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At least 73 records · Page 4

A Simplified Approach Based on Cellular Automata for Describing Direct Reduced Iron Production in Different Reducing Conditions

A quick computation approach based on cellular automata is developed and implemented to describe the reduction of iron ore pellets by a mixture of reducing agents featured by different H 2 /CO ratios. The evolution of oxygen concentration inside the pellet is followed from the beginning to the end of contact between reducing agent and pellet. The variation of thermal state of pellets and gas mixture is computed based on their initial temperature, considering the heat involved and the convective heat exchange between pellet and gas mixture. The use of cellular automata and finite‐difference method to solve the diffusion equation point out the absence of any diffusion coefficient value, allowing to make the model fit the experimental trial, because the problem is that it is not ruled just by diffusion but also by the concentration variation of reducing agent inside the pellet due to porosity increasing during reduction. The updating of the reducing agents concentration implies a sharp decrease of oxygen concentration that the cellular automata model considers. The developed model is able to provide the in‐line control of reduction process and could be used to adjust the chemical concentration and temperature of injected reducing agents.

Metallurgy & Metallurgical Engineering↗

Engineering microbial consortia with rationally designed cellular interactions

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. Here, we then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

42 ENGINEERING↗

The regulation of animal behavior by cellular stress responses

Cellular stress responses exist to detect the effects of stress on cells, and to activate protective mechanisms that promote resilience. As well as acting at the cellular level, stress response pathways can also regulate whole organism responses to stress. One way in which animals facilitate their survival in stressful environments is through behavioral adaptation; this review considers the evidence that activation of cellular stress responses plays an important role in mediating the changes to behavior that promote organismal survival upon stress.

60 APPLIED LIFE SCIENCES↗

Simulating Mixed‐Phase Open Cellular Clouds Observed During COMBLE: Evaluation of Parameterized Turbulence Closure

Marine cold-air outbreaks, or CAOs, are airmass transformations whereby relatively cold boundary layer (BL) air is transported over relatively warm water. To more deeply understand BL and mixed-phase cloud properties during CAO conditions, the Cold-Air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) took place from late 2019 into early 2020. During COMBLE, the U.S. Department of Energy's first Atmospheric Radiation Measurement Mobile Facility (AMF1) was deployed to Andenes, Norway, far downstream (~1,000 km) from the Arctic pack ice. This study examines the two most intense CAOs sampled at the AMF1 site. The observed BL structures are open cellular with high (~3–5 km) and cold (–30 to –50 °C) cloud tops, and they often have pockets of high liquid water paths (LWPs; up to ~1,000 g m –2 ) associated with strong updrafts and enhanced turbulence. We use a high-resolution mesoscale model to explore how well four turbulence closure methods represent open cellular clouds. After applying a radar simulator to model outputs for direct evaluation, cloud top properties agree well with AMF1 observations (within ~10%), but radar reflectivity and LWP agreement is more variable. Results suggest that the turbulent Prandtl number may play an important role for the simulated BL and cloud properties. All simulations produce enhanced precipitation rates that are well-correlated with a cloud transition. Finally, the eddy-diffusivity/mass-flux approach produces the deepest cloud layer and therefore the largest and most coherent cellular structures. Furthermore, we recommend the use of a non-local turbulence closure approach to better capture turbulent processes in intense CAOs.

54 ENVIRONMENTAL SCIENCES↗

Phosphatidic acid: an emerging versatile class of cellular mediators

Abstract Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Biochemistry & Molecular Biology↗

The Role of Unit-Cell Topology in Modulating the Compaction Response of Additively Manufactured Cellular Materials using Simulations and Validation Experiments

Additive manufacturing has enabled a transformational ability to create cellular structures (or foams) with tailored topology. Compared to their monolithic polymer counterparts, cellular structures are potentially suitable for systems requiring materials with high specific energy-absorbing capability to provide enhanced damping. In this work, we demonstrate the utility of controlling unit-cell topology with the intent of obtaining a desired stress–strain response and energy density. Using mesoscale simulations that resolve the unit-cell sub-structures, we validate the role of unit-cell topology in selectively activating a buckling mode and thereby modulating the characteristic stress–strain response. Simulations incorporate a linear viscoelastic constitutive model and a hyperelastic model for simulating large deformation of the polymer under both tension and compression. Simulated results for nine different cellular structures are compared with experimental data to gain insights into three different modes of buckling and the corresponding stress–strain response.

36 MATERIALS SCIENCE↗

Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast

Soft X-ray tomography (SXT) is an invaluable tool for quantitatively analyzing cellular structures at suboptical isotropic resolution. However, it has traditionally depended on manual segmentation, limiting its scalability for large datasets. Here, we leverage a deep learning-based autosegmentation pipeline to segment and label cellular structures in hundreds of cells across three Saccharomyces cerevisiae strains. This task-based pipeline uses manual iterative refinement to improve segmentation accuracy for key structures, including the cell body, nucleus, vacuole, and lipid droplets, enabling high-throughput and precise phenotypic analysis. Using this approach, we quantitatively compared the three-dimensional (3D) whole-cell morphometric characteristics of wild-type, VPH1-GFP, and vac14 strains, uncovering detailed strain-specific cell and organelle size and shape variations. We show the utility of SXT data for precise 3D curvature analysis of entire organelles and cells and detection of fine morphological features using surface meshes. Our approach facilitates comparative analyses with high spatial precision and statistical throughput, uncovering subtle morphological features at the single-cell and population level. This workflow significantly enhances our ability to characterize cell anatomy and supports scalable studies on the mesoscale, with applications in investigating cellular architecture, organelle biology, and genetic research across diverse biological contexts.

Chen, Jianhua [Lawrence Berkeley National Laborato↗

Base Station Antenna Uptilt Optimization for Cellular-Connected Drone Corridors

Reliable wireless coverage in drone corridors is critical to enable a connected, safe, and secure airspace. To support beyond visual line of sight (BVLOS) operations of aerial vehicles in a drone corridor, cellular base stations (BSs) can serve as a convenient infrastructure as they are widely deployed to provide seamless wireless coverage. However, antennas in the existing cellular networks are down-tilted to optimally serve their ground users, which results in coverage holes at higher altitudes when they are used to serve drones. In this paper, we consider the use of additional uptilted antennas at each cellular BS and optimize the uptilt angle to maximize the wireless coverage probability across a given drone corridor. Through numerical results, we can characterize the optimal value of the antenna uptilt angle for a given antenna pattern as well as the minimum/maximum altitudes of the drone corridor.

42 ENGINEERING↗

Extensive cellular multi-tasking within Bacillus subtilis biofilms

Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells “multi-task,” simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive Optical Two-Photon Fluorescence Microscopy Probes Cellular Organization of Ocular Lenses In Vivo

The mammalian ocular lens is an avascular multicellular organ that grows continuously throughout life. Traditionally, its cellular organization is investigated using dissected lenses, which eliminates in vivo environmental and structural support. Therefore, in vivo optical imaging methods for studying lenses in their native context in live animals are urgently needed. Here, we demonstrated that two-photon fluorescence microscopy can visualize lens cells in vivo. To maintain subcellular resolution at depth, we used adaptive optics to correct aberrations owing to ocular and lens tissues, which led to substantial signal and resolution improvements. Imaging lens cells up to 980 µm deep, we observed novel cellular organizations including suture-associated voids, enlarged vacuoles, and large cavities, contrary to the conventional view of a highly ordered organization. We tracked these features longitudinally over weeks and observed the incorporation of new cells during growth. Taken together, noninvasive longitudinal in vivo imaging of lens morphology using adaptive optics two-photon fluorescence microscopy will allow us to observe the development or alterations of lens cellular organization in living animals directly.

60 APPLIED LIFE SCIENCES↗

Study of impacts of two types of cellular aging on the yeast bud morphogenesis

Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed and used to suggest and test hypothesized impacts of aging on bud morphogenesis. Experimentally calibrated model simulations showed that during the early stage of budding, tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip, a process guided by the polarized Cdc42 signal. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage as observed in experiments in this work. The model simulation results suggest that the localization of new cell surface material insertion, regulated by chemical signal polarization, could be weakened due to cellular aging in yeast and other cell types, leading to the change and stabilization of the bud aspect ratio.

Tsai, Kevin↗

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.

97 MATHEMATICS AND COMPUTING↗

Where Have All of the Electrons Gone? Understanding the Role of Alternative Electron Flow and O 2 Reduction in Balancing Cellular Redox (Final Technical Report)

An informed understanding of the fundamentals of light-driven electron transfer reactions in photoautotrophic organisms is necessary to enable improved photosynthetic efficiencies for the production of renewable fuels and novel biomaterials. To obtain high photosynthetic yields, light energy must be efficiently coupled to the fixation of CO 2 . Sub-optimal environmental conditions and metabolic routing (caused by blocks in biosynthetic routes) can severely impact the conversion of light energy to biomass and lead to reactive oxygen production, which in turn can cause cellular damage and productivity losses. Hence, plants, algae, and photosynthetic bacteria have evolved a network of alternative outlets to sustain the flow of photosynthetically derived-electrons. Our research was focused on the nature and integration of these outlets. The data obtained in this project will inform efforts to rationally engineer crop plants and algae to improve photosynthetic yields by enhancing electron transfer reactions to CO 2 reduction and targeted biomass accumulation. A major project research thrust was focused on identifying and quantifying the flow of photosynthetic reductant through electron transfer circuits that result in the light-dependent reduction of O 2 . New energy management strategies were identified that are used when normal carbon assimilation pathways are compromised due to nutrient deprivation, and/or by a reduction in starch synthesis/carbon storage, all conditions resulting in highly reduced intracellular redox pools. The green alga Chlamydomonas reinhardtii, and likely many other algae, have multiple O 2 -reducing pathways that play critical roles in maintaining cellular metabolic balance and scavenging electrons that could potentially cause cellular damage, which in some instances leads to reduced photosynthetic yields but increased fitness. We explored the activities of three essential outlets associated with Chlamydomonas reinhardtii photosynthetic electron transport: (1) reduction of O 2 to H 2 O through Flavodiiron proteins (FLVs) and (2) Plastid Terminal Oxidases (PTOX), and (3) the synthesis of starch. Real-time measurements of O 2 exchange demonstrated that FLVs immediately engage during dark to light transitions, allowing electron transport when the CBBC is not fully activated. Under these conditions, we quantified, for the first time, maximal FLV activity and its overall capacity to direct photosynthetic electrons towards O 2 reduction. However, when starch synthesis is compromised, a greater proportion of electrons is directed toward O 2 reduction through the FLVs, while PTOX, which is sensitive to the PQ pool redox state, is activated. This suggests, that starch synthesis has an important role in priming/regulating CBBC and electron transport. We also identified a biological ‘switch’ in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b 6 f complex when reductant and ATP generated by PET are in excess of the capacity of carbon metabolism to utilize these products; we specifically show a restriction at this switch when sta6 mutant cells, which cannot synthesize starch, are limited for nitrogen (growth inhibition) and subjected to a dark to light transition. This restriction causes diminished electron flow to PSI, which prevents PSI photodamage, and the plastid alternative oxidase (PTOX) becomes fully activated, serving as an electron valve that dissipates excitation energy absorbed by PSII, thereby lessening PSII photoinhibition. Furthermore, illumination of the cells following the dark acclimation gradually diminishes the restriction at the switch. Future engineering of these switches may allow more effective electron transfer to lipid (biofuel) pathways and diminish the number of electrons “wasted” in the reduction of O 2 to water. Lastly, we explored metabolic routing of electrons during algal fermentation and discovered multiple novel pathways that are activated when the preferred anoxic routes are blocked. These provide valuable products (e.g. lactate, glycerol) that can be used in broad portfolio of biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of Interior Cellular Shades in a Residential Building

Windows are major contributors to energy demand in residential homes because of their inferior thermal resistance compared with the opaque envelope and sometimes from unwanted solar heat gain. Window attachments can help to mitigate this demand by controlling the solar heat gains and enhancing the thermal resistance of the windows. In this study, the energy savings potential of cellular shades in residential homes is studied using experimental testing and energy simulations. The energy performance of the shading devices was experimentally tested during the heating season from December 2019 to May 2020 with a focus on cellular shades. Five shading devices—three single and two double cellular/cell-in-cell shades—were used to compare the performance with generic horizontal (venetian) blinds using two nearly identical sideby-side rooms in a residential building with their exterior window facing east. Another objective of the experimental testing was to evaluate any impact of the side-channel of the shading device on energy savings. To observe the impact of the side-channels on energy savings, from shades in two of the test cases, cellular shades with side-channels were used. From the experimental testing, daily energy savings in the range of 9% to 23% were observed by considering data from 6 p.m. until 6 a.m. of the next day.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

The role of unit cell topology in modulating the compaction response of additively manufactured cellular materials using simulations and validation experiments

Additive manufacturing has enabled a transformational ability to create cellular structures (or foams) with tailored topology. Compared to their monolithic polymer counterparts, cellular structures are potentially suitable for systems requiring materials with high specific energy-absorbing capability to provide enhanced damping. In this work, we demonstrate the utility of controlling unit-cell topology with the intent of obtaining a desired stress–strain response and energy density. Using mesoscale simulations that resolve the unit-cell sub-structures, we validate the role of unit-cell topology in selectively activating a buckling mode and thereby modulating the characteristic stress–strain response. Simulations incorporate a linear viscoelastic constitutive model and a hyperelastic model for simulating large deformation of the polymer under both tension and compression. Simulated results for nine different cellular structures are compared with experimental data to gain insights into three different modes of buckling and the corresponding stress–strain response.

36 MATERIALS SCIENCE↗

Enabling The Next Generation of Smart Sensors in Coal Fired Power Plants using Cellular 5G Technology

Ohio University (OHIO), West Virginia University (WVU), and American Electric Power (AEP) proposed to study and report on the benefits of 5G wireless cellular technologies for coal-fired power plants. The significant advantages, cost savings, and potential of 5G wireless data communications based sensors promised to usher in a new era of reliable, inexpensive, and powerful embedded systems that had not previously been available for coal-fired power plants. The team built upon existing experience with cellular-based systems, power plant water quality sensing, and high temperature sensors developed during past projects. Principal Investigator Wilhelm had been developing cellular-based sensor data systems with a commercial partner for 10 years, pioneering innovative solar-powered devices that began with 2G technology. The lessons and knowledge gained served as a foundation to demonstrate innovations and potential impacts specific to coal fired power plants enabled by 5G technology, along with integration with existing sensors and systems.

20 FOSSIL-FUELED POWER PLANTS↗

Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life

Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.

59 BASIC BIOLOGICAL SCIENCES↗

Contrasting characteristics of open- and closed-cellular stratocumulus cloud in the eastern North Atlantic

Abstract. Extensive regions of marine boundary layer cloud impact the radiative balance through their significant shortwave albedo while having little impact on outgoing longwave radiation. Despite this importance, these cloud systems remain poorly represented in large-scale models due to difficulty in representing the processes that drive their life cycle and coverage. In particular, the mesoscale organization and cellular structure of marine boundary clouds have important implications for the subsequent cloud feedbacks. In this study, we use long-term (2013–2018) observations from the Atmospheric Radiation Measurement (ARM) Facility's Eastern North Atlantic (ENA) site on Graciosa Island, Azores, Portugal, to identify cloud cases with open- or closed-cellular organization. More than 500 h of each organization type are identified. The ARM observations are combined with reanalysis and satellite products to quantify the cloud, precipitation, aerosol, thermodynamic, and large-scale synoptic characteristics associated with these cloud types. Our analysis shows that both cloud organization populations occur during similar sea surface temperature conditions, but the open-cell cases are distinguished by stronger cold-air advection and large-scale subsidence compared to the closed-cell cases, consistent with their formation during cold-air outbreaks. We also find that the open-cell cases were associated with deeper boundary layers, stronger low-level winds, and higher rain rates compared to their closed-cell counterparts. Finally, raindrops with diameters larger than 1 mm were routinely recorded at the surface during both populations, with a higher number of large drops during the open-cellular cases. The similarities and differences noted herein provide important insights into the environmental and cloud characteristics during varying marine boundary layer cloud mesoscale organization and will be useful for the evaluation of model simulations for ENA marine clouds.

54 ENVIRONMENTAL SCIENCES↗