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At least 109 records · Page 6

Multi-stage preconditioners for thermal–compositional–reactive flow in porous media

We present a family of multi-stage preconditioners for coupled thermal-compositional-reactive reservoir simulation problems. The most common preconditioner used in industrial practice, the Constrained Pressure Residual (CPR) method, was designed for isothermal models and does not offer a specific strategy for the energy equation. For thermal simulations, inadequate treatment of the temperature unknown can cause severe conver-gence degradation. When strong thermal diffusion is present, the energy equation exhibits significant elliptic behavior that cannot be accurately corrected by CPR's second stage. In this work, we use Schur-complement decompositions to extract a temperature subsystem and apply an Algebraic MultiGrid (AMG) approximation as an additional preconditioning stage to improve the treatment of the energy equation. We present results for several two-dimensional hot air injection problems using an extra heavy oil, including challenging reactive In-Situ Combustion (ISC) cases. We show improved performance and robustness across different thermal regimes, from advection dominated (high Péclet number) to diffusion dominated (low Péclet number). The number of linear iterations is reduced by 40–85% compared to standard CPR for both homogeneous and heterogeneous media, and the new methods exhibit almost no sensitivity to the thermal regime.

42 ENGINEERING↗

Evaluating Stage Motion for Automated Electron Microscopy

Abstract Precise control is an essential and elusive quality of emerging self-driving transmission electron microscopes (TEMs). It is widely understood these instruments must be capable of performing rapid, high-volume, and arbitrary movements for practical self-driving operation. However, stage movements are difficult to automate at scale, owing to mechanical instability, hysteresis, and thermal drift. Such difficulties pose major barriers to artificial intelligence-directed microscope designs that require repeatable, precise movements. To guide design of emerging instruments, it is necessary to understand the behavior of existing mechanisms to identify rate limiting steps for full autonomy. Here, we describe a general framework to evaluate stage motion in any TEM. We define metrics to evaluate stage degrees of freedom, propose solutions to improve performance, and comment on fundamental limits to automated experimentation using present hardware.

47 OTHER INSTRUMENTATION↗

Understanding the Impact of Data Staging for Coupled Scientific Workflows

We report the rate of data generated by cutting-edge experimental science facilities and large-scale simulations enabled by current high-performance computing (HPC) systems has continued to grow at a far greater pace than the development of the network and storage capabilities on which these systems rely. To cope with this challenge, scientist are moving toward the creation of autonomous experiments and HPC simulations using machine learning. However, efficiently moving, storing, and processing large amounts of data away from the point of origin presents an incredible challenge. In-memory computing, in situ analysis, data staging, and data streaming are recognized viable alternatives to traditional file-based methods for transferring data between coupled workflows. However, the performance trade-offs and limitations for these methods are not fully understood when used in HPC applications. This article presents a comprehensive performance assessment of the current solutions for data staging when applied to applications that are not necessary I/O intensive which makes them not ideal candidates for these methods. Our study is based on experiments running at scale on Oak Ridge National Laboratory's Summit supercomputer using applications and simulations that cover typical computational motifs and patterns. We investigated the usability and cost/benefit trade-offs of staging algorithms for HPC applications under different scenarios and highlight opportunities for optimizing the dataflow between coupled simulation workflows.

97 MATHEMATICS AND COMPUTING↗

Visualizing the Nanoscale Oxygen and Cation Transport Mechanisms during the Early Stages of Oxidation of Fe–Cr–Ni Alloy Using In Situ Atom Probe Tomography

Abstract Understanding the early stages of interactions between oxygen and material surfaces—especially at very high spatial resolutions—is highly beneficial for fields ranging from materials degradation, corrosion, geological sciences, forensics, and catalysis. The ability of in situ atom probe tomography (APT) is demonstrated to track the diffusion of oxygen and metal ions at nanoscale spatial resolution during the early stages of oxidation of a model Fe–Cr–Ni alloy. Using 18 O isotope tracers in these in situ APT experiments and complementary ex situ multimodal microscopy, spectroscopy, and computational simulations allows to precisely analyze the kinetics of oxidation and determine that outward cation diffusion to oxide/air interface is the primary mechanism for intragranular oxide growth in this alloy at 300 °C. This unique in situ isotopic tracer APT approach and the insights gained can be highly beneficial for studying early stages of gas–surface reactions in a broad array of materials.

36 MATERIALS SCIENCE↗

Continuous precipitation‐filtration process for initial capture of a monoclonal antibody product using a four‐stage countercurrent hollow fiber membrane washing step

The significant increase in product titers, coupled with the growing focus on continuous bioprocessing, has renewed interest in using precipitation as a low‐cost alternative to Protein A chromatography for the primary capture of monoclonal antibody (mAb) products. In this work, a commercially relevant mAb was purified from clarified cell culture fluid using a tubular flow precipitation reactor with dewatering and washing provided by tangential flow microfiltration. The particle morphology was evaluated using an inline high‐resolution optical probe, providing quantitative data on the particle size distribution throughout the precipitation process. Data were obtained in both a lab‐built 2‐stage countercurrent washing system and a commercial countercurrent contacting skid that provided 4 stages of continuous washing. The processes were operated continuously for 2 h with overall mAb yield of 92 ± 3% and DNA removal of nearly 3 logs in the 4‐stage system. The high DNA clearance was achieved by selective redissolution of the mAb using a low pH acetate buffer. Host cell protein clearance was 0.59 ± 0.08 logs, comparable to that based on model predictions. The process mass intensity was slightly better than typical Protein A processes and could be significantly improved by preconcentration of the antibody feed material.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Metal-Alkyls on Early-Stage Ethylene Polymerization over a Cr/SiO 2 Phillips Catalyst: A Bulk Characterization and X-ray Chemical Imaging Study

The Cr/SiO 2 Phillips catalyst has taken a central role in ethylene polymerization since its invention in 1953. The uniqueness of this catalyst is related to its ability to produce broad molecular weight distribution (MWD) PE materials as well as that no co-catalysts are required to attain activity. Nonetheless, co-catalysts in the form of metal-alkyls can be added for scavenging poisons, enhancing catalyst activity, reducing the induction period, and tailoring polymer characteristics. The activation mechanism and related polymerization mechanism remain elusive, despite extensive industrial and academic research. Here, we show that by varying the type and amount of metal-alkyl co-catalyst, we can tailor polymer properties around a single Cr/SiO 2 Phillips catalyst formulation. Furthermore, we show that these different polymer properties exist in the early stages of polymerization. We have used conventional polymer characterization techniques, such as size exclusion chromatography (SEC) and 13 C NMR, for studying the metal-alkyl co-catalyst effect on short-chain branching (SCB), long-chain branching (LCB) and molecular weight distribution (MWD) at the bulk scale. In addition, scanning transmission X-ray microscopy (STXM) was used as a synchrotron technique to study the PE formation in the early stages: allowing us to investigate the produced type of early-stage PE within one particle cross-section with high energy resolution and nanometer scale spatial resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors

Aims/hypothesis Progression to type 1 diabetes is associated with genetic factors, the presence of autoantibodies and a decline in beta cell insulin secretion in response to glucose. Very little is known regarding the molecular changes that occur in human insulin-secreting beta cells prior to the onset of type 1 diabetes. Herein, we applied an unbiased proteomics approach to identify changes in proteins and potential mechanisms of islet dysfunction in islet-autoantibody-positive organ donors with pre-symptomatic stage 1 type 1 diabetes (HbA1c ≤42 mmol/mol [6.0%]). We aimed to identify pathways in islets that are indicative of beta cell dysfunction. Methods Multiple islet sections were collected through laser microdissection of frozen pancreatic tissues from organ donors positive for single or multiple islet autoantibodies (AAb + , n=5), and age (±2 years)- and sex-matched non-diabetic (ND) control donors (n=5) obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD). Islet sections were subjected to MS-based proteomics and analysed with label-free quantification followed by pathway and functional annotations. Results Analyses resulted in ~4500 proteins identified with low false discovery rate (<1%), with 2165 proteins reliably quantified in every islet sample. We observed large inter-donor variations that presented a challenge for statistical analysis of proteome changes between donor groups. We therefore focused on only the donors with stage 1 type 1 diabetes who were positive for multiple autoantibodies (mAAb + , n=3) and genetic risk compared with their matched ND controls (n=3) for the final statistical analysis. Approximately 10% of the proteins (n=202) were significantly different (unadjusted p<0.025, q<0.15) for mAAb + vs ND donor islets. The significant alterations clustered around major functions for upregulation in the immune response and glycolysis, and downregulation in endoplasmic reticulum (ER) stress response as well as protein translation and synthesis. The observed proteome changes were further supported by several independent published datasets, including a proteomics dataset from in vitro proinflammatory cytokine-treated human islets and single-cell RNA-seq datasets from AAb + individuals. Conclusions/interpretation In situ human islet proteome alterations in stage 1 type 1 diabetes centred around several major functional categories, including an expected increase in immune response genes (elevated antigen presentation/HLA), with decreases in protein synthesis and ER stress response, as well as compensatory metabolic response. The dataset serves as a proteomics resource for future studies on beta cell changes during type 1 diabetes progression and pathogenesis. Data availability The LC-MS raw datasets that support the findings of this study have been deposited in the online repository: MassIVE (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with accession no. MSV000090212.

Autoantibody-positive↗

Stage-local partitioned two-step runge-kutta methods for large systems of ordinary differential equations

We introduce stage-local partitioned two-step Runge-Kutta methods are an extension of standard two-step Runge-Kutta methods, which are an alternative to the standard additive two-step Runge-Kutta methods currently existing in the literature. Furthermore, these new schemes are designed with an eye towards truly N-partitioned systems and leverage local stage approximations to make several computationally interesting approximations viable. Specifically, the focus on local stage approximations makes possible the construction of truly asynchronous schemes, in the parallel sense, possible. In addition, we show that an implicit-explicit approach to these schemes can lead to methods that require the inversion of only local nonlinear systems.

Applied Dynamical Systems↗

Reliability-informed end-of-use decision making for product sustainability using two-stage stochastic optimization

The concept of circular economy has been diffused in recent decades to promote economic growth that does not add to the burden on natural resource extraction. Re-X options (e.g., reuse, repair, refurbish, remanufacture, recycle) have been gradually adopted in the product development process and optimized to reduce or eliminate waste and pollution. Although manufacturing incorporating Re-X options can be more environmentally friendly, it involves more sources of uncertainty than traditional manufacturing since the end-of-use products can be collected from multiple origins with various quantities and qualities, and the market demand for both new and remanufactured products cannot be forecasted perfectly. Thus, there is a need to optimize the Re-X policy to alleviate the negative impacts of the higher uncertainty. One option is using the reliability information of new products to estimate the end-of-use conditions and applying multi-stage stochastic optimization to capture multiple demand scenarios. This paper develops a two-stage stochastic optimization model to optimize the quality thresholds for reuse, recycling, and remanufacturing options. Our objective is to minimize the total cost, energy consumption, and environmental impact of producing and providing warranty service for a product family. The model employs reliability information of product components to estimate the warranty service cost and the end-of-use conditions of the returned resources. A case study on a general product family is implemented to illustrate the efficacy of the optimization model. Finally, results show that the two-stage optimization can achieve cost and environmental impact reduction for a hybrid manufacturing and remanufacturing process.

97 MATHEMATICS AND COMPUTING↗

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

Anaerobic gut fungi of the phylum Neocallimastigomycota are microbes proficient in valorizing low-cost but difficult-to-breakdown lignocellulosic plant biomass. Characterization of different fungal life stages and how they contribute to biomass breakdown are critical for biotechnological applications, yet we lack foundational knowledge about the transcriptional, metabolic, and enzyme secretion behavior of different life stages of anaerobic gut fungi: zoospores, germlings, immature thalli, and mature zoosporangia. A Miracloth-based technique was developed to enrich cell pellets with zoospores - the free-swimming, flagellated, young life stage of anaerobic gut fungi. By contrast, fungal mats contained relatively more vegetative, encysted, mature sporangia that form films. Global gene expression profiles were compared from two sample types (zoospore-enriched cell pellets vs. mature mats) harvested from the anaerobic gut fungal strain Neocallimastix californiae G1. Despite cultures being grown on glucose, the fungal zoospore-enriched samples were transcriptionally primed to encounter plant matter substrate, as evidenced by upregulation of catabolic carbohydrate-active enzymes and putative carbohydrate transporters. Furthermore, we report significant differential gene expression for gene annotation groups, including putative secondary metabolites and transcription factors. Understanding global gene expression differences between the fungal zoospore-enriched cells and mature fungi aid in characterizing fungal development, unmasking gene function, and guiding cultivation conditions and engineering targets to promote enzyme secretion.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling information flow in a computer processor with a multi-stage queuing model

In this paper, we introduce a nonlinear stochastic model to describe the propagation of information inside a computer processor. In this model, a computational task is divided into stages, and information can flow from one stage to another. The model is formulated as a spatially-extended, continuous-time Markov chain where space represents different stages. This model is equivalent to a spatially-extended version of the M/M/s queue. The main modeling feature is the throttling function which describes the processor slowdown when the amount of information falls below a certain threshold. We derive the stationary distribution for this stochastic model and develop a closure for a deterministic ODE system that approximates the evolution of the mean and variance of the stochastic model. In conclusion, we demonstrate the validity of the closure with numerical simulations.

97 MATHEMATICS AND COMPUTING↗

A theoretical study of the upper bound of surface elevation variance in the Phillips initial stage during wind-wave generation

The resonance mechanism in the initial of wind-wave generation proposed by Phillips is a foundation of wind-wave generation theory, but a precise theoretical quantification of wave energy growth in this initial stage has not been obtained yet after more than six decades of research. In this study, we aim to address this knowledge gap by developing an analytical approach based on a novel complex analysis method to theoretically investigate the temporal evolution of the wave energy in the Phillips initial stage. We quantitatively derive and analyse the growth behaviour of the surface wave energy and obtain an analytical solution for its upper bound. Our result highlights the crucial effects of surface tension. Because the phase velocity of gravity–capillary waves has a minimal value at a critical wavenumber, gravity–capillary waves and gravity waves (which neglect surface tension) exhibit distinct resonance curve properties and wave energy growth behaviours. For gravity waves, the resonance curve extends indefinitely; for gravity–capillary waves, it either forms a finite-length curve or does not exist, depending on the wind speed. The leading-order term of the upper-bound solution of the energy of gravity waves increases linearly over time, while for gravity–capillary waves, the term increases linearly over time under strong wind conditions but remains finite under weak wind conditions. This theoretical study provides an analytical framework for the generation of wind-waves in the Phillips initial stage, which may inspire further theoretical, numerical and experimental research.

58 GEOSCIENCES↗

Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes

Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. Here, in this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of dual-layer solid-electrolyte interphase inhomogeneities on early-stage defect formation in Si electrodes

While intensive efforts have been devoted to studying the nature of the solid-electrolyte interphase (SEI), little attention has been paid to understanding its role in the mechanical failures of electrodes. Here we unveil the impact of SEI inhomogeneities on early-stage defect formation in Si electrodes. Buried under the SEI, these early-stage defects are inaccessible by most surface-probing techniques. With operando full field diffraction X-ray microscopy, we observe the formation of these defects in real time and connect their origin to a heterogeneous degree of lithiation. This heterogeneous lithiation is further correlated to inhomogeneities in topography and lithium-ion mobility in both the inner- and outer-SEI, thanks to a combination of operando atomic force microscopy, electrochemical strain microscopy and sputter-etched X-ray photoelectron spectroscopy. Our multi-modal study bridges observations across the multi-level interfaces (Si/LixSi/inner-SEI/outer-SEI), thus offering novel insights into the impact of SEI homogeneities on the structural stability of Si-based lithium-ion batteries. Severe structural deformation during (de)lithiation is the main factor limiting the stability of Si anodes in Li-ion batteries. Here, a multi-modal approach is used to visualize these deformations in their early-stage and link them to inhomogeneities in the dual-layer solid-electrolyte interphase.

25 ENERGY STORAGE↗

Comparative transcriptome analysis of cells from different areas reveals ROS responsive mechanism at sclerotial initiation stage in Morchella importuna

Morels are some of the most highly prized edible and medicinal mushrooms, with great economic and scientific value. Outdoor cultivation has been achieved and expanded on a large scale in China in recent years. Sclerotial formation is one of the most important phases during the morel life cycle, and previous reports indicated that reactive oxygen species (ROS) play an important role. However, ROS response mechanisms at sclerotial initiation (SI) stage are poorly understood. In this study, comparative transcriptome analyses were performed with sclerotial and hyphal cells at different areas in the same plate at SI stage. Gene expression was significantly different at SI stage between sclerotial formation and mycelia growth areas. GO and KEGG analyses indicated more vigorous metabolic characteristics in the hyphae area, while transcription process, DNA repair, and protein processing were enriched in sclerotial cells. Gene expression related to H 2 O 2 production was high in the hyphae area, while expression of H 2 O 2 -scavenging genes was high in sclerotial cells, leading to a higher H 2 O 2 concentration in the hyphal region than in the sclerotium. Minor differences were observed in gene expression of H 2 O 2 -induced signaling pathway in sclerotial and hyphal cells; however, expression levels of the target genes of transcription factor MSN2, important in the H 2 O 2 -induced signaling pathways, were significantly different. MSN2 enhanced stress response regulation in sclerotia by regulating these target genes. Small molecular HSPs were also found upregulated in sclerotial cells. This study indicated that sclerotial cells are more resistant to ROS stress than hyphal cells through transcriptional regulation of related genes.

59 BASIC BIOLOGICAL SCIENCES↗

A two-stage service restoration method for electric power distribution systems

Improving the reliability of power distribution systems is critically important for both utilities and customers. This calls for an efficient service restoration module within a distribution management system to support the implementation of self-healing smart grid networks. Although the emerging smart grid technologies, including distributed generators (DGs) and remote-controlled switches, enhance the self-healing capability and allow faster recovery, they still pose additional complexity to the service restoration problem, especially under cold load pickup (CLPU) conditions. Herein, a novel two-stage restoration framework is proposed to generate a restoration solutions with a sequence of control actions. The first stage generates a restoration plan that supports both the traditional service restoration using feeder reconfiguration and the grid-forming DG-assisted intentional islanding methods. The second stage generates an optimal sequence of switching operations to bring the outaged system quickly to the final restored configuration. The problem is formulated as a mixed-integer linear program that incorporates system connectivity, operating constraints, and the CLPU models. It is demonstrated that on using a multi-feeder test case, the proposed framework is effective in utilizing all available resources to quickly restore the service and generate an optimal sequence of switching actions to be used by the operator to reach the desired optimal configuration.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Emittance preservation for the electron arm in a single PWFA-LC stage using quasi-adiabatic plasma density ramp matching sections

Plasma-based acceleration (PBA) is being considered for a next generation linear collider (LC). In some PBA-LC designs for the electron arm, the extreme beam parameters are expected to trigger background ion motion within the witness beam, which can lead to longitudinally varying nonlinear focusing forces and result in an unacceptable emittance growth of the beam. To mitigate this, we propose to use quasi-adiabatic plasma density ramps as matching sections at the entrance and exit of each stage. We match the witness electron beam to the low density plasma entrance, where the beam initially has a large matched spot size so the ion motion effects are relatively small. As the beam propagates in the plasma density upramp, it is quasi-adiabatically focused, and its distribution maintains a non-Gaussian equilibrium distribution in each longitudinal slice throughout the process, even when severe ion collapse has occurred. This only causes small amounts of slice emittance growth. The phase mixing between slices with different betatron frequencies leads to additional projected emittance growth within the acceleration stage. A density downramp at the exit of an acceleration section can eliminate much of the slice and projected emittance growth as the beam and ion motion adiabatically defocuses and decreases, respectively. Simulation results from QuickPIC with Azimuthal Decomposition show that within a single acceleration stage with a 25 GeV energy gain, this concept can limit the projected emittance growth to only ∼2% for a 25 GeV, 100 nm emittance witness beam and ∼20% for a 100 GeV, 100 nm normalized emittance witness beam. The trade-off between the adiabaticity of the plasma density ramp and the initial ion motion at the entrance for a given length of the plasma density ramp is also discussed.

Physics↗

Staged Z-pinch experiment at the double-EAGLE pulsed power facility

The staged Z-pinch is a potential high-energy gain fusion concept where a high atomic number liner implodes on a deuterium target using a pulsed multi-MA current source. Over the past several years this concept has been studied on 0.5–1.0 MA facilities using Ar and Kr gas puffs injected at R = 1.2 cm. Neutron yield up to (2.5 ± 0.34) x 10 10 was measured, Ruskov et al (2023 IEEE Trans. Plasma Sci. 51 3310–6). Here, in this study, we present experimental results from the 4 MA, 110 ns current rise time Double-EAGLE facility at L3Harris (currently, Fisica Inc.) where a larger radius nozzle created gas density profiles peaked at R = 2.5 cm. Modeling with the MACH2 and FLASH codes indicates that the larger radius allows stronger acceleration of the liner plasma and generation of shock waves that preheat a target plasma layer next to the liner to temperatures $T_i >$1 keV. The resulting counter thermal pressure on the liner plasma limits the growth of the Magneto-Rayleigh–Taylor (MRT) instability at the liner-vacuum boundary and the implosion proceeds in a relatively stable manner. Near bang time the enormous target plasma thermal pressure smoothens the MRT perturbations developed during the earlier implosion stages. Time integrated x-ray pinhole images with cutoff energy of 100 eV confirm that a long (∼3 cm), stable and uniform high energy density plasma column is formed in the final implosion stage. Consistent neutron yield in the 10 10 –10 11 range was measured for both Ar and Kr liners imploding on a deuterium target.

Physics - Plasma physics↗