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At least 343 records · Page 19

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗

EHR-BERT: A BERT-based model for effective anomaly detection in electronic health records

Objective: Physicians and clinicians rely on data contained in electronic health records (EHRs), as recorded by health information technology (HIT), to make informed decisions about their patients. The reliability of HIT systems in this regard is critical to patient safety. Consequently, better tools are needed to monitor the performance of HIT systems for potential hazards that could compromise the collected EHRs, which in turn could affect patient safety. In this paper, we propose a new framework for detecting anomalies in EHRs using sequence of clinical events. This new framework, EHR-Bidirectional Encoder Representations from Transformers (BERT), is motivated by the gaps in the existing deep-learning related methods, including high false negatives, sub-optimal accuracy, higher computational cost, and the risk of information loss. EHR-BERT is an innovative framework rooted in the BERT architecture, meticulously tailored to navigate the hurdles in the contemporary BERT method; thus, enhancing anomaly detection in EHRs for healthcare applications.Methods: The EHR-BERT framework was designed using the Sequential Masked Token Prediction (SMTP) method. This approach treats EHRs as natural language sentences and iteratively masks input tokens during both training and prediction stages. This method facilitates the learning of EHR sequence patterns in both directions for each event and identifies anomalies based on deviations from the normal execution models trained on EHR sequences.Results: Extensive experiments on large EHR datasets across various medical domains demonstrate that EHR-BERT markedly improves upon existing models. It significantly reduces the number of false positives and enhances the detection rate, thus bolstering the reliability of anomaly detection in electronic health records. This improvement is attributed to the model’s ability to minimize information loss and maximize data utilization effectively.Conclusion: EHR-BERT showcases immense potential in decreasing medical errors related to anomalous clinical events, positioning itself as an indispensable asset for enhancing patient safety and the overall standard of healthcare services. The framework effectively overcomes the drawbacks of earlier models, making it a promising solution for healthcare professionals to ensure the reliability and quality of health data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Optimization-based mesh correction with volume and convexity constraints

Here, we consider the problem of finding a mesh such that 1) it is the closest, with respect to a suitable metric, to a given source mesh having the same connectivity, and 2) the volumes of its cells match a set of prescribed positive values that are not necessarily equal to the cell volumes in the source mesh. Also, this volume correction problem arises in important simulation contexts, such as satisfying a discrete geometric conservation law and solving transport equations by incremental remapping or similar semi-Lagrangian transport schemes. In this paper we formulate volume correction as a constrained optimization problem in which the distance to the source mesh defines an optimization objective, while the prescribed cell volumes, mesh validity and/or cell convexity specify the constraints. We solve this problem numerically using a sequential quadratic programming (SQP) method whose performance scales with the mesh size. To achieve scalable performance we develop a specialized multigrid-based preconditioner for optimality systems that arise in the application of the SQP method to the volume correction problem. Numerical examples illustrate the importance of volume correction, and showcase the accuracy, robustness and scalability of our approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Lubricated immersed boundary method in two dimensions

Many biological examples of fluid-structure interaction, including the transit of red blood cells through the narrow slits in the spleen and the intracellular trafficking of vesicles into dendritic spines, involve the near-contact of elastic structures separated by thin layers of fluid. Motivated by such problems, we introduce an immersed boundary method that uses elements of lubrication theory to resolve thin fluid layers between immersed boundaries. We demonstrate 2nd-order accurate convergence for simple two-dimensional flows with known exact solutions to showcase the increased accuracy of this method compared to the standard immersed boundary method. Motivated by the phenomenon of wall-induced migration, we apply the lubricated immersed boundary method to simulate an elastic vesicle near a wall in shear flow. We also simulate the dynamics of a vesicle traveling through a narrow channel and observe the ability of the lubricated method to capture the vesicle motion on relatively coarse fluid grids.

59 BASIC BIOLOGICAL SCIENCES↗

Mesoscale informed parameter estimation through machine learning: A case-study in fracture modeling

Scale bridging is a critical need in computational sciences, where the modeling community has developed accurate physics models from first principles, of processes at lower length and time scales that influence the behavior at the higher scales of interest. However, it is not computationally feasible to incorporate all of the lower length scale physics directly into upscaled models. This is an area where machine learning has shown promise in building emulators of the lower length scale models, which incur a mere fraction of the computational cost of the original higher fidelity models. We demonstrate the use of machine learning using an example in materials science estimating continuum scale parameters by emulating, with uncertainties, complicated mesoscale physics. Additionally, we describe a new framework to emulate the fine scale physics, especially in the presence of microstructures, using machine learning, and showcase its usefulness by providing an example from modeling fracture propagation. Our approach can be thought of as a data-driven dimension reduction technique that yields probabilistic emulators. Our results show well-calibrated predictions for the quantities of interests in a low-strain simulation of fracture propagation at the mesoscale level. Furthermore, on average, we achieve ~10% relative errors on time-varying quantities like total damage and maximum stresses. Successfully replicating mesoscale scale physics within the continuum models is a crucial step towards predictive capability in multi-scale problems.

36 MATERIALS SCIENCE↗

Accurate numerical, integral methods for computing drift-kinetic Trubnikov-Rosenbluth potentials

A novel numerical method is employed to compute the integral form of the axi-symmetric Trubnikov-Rosenbluth potentials. Two methods for quadrature in pitch-angle are described and their convergence properties are studied. Careful attention is given to quadrature over a singular Green's function. Here it is shown that an infinite series representation of the Green's function can be used more efficiently than its closed form involving complete elliptic integrals. Then a collocation method in speed, with its associated quadrature scheme, is laid out and its convergence properties are studied. Using the proposed scheme, accurate low-order moments of the field collision operator are obtained using relatively few velocity space degrees of freedom. The scheme is showcased by solving for the equilibrium, axi-symmetric bootstrap current in tokamaks. A C 0 Gauss-Lobatto-Legendre finite element pitch-angle basis with vertex nodes at the trapped/passing boundary is shown, in the context of the integral methods used, to be much more efficient than the more common Legendre polynomial expansion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A fully-integrated lattice Boltzmann method for fluid–structure interaction

Here we present a fully-integrated lattice Boltzmann (LB) method for fluid–structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid–fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. The LBRMT achieves a spatial convergence rate between first-order and second-order for FSI simulations and is designed for low to intermediate Reynolds number flows with finite inertia at small Mach numbers. With simulations of complex suspensions mixing, we highlight the potential of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.

97 MATHEMATICS AND COMPUTING↗

Structure preservation using discrete gradients in the Vlasov-Poisson-Landau system

We present a novel structure-preserving framework for solving the Vlasov-Poisson-Landau system of equations using a particle in cell (PIC) discretization combined with discrete gradient time integrators. The Vlasov-Poisson-Landau system is an accurate model for studying hot plasma dynamics at a kinetic scale where small-angle Coulomb collisions dominate. Our scheme guarantees conservation of mass, momentum and energy as well as preservation of the monotonicity of entropy production in both the time-continuous and discrete systems. We employ the conservative integrator for both the Hamiltonian Vlasov-Poisson equations and the dissipative Landau equation using the PETSc library (www.mcs.anl.gov/petsc) to showcase structure-preserving properties.

Discrete gradients↗

A fourth order sharp immersed method for the incompressible Navier-Stokes equations with stationary and moving boundaries and interfaces

We propose a fourth order Navier-Stokes solver based on the immersed interface method (IIM), for flow problems with stationary and one-way coupled moving boundaries and interfaces. Our algorithm employs a Runge-Kutta-based projection method that maintains high-order temporal accuracy in both velocity and pressure for steady and unsteady velocity boundary conditions. Fourth order spatial accuracy is achieved through a novel fifth order IIM discretization scheme for the advection term, as well as existing high-order interface-corrected finite difference schemes for the other differential operators. Using a set of manufactured flow problems with stationary and moving boundaries, we demonstrate fourth order convergence of velocity and pressure in the infinity norm, both inside the domain and on the immersed boundaries. The solver’s performance is further validated through a range of practical flow simulations, highlighting its efficiency over a second order scheme. Finally, we showcase the ability of our immersed discretization scheme to handle interface-coupled multiphysics problems by solving a conjugate heat transfer problem with multiple immersed solids. Overall, the proposed approach robustly combines the efficiency of high order discretization schemes with the flexibility of immersed discretizations for flow problems with complex, moving boundaries and interfaces.

42 ENGINEERING↗

Advancing process-based flood frequency analysis for assessing flood hazard and population flood exposure

Recent studies have showcased the use of process-based hydrological models with Stochastic Storm Transposition (SST) techniques to conduct Flood Frequency Analysis (FFA). This framework, referred hereby FFA-SST, has proved to be a robust strategy to estimate peak flows of specific annual exceedance probability (e.g., 100-year peak flow) that can reflect natural and anthropogenic disturbances, including changes in land use and meteorological patterns. With the objective of advancing the FFA-SST framework, this study presents for the first time the use of an Integrated Surface-Subsurface Hydrological Model (ISSHM) to conduct FFA-SST by extending the analysis from peak flow responses to flood extent, enabling a unique view and analysis of flood hazard and population flood exposure at the basin scale. As a proof-of-concept, we used the ISSHM, Advanced Terrestrial Simulator (Amanzi-ATS) model, and the SST model, RainyDay, to conduct FFA-SST by simulating the flood response to 5,000 annual synthetic storm events in a 2,227 $km^2$ Southeast Texas watershed. We demonstrate that ATS, without site-specific calibration, provides a robust process-based representation of peak flows, flood extent, streamflow, evapotranspiration, soil moisture content, and water storage changes. Our results and analyses, covering frequency curves up to a 500-year return period for peak flows, basin inundation fractions, and the number of people exposed to flooding, offer a unique perspective to analyze flood impacts across spatial scales. Overall, this study provides critical insights for flood risk management by extending the FFA-SST framework to include both flood hazard and population flood exposure analyses at the basin scale. Such an approach will empower stakeholders and disaster emergency agencies with a more comprehensive understanding of flood impacts across the entire basin domain, facilitating informed decision-making for flood risk assessment and management.

58 GEOSCIENCES↗

Advanced magnetic X-ray spectro-microscopies to characterize mesoscopic magnetic materials

Here, this article provides a brief overview of advanced magnetic X-ray spectro-microscopies that are widely used in characterizing mesoscopic magnetic materials. Common to those techniques are various X-ray magnetic dichroism effects that are used as magnetic contrast mechanism. A particular interest is to use those techniques to image the underlying microscopic spin structures in magnetic materials with high spatial resolution and to ultimately resolve their full 3D mesoscale characteristics with elemental sensitivity, as well as their ultrafast dynamics upon excitations with field and current pulses. Recent research examples using various magnetic X-ray spectro-microscopies are presented to showcase their specific features with a focus on imaging novel topological spin textures, such as vortices, skyrmions and Hopfions, which are considered as potential building blocks towards low power, high-speed and high-density magnetic devices that could transform information technologies and potentially be used in biomedical applications. Future developments with magnetic X-ray spectro-microscopies harness the full coherence of next generation X-ray sources and could open the path towards single shot imaging with spatial and temporal resolutions down to fundamental magnetic length and time scales.

36 MATERIALS SCIENCE↗

Bulk synthesis of radiation resistant W – Ti – Cr – V compositionally complex alloys

Refractory compositionally complex alloys are candidate material systems for next generation advanced nuclear reactors. This work showcases the first successful bulk synthesis of low activation W–Ti based refractory compositionally complex alloys using arc melting and provides insights on using additive manufacturing for these compositions using directed energy deposition. Both techniques produce equiaxed grains composed of a tungsten matrix with Ti–V–Cr dendritic boundaries. The arc melted specimen possesses a multi-modal grain size distribution, while the directed energy deposition specimen possesses a more gaussian distribution of grain size. Both arc melted and directed energy deposition specimens demonstrate high thermal stability up to 900 °C, as well as promising radiation resistance with low loop formation and the presence of homogeneously distributed helium cavities maintaining small diameters at ≥10 dpa under simultaneous light (helium) and heavy (krypton) ion irradiation at 900 °C.

Arc melting (AM)↗

The effects of hydrogen absorption in U 3 Si 5 and its thermodynamic properties

The hydrogen absorption behavior of U 3 Si 5 was examined using a Sieverts apparatus. Experimental results revealed the formation of a hydride phase with a stoichiometry reaching U 3 Si 5 H 1.23 at pressures up to 250 kPa and temperatures below 300°C. Further, by employing Van 't Hoff analysis, the enthalpy and entropy of formation for the newly formed hydride phase were measured as -19.73 $kJ$ ∙ $mol$ -1 and -251.18 $J$ ∙ $mol$ -1 ∙ $T$ -1 , respectively. Rietveld refinement showcased an expansion in lattice parameters a and c, resulting in an overall increase in unit cell volume of up to 8%; volume expansion can induce structural failures within the material.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Origin of deactivation of aqueous Na–CO 2 battery and mitigation for long-duration energy storage

Here, the development of long-duration energy storage technology is crucial to facilitate the efficient utilization of renewable energy sources while mitigating carbon dioxide production. In this study, we investigate the deactivation and reactivation mechanisms of the aqueous Na–CO 2 battery during extended cycling. We have designed the cathode to include non-precious intermetallic catalysts. As the cell undergoes repeated cycles, the voltage polarization during discharge progressively rises, eventually leading to the cell's deactivation and formation of decomposition products clogging the electrode surface. Results obtained from comprehensive characterization techniques, including conductive atomic force microscopy (cAFM), Raman spectroscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and inductively coupled plasma-mass spectrometry provide insight into the decomposition products. We also showcase an electrochemical approach for regeneration of these aqueous cells. Our findings, along with the insights we have gained, provide a path toward creating long-duration systems with self-healing properties.

25 ENERGY STORAGE↗

Assessing the coating implications of slurry formulations in NCMA and LFMP blend cathodes for lithium-ion batteries

This paper investigates the implications of slurry formulations and electrode processing on the performance of lithium-ion battery (LIB) cathodes, focusing on Nickel Cobalt Manganese Aluminum (NCMA) and Lithium Ferro Manganese Phosphate (LFMP) blends. Through a comprehensive examination of electrode processing steps, from material selection to coating application, we elucidate the critical role of processing parameters in shaping electrode morphology and electrochemical behavior. Rheological studies reveal the influence of slurry composition on viscosity and flow behavior, highlighting the importance of achieving optimal rheological properties for uniform coating deposition. Electrochemical characterization, including cyclic voltammetry and rate capability tests, unveils the electrochemical behavior of NCMA, LFMP, and their blend, showcasing the synergistic effects of material blending on battery performance. In conclusion, our findings underscore the intricate relationship between slurry formulation, electrode processing, and LIB performance, offering valuable insights for the design and optimization of high-performance electrode materials for next-generation batteries.

25 ENERGY STORAGE↗

Agro-waste shaped porous Al2O3/Ni composites: Corrosion resistance performance and artificial neural network modelling

Highlights: • Porous Al{sub 2}O{sub 3}/Ni composites were developed with agro-waste pore-forming agents. • The RH and SCB graded composites showed Ni{sub 3}Al{sub 2}SiO{sub 8} and NiAl{sub 2}O{sub 4} spinels respectively. • Superior chemical stability was demonstrated by the Al{sub 2}O{sub 3}-2Ni-RH composite. • The ANN model demonstrated a good performance with R{sup 2} value of approx. 0.99. - Abstract: In the present study, an analysis on the combined effect of nickel (Ni) reinforcement and pore former type in characterizing the corrosion behavior of composite porous alumina ceramics was performed. In order to showcase the potential of the new porous ceramics, pore-forming agents (PFAs) from rice husk (RH) and sugarcane bagasse (SCB) were used in shaping the plain and composite porous alumina samples having sample formulation of Al{sub 2}O{sub 3}-xNi-PFA; x = 0, 2, 4, 6 and 8 wt%. Results showed that the emergence of a highly stable Ni{sub 3}Al{sub 2}SiO{sub 8} spinelloid phase in the RH-graded composites enhanced their chemical stability in the corrosive mediums (10 wt% NaOH and 20 wt% H{sub 2}SO{sub 4}) relative to the plain and the corresponding SCB-graded counterparts. An artificial neural network (ANN) model has been developed for predicting the corrosion behavior of the plain and composite porous alumina ceramics based on the experimental data. The developed ANN model satisfactorily predicted the percent mass losses of the porous ceramics in strong alkali and strong acid solutions with coefficient of determination (R{sup 2}) of approximately 0.99.

36 MATERIALS SCIENCE↗