulation

Abstract We present a hybrid particle/grid approach for simulating incompressible fluids on collocated velocity grids. Our approach supports both particle‐based Lagrangian advection in very detailed regions of the flow and efficient Eulerian grid‐based advection in other regions of the flow. A novel Backward Semi‐Lagrangian method is derived to improve accuracy of grid based advection. Our approach utilizes the implicit formula associated with solutions of the inviscid Burgers’ equation. We solve this equation using Newton's method enabled by C 1 continuous grid interpolation. We enforce incompressibility over collocated, rather than staggered grids. Our projection technique is variational and designed for B‐spline interpolation over regular grids where multiquadratic interpolation is used for velocity and multilinear interpolation for pressure. Despite our use of regular grids, we extend the variational technique to allow for cut‐cell definition of irregular flow domains for both Dirichlet and free surface boundary conditions.

Gagniere, S.↗

Disk transport rates from Ti isotopic signatures of refractory inclusions

Abstract The early solar system was a dynamic period during which the formation of early solids set into motion the process of planet building. Although both astrophysical observations and theoretical modeling demonstrate the presence of widespread transport of material, we lack concrete quantitative constraints on timings, distances, and mechanisms thereof. To trace these transport processes, one needs objects of known early formation times and these objects would need to be distributed throughout parent bodies with known accretion times and distances. Generally, these criteria are met by “regular” (i.e., non–fractionated and unidentified nuclear and excluding hibonite‐rich) Ca‐Al‐rich inclusions (CAIs) as these objects formed very early and close to the young Sun and contain distinctive nucleosynthetic isotope anomalies that permit provenance tracing. However, nucleosynthetic isotopic signatures of such refractory inclusions have so far primarily been analyzed in chondritic meteorites that formed within ~4 AU from the Sun. Here, we investigate Ti isotopic signatures of four refractory inclusions from the ungrouped carbonaceous chondrite WIS 91600 that was previously suggested to have formed beyond ~10 AU from the Sun. We show that these inclusions exhibit correlated excesses in 50 Ti and 46 Ti and lack large Ti isotopic anomalies that would otherwise be indicative of more enigmatic refractory materials with unknown formation ages. Instead, these isotope systematics suggest the inclusions to be genetically related to regular CAIs commonly found in other chondrites that have a broadly known formation region and age. Collectively, this implies that a common population of CAIs was distributed over the inner ~10 AU within ~3.5 Myr, yielding an average (minimum) speed for the transport of millimeter‐scale material in the early solar system of ~1 cm s −1 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monotonic Gaussian Process for Physics-Constrained Machine Learning With Materials Science Applications

Physics-constrained machine learning is emerging as an important topic in the field of machine learning for physics. One of the most significant advantages of incorporating physics constraints into machine learning methods is that the resulting model requires significantly less data to train. By incorporating physical rules into the machine learning formulation itself, the predictions are expected to be physically plausible. Gaussian process (GP) is perhaps one of the most common methods in machine learning for small datasets. In this paper, we investigate the possibility of constraining a GP formulation with monotonicity on three different material datasets, where one experimental and two computational datasets are used. The monotonic GP is compared against the regular GP, where a significant reduction in the posterior variance is observed. The monotonic GP is strictly monotonic in the interpolation regime, but in the extrapolation regime, the monotonic effect starts fading away as one goes beyond the training dataset. Imposing monotonicity on the GP comes at a small accuracy cost, compared to the regular GP. The monotonic GP is perhaps most useful in applications where data are scarce and noisy, and monotonicity is supported by strong physical evidence.

36 MATERIALS SCIENCE↗

Investigating the Impact of Power-Take-Off System Parameters and Control Law on a Rotational Wave Energy Converter’s Peak-to-Average Power Ratio Reduction

Due to the irregular nature of real waves, the power captured in a wave energy converter (WEC) system is highly variable. This is an important barrier to the effective use of WECs. To address this challenge, this study focuses on a rotational WEC power-take-off system in which high-speed and high-efficiency generators along with a torque/power smoothing inertia element can be effectively utilized. In the first phase of this study, the U.S. Department of Energy’s reference model 3 (WEC-Sim RM3; two-body point absorber), along with a slider-crank WEC, were integrated for linear to rotational conversion. Relative motion between the float and spar in RM3 was the driving force for this slider-crank WEC, which is connected to a motor/generator set through a gearbox. RM3 geometry was scaled down by 25 times to work within the limits of the physical motor/generator set used in the experimentation. Once the integration in a hardware-in-the-loop simulation environment was successfully completed, data on the peak-to-average power ratio was collected for various wave conditions including regular and irregular waves. The control algorithm designed to keep the system in resonance with waves was able to maintain relatively high speed depending on the specific gear ratio and wave period. Initial results with hardware-in-the-loop simulations reveal that gear ratio and crank radius have a strong impact on the peak-to-average power ratio. In addition, it was found that output power from the generator was maximized at a larger gear ratio, as the crank radius was increased.

50 EE - Wind and Water Power Program - Water (EE-4↗

Investigation of Theoretical Solutions to a Bottom-Raised Oscillating Surge Wave Energy Converter (OSWEC) Through Experimental and Parametric Studies

Experiments were conducted on a wave tank model of a bottom raised oscillating surge wave energy converter (OSWEC) model in regular waves. The OSWEC model shape was a thin rectangular flap, which was allowed to pitch in response to incident waves about a hinge located at the intersection of the flap and the top of the supporting foundation. Torsion springs were added to the hinge in order to position the pitch natural frequency at the center of the wave frequency range of the wave maker. The flap motion as well as the loads at the base of the foundation were measured. The OSWEC was modeled analytically using elliptic functions in order to obtain closed form expressions for added mass and radiation damping coefficients, along with the excitation force and torque. These formulations were derived and reported in a previous publication by the authors. While analytical predictions of the foundation loads agree very well with experiments, large discrepancies are seen in the pitch response close to resonance. These differences are analyzed by conducting a sensitivity study, in which system parameters, including damping and added mass values, are varied. The likely contributors to the differences between predictions and experiments are attributed to tank reflections, standing waves that can occur in long, narrow wave tanks, as well as the thin plate assumption employed in the analytical approach.

analytical↗

Exploiting voxel-sparsity for bone imaging with sparse-view cone-beam computed tomography

An optimization-based image reconstruction frame work is developed specifically for bone imaging. This framework exploits voxel-sparsity by use of ℓ 1 -norm image regularization and it enables image reconstruction from sparse-view cone-beam computed tomography (CBCT) acquisition. The effectiveness of the voxel-sparsity regularization is enhanced by using a blurred image representation. Ramp-filtering is included in the data discrepancy term and it has the effect of acting as a preconditioner, reducing the necessary number of iterations. The bone image reconstruction framework is demonstrated on CBCT data taken from an equine metacarpal condyle specimen.

Bone imaging↗

Running Primal-Dual Gradient Method for Time-Varying Nonconvex Problems

This paper focuses on a time-varying constrained nonconvex optimization problem, and considers the synthesis and analysis of online regularized primal-dual gradient methods to track a Karush-Kuhn-Tucker (KKT) trajectory. The proposed regularized primal-dual gradient method is implemented in a running fashion, in the sense that the underlying optimization problem changes during the execution of the algorithms. In order to study its performance, we first derive its continuous-time limit as a system of differential inclusions. We then study sufficient conditions for tracking a KKT trajectory, and also derive asymptotic bounds for the tracking error (as a function of the time-variability of a KKT trajectory). Further, we provide a set of sufficient conditions for the KKT trajectories not to bifurcate or merge, and also investigate the optimal choice of the parameters of the algorithm. Illustrative numerical results for a time-varying nonconvex problem are provided.

differential inclusion↗

Space-Split Algorithm for Sensitivity Analysis of Discrete Chaotic Systems With Multidimensional Unstable Manifolds

Accurate approximations of the change of a system's output and its statistics with respect to the input are highly desired in computational dynamics. Ruelle's linear response theory provides breakthrough mathematical machinery for computing the linear response of chaotic dynamical systems. In this paper, we propose an algorithm for sensitivity analysis of discrete chaos with an arbitrary number of positive Lyapunov exponents. We combine the concept of perturbation space-splitting, which regularizes Ruelle's original expression, together with measure-based parameterization of the expanding subspace. We use these tools to rigorously derive trajectory-following recursive relations that converge exponentially fast, and construct a memory-efficient Monte Carlo scheme for derivatives of the output statistics. Thanks to the regularization and lack of simplifying assumptions on the system's behavior, our method is immune to the common problems of other popular methods such as the exploding tangent solutions and unphysical shadowing directions. Here, we provide a ready-to-use algorithm, analyze its complexity, and demonstrate several numerical examples of sensitivity computation using physically-inspired low-dimensional systems.

97 MATHEMATICS AND COMPUTING↗

Stochastic Approximation for Multi-period Simulation Optimization with Streaming Input Data

We consider a continuous-valued simulation optimization (SO) problem, where a simulator is built to optimize an expected performance measure of a real-world system while parameters of the simulator are estimated from streaming data collected periodically from the system. At each period, a new batch of data is combined with the cumulative data and the parameters are re-estimated with higher precision. The system requires the decision variable to be selected in all periods. Therefore, it is sensible for the decision-maker to update the decision variable at each period by solving a more precise SO problem with the updated parameter estimate to reduce the performance loss with respect to the target system. We define this decision-making process as the multi-period SO problem and introduce a multi-period stochastic approximation (SA) framework that generates a sequence of solutions. Two algorithms are proposed: Re-start SA (ReSA) reinitializes the stepsize sequence in each period, whereas Warm-start SA (WaSA) carefully tunes the stepsizes, taking both fewer and shorter gradient-descent steps in later periods as parameter estimates become increasingly more precise. We show that under suitable strong convexity and regularity conditions, ReSA and WaSA achieve the best possible convergence rate in expected sub-optimality either when an unbiased or a simultaneous perturbation gradient estimator is employed, while WaSA accrues significantly lower computational cost as the number of periods increases. In addition, we present the regularized ReSA, which obviates the need to know the strong convexity constant and achieves the same convergence rate at the expense of additional computation.

Computer Science↗

Optimizing Fast Charging and Wetting in Lithium-Ion Batteries with Optimal Microstructure Patterns Identified by Genetic Algorithm

To sustain the high-rate current required for fast charging electric vehicle batteries, electrodes must exhibit sufficiently high effective ionic diffusion. Additionally, to reduce battery manufacturing costs, wetting time must decrease. Both of these issues can be addressed by structuring the electrodes with mesoscale pore channels. However, their optimal spatial distribution, or patterns, is unknown. Herein, a genetic algorithm has been developed to identify these optimal patterns using a CPU-cheap proxy distance-based model to evaluate the impact of the added pore networks. Both coin-cell and pouch cell form factors have been considered for the wetting analysis, with their respective electrolyte infiltration mode. Regular hexagonal and mud-crack-like patterns, respectively, for fast charging and fast wetting were found to be optimal and have been compared with pre-determined, easier to manufacture, patterns. The model predicts that using cylindrical channels arranged in a regular hexagonal pattern is ∼6.25 times more efficient for fast charging as compared to grooved lines with both structuring strategies being restricted to a 5% electrode total volume loss. The model also shows that only a very limited electrode volume loss (1%–2%) is required to dramatically improve the wetting (5–20 times) compared to an unstructured electrode.

25 ENERGY STORAGE↗

A Systematic Review and Meta-Analysis of Tai Chi Training in Cardiorespiratory Fitness of Elderly People

Objectives. The purpose of this study was to investigate the influence of Tai Chi on cardiorespiratory fitness (CRF) in elderly people using meta-analysis. Methods. This study used seven electronic databases and data retrieved from randomized controlled trials (RCTs) investigating the role of Tai Chi on CRF in the elderly. All these 24 RCTs were screened and selected from 7 literature databases. The Stata 11.2 software (StataCorp, USA) was used for the meta-analysis, subgroup analysis, and bias test, while the Cochrane Collaboration’s tool was used for the assessment of the risk of bias (RoB). 4 researchers independently participated in sample selection, data extraction, and RoB assessment. Results. Following the inclusion criteria, 24 eligible studies were included in our analysis. The meta-analysis indicated that Tai Chi practice significantly increased the maximum rate of oxygen consumption (VO2 max) (weighted mean difference (WMD) = 3.76, 95% CI: 1.25 to 6.26, P < 0.1 ), leading to an overall reduction in the heart rate (HR) (WMD = −1.84, 95% CI: −2.04 to −1.63, P ≤ 0.001 ) and an increase in the O2 pulse (WMD = 0.94, 95% CI: 0.60 to 1.28, P ≤ 0.001 ) in individuals who practiced Tai Chi regularly compared with those who did not. The subgroup analysis suggested that overall in those who practiced Tai Chi, males (WMD = 1.48, 95% CI: 0.85 to 2.12, P ≤ 0.001 ) had higher O2 pulse than females (WMD = 0.73, 95% CI: 0.33 to 1.12, P ≤ 0.001 ). The subgroup analysis also showed an increase in the vital capacity (VC) (WMD = 316.05, 95% CI: 239.74 to 392.35, P ≤ 0.001 ) in individuals practicing Tai Chi. When the samples were further stratified by Tai Chi practicing time, the subgroup analysis suggested that individuals practicing Tai Chi over a period of 24 weeks showed no significant difference in VC (WMD = 82.95, 95% CI: -98.34 to 264.23, P = 0.370 ), while those practicing Tai Chi over a period of 48 weeks showed a significant increase (WMD = 416.62, 95% CI: 280.68 to 552.56, P ≤ 0.001 ). Furthermore, the subgroup analysis demonstrated that the increase in VC is significantly correlated with the Tai Chi practicing time (WMD = 344.97, 95% CI: 227.88 to 442.06, P ≤ 0.001 ). Conclusion. Regular Tai Chi practice could improve the CRF in the elderly, as indicated by significant improvement in indicators including VO2max, O2pulse, VC, and HR. However, gender and practice time might influence the overall beneficial outcomes.

Tan, Tianyang↗

ForceFinder

SAND2025-11750O ForceFinder extends the Structural Dynamics Python Libraries (SDynPy) with comprehensive tools for inverse source estimation (ISE) tasks via frequency response function (FRF) matrix inversion. The software is designed for transfer path analysis and multiple-input/multiple-output (MIMO) vibration control problems. It allows users to estimate sources through various algorithms, from the basic Moore-Penrose pseudo-inverse to statistical learning methods such as Tikhonov regularization via an L-curve and elastic net regularization via an information criterion. ForceFinder uses an object-oriented framework, where all components of the ISE problem—such as FRFs, responses, and transformations—are stored in a "SourcePathReceiver" object. This software can be applied to any noise and vibration problem. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Carter, Steven [Sandia National Lab. (SNL-CA), Liv↗