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At least 811 records · Page 45

Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

Abstract Background and aims Hakea prostrata (Proteaceae) is a highly phosphorus-use-efficient plant native to southwest Australia. It maintains a high photosynthetic rate at low leaf phosphorus (P) and exhibits delayed leaf greening, a convergent adaptation that increases nutrient-use efficiency. This study aimed to provide broad physiological and gene expression profiles across leaf development, uncovering pathways leading from young leaves as nutrient sinks to mature leaves as low-nutrient, energy-transducing sources. Methods To explore gene expression underlying delayed greening, we analysed a de novo transcriptome for H. prostrata across five stages of leaf development. Photosynthesis and respiration rates, and foliar pigment, P and nitrogen (N) concentrations were determined, including the division of P into five biochemical fractions. Key results Transcripts encoding functions associated with leaf structure generally decreased in abundance across leaf development, concomitant with decreases in foliar concentrations of 85% for anthocyanins, 90% for P and 70% for N. The expression of genes associated with photosynthetic function increased during or after leaf expansion, in parallel with increases in photosynthetic pigments and activity, much later in leaf development than in species that do not have delayed greening. As leaves developed, transcript abundance for cytosolic and mitochondrial ribosomal proteins generally declined, whilst transcripts for chloroplast ribosomal proteins increased. Conclusions There was a much longer temporal separation of leaf cell growth from chloroplast development in H. prostrata than is found in species that lack delayed greening. Transcriptome-guided analysis of leaf development in H. prostrata provided insight into delayed greening as a nutrient-saving strategy in severely phosphorus-impoverished landscapes.

59 BASIC BIOLOGICAL SCIENCES↗

The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae

Abstract Cyanidioschyzon merolae is an extremophilic red microalga which grows in low-pH, high-temperature environments. The basis of C. merolae ’s environmental resilience is not fully characterized, including whether this alga uses a carbon-concentrating mechanism (CCM). To determine if C. merolae uses a CCM, we measured CO 2 uptake parameters using an open-path infra-red gas analyzer and compared them to values expected in the absence of a CCM. These measurements and analysis indicated that C. merolae had the gas-exchange characteristics of a CCM-operating organism: low CO 2 compensation point, high affinity for external CO 2 , and minimized rubisco oxygenation. The biomass δ 13 C of C. merolae was also consistent with a CCM. The apparent presence of a CCM in C. merolae suggests the use of an unusual mechanism for carbon concentration, as C. merolae is thought to lack a pyrenoid and gas-exchange measurements indicated that C. merolae primarily takes up inorganic carbon as carbon dioxide, rather than bicarbonate. We use homology to known CCM components to propose a model of a pH-gradient-based CCM, and we discuss how this CCM can be further investigated.

60 APPLIED LIFE SCIENCES↗

Macroscale structural changes of thylakoid architecture during high light acclimation in Chlamydomonas reinhardtii

Abstract Photoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure during acclimation to growth in HL has not been fully understood. Here, we combined live-cell super-resolution microscopy and analytical membrane subfractionation to investigate macroscale structural changes of thylakoid membranes during HL acclimation in Chlamydomonas . Subdiffraction-resolution live-cell imaging revealed that the overall thylakoid structures became thinned and shrunken during HL acclimation. The stromal space around the pyrenoid also became enlarged. Analytical density-dependent membrane fractionation indicated that the structural changes were partly a consequence of membrane unstacking. The analysis of both an LHCSR loss-of-function mutant , npq4 lhcsr1 , and a regulatory mutant that over-expresses LHCSR, spa1-1 , showed that structural changes occurred independently of LHCSR protein levels, demonstrating that LHCSR was neither necessary nor sufficient to induce the thylakoid structural changes associated with HL acclimation. In contrast, stt7-9 , a mutant lacking a kinase of major light-harvesting antenna proteins, had a slower thylakoid structural response to HL relative to all other lines tested but still showed membrane unstacking. These results indicate that neither LHCSR- nor antenna-phosphorylation-dependent HL acclimation are required for the observed macroscale structural changes of thylakoid membranes in HL conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and characterization of the low molecular mass ferredoxins involved in central metabolism in Heliomicrobium modesticaldum

The homodimeric Type I reaction center (RC) from Heliomicrobium modesticaldum lacks the PsaC subunit found in Photosystem I and instead uses the interpolypeptide [4Fe–4S] cluster F X as the terminal electron acceptor. Our goal was to identify which of the small mobile dicluster ferredoxins encoded by the H. modesticaldum genome are capable of accepting electrons from the heliobacterial RC (HbRC) and pyruvate:ferredoxin oxidoreductase (PFOR), a key metabolic enzyme. Analysis of the genome revealed seven candidates: HM1_1462 (PshB1), HM1_1461 (PshB2), HM1_2505 (Fdx3), HM1_0869 (FdxB), HM1_1043, HM1_0357, and HM1_2767. Heterologous expression in Escherichia coli and studies using time-resolved optical spectroscopy revealed that only PshB1, PshB2, and Fdx3 are capable of accepting electrons from the HbRC and PFOR. Modeling studies using AlphaFold show that only PshB1, PshB2, and Fdx3 should be capable of docking on PFOR at a positively charged patch that overlays a surface-proximal [4Fe–4S] cluster. Proteomic analysis of wild-type and gene deletion strains ΔpshB1, ΔpshB2, ΔpshB1pshB2, and Δfdx3 grown under nitrogen-replete conditions revealed that Fdx3 is undetectable in the wild-type, ΔpshB1, and Δfdx3 strains, but it is present in the ΔpshB2 and ΔpshB1pshB2 strains, implying that Fdx3 may substitute for PshB2. When grown under nitrogen-deplete conditions, Fdx3 is present in the wild-type and all deletion strains except for Δfdx3. None of the knockout strains demonstrated significant impairment during chemotrophic dark growth on pyruvate, photoheterotrophic light growth on pyruvate, or phototrophic growth on acetate+CO 2 , indicating a high degree of redundancy among these three electron transfer proteins. As a result, loss of both PshB1 and PshB2, but not FdxB, resulted in poor growth under N 2 -fixing conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning models for segmentation and classification of cyanobacterial cells

Abstract Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells. Here, we describe a newly developed software package called Cypose which uses machine learning (ML) models to solve two specific tasks: segmentation of individual cyanobacterial cells, and classification of cellular phenotypes. The segmentation models are based on the Cellpose framework, while classification is performed using a convolutional neural network named Cyclass. To our knowledge, these are the first developed ML-based models for cyanobacteria segmentation and classification. When compared to other methods, our segmentation models showed improved performance and were able to segment cells with varied morphological phenotypes, as well as differentiate between live and lysed cells. We also found that our models were robust to imaging artifacts, such as dust and cell debris. Additionally, the classification model was able to identify different cellular phenotypes using only images as input. Together, these models improve cell segmentation accuracy and enable high-throughput analysis of dense cyanobacterial colonies and filamentous cyanobacteria.

Huffine, Clair A.↗

Enhancing scalability and accuracy of quantum poisson solver

The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far either suffer from lack of accuracy and/or are limited to very small sizes of the problem and thus have no practical usage. In this regard, our previous work showed a proof-of-concept demonstration in advancing quantum Poisson solver algorithm and validated preliminary results for a simple case of 3 x 3 problem. In this work, we delve into comprehensive research details, presenting the results on up to 15 x 15 problems that include step-by-step improvements in Poisson equation solutions, scaling performance, and experimental exploration. In particular, we demonstrate the implementation of eigenvalue amplification by a factor of up to 2 8 , achieving a significant improvement in the accuracy of our quantum Poisson solver and comparing that to the exact solution. Additionally, we present success probability results, highlighting the reliability of our quantum Poisson solver. Moreover, we explore the scaling performance of our algorithm against the circuit depth and width, demonstrating how our approach scales with larger problem sizes and thus further solidifies the practicality of easy adaptation of this algorithm in real-world applications. We also discuss a multilevel strategy for how this algorithm might be further improved to explore much larger problems with greater performance. Finally, through our experiments on the IBM quantum hardware, we conclude that though overall results on the existing NISQ hardware are dominated by the error in the CNOT gates, this work opens a path to realizing a multidimensional Poisson solver on near-term quantum hardware.

97 MATHEMATICS AND COMPUTING↗

Formal verification and validation of run-to-completion style state charts using Event-B

State chart notations with ‘run to completion’ semantics are popular with engineers for designing controllers that react to environment events with a sequence of state transitions but lack formal refinement and rigorous verification methods. State chart models are typically used to design complex control systems that respond to environmental triggers with a sequential process. The model is usually constructed at a concrete level and verified and validated using animation techniques relying on human judgement. Event-B, on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. Abstraction and formal verification provide greater assurance that critical (e.g. safety or security) properties are not violated by the control system. In this paper, we introduce a notion of refinement into a ‘run to completion’ state chart modelling notation and leverage Event-B’s tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Event-B refinements and suggest a solution. We illustrate our approach and show how models can be validated at different refinement levels using our scenario checker animation tools. We show how critical invariant properties can be verified by proof despite the reactive nature of the system and how behavioural aspects of the system can be verified by testing the expected reactions using a temporal logic, model checking approach. To verify liveness, we outline a proof that the run to completion is deadlock-free and converges to complete the run.

97 MATHEMATICS AND COMPUTING↗

Physics-Informed and Data-Driven Prediction of Residual Stress in Three-Dimensional Machining

Efficient and reliable prediction of machining-induced residual stress (RS) is a key requirement for truly integrated computational materials engineering (ICME). Currently available process modeling approaches, including empirical, analytical, and numerical methodologies lack predictive power and require substantial calibration and validation data. Moreover, most model-based approaches consider only two-dimensional (2D) (i.e., orthogonal), cutting processes. Meanwhile, industrial processes such as milling, turning, and drilling are inherently three-dimensional (3D). The present work attempts to bridge the gap between 2D and 3D through careful consideration of the process physics, including geometric, kinematic, and size-effect constraints to realize robust prediction of how RS develops in 3D machining. Using a novel in-situ experimental technique and digital image correlation (DIC) to determine equivalent Hertzian contact widths, contact pressures, and friction coefficients, the proposed methodology leverages a discretized conversion algorithm that includes multi-pass shakedown effects. This paper presents a semi-analytical model to predict machining-induced RS in 3D turning operations, which are used representatively for 3D processes more generally. Rather than follow a ‘brute force’ 3D FEM approach or conduct countless experiments to train a purely data-driven machine learning algorithm, the proposed approach builds on previous 2D modeling work. Through careful consideration of the process physics, including complex geometry/kinematic considerations of 3D turning, the authors demonstrated an experimentally calibrated approach, as well as validation based on published RS data. Model predictions and previously published measurement data of RS depth profiles for turning of Inconel 718 were compared for a range of process parameters. Correlation between the proposed 3D model and validation data was found to be within the margin of experimental error for most conditions. The proposed model appears to capture the overall behavior of 3D RS depth profiles with acceptable accuracy, particularly the key metrics of near-surface stress, peak stress magnitude and location, as well as overall stress profile depth. This report presents a physics-informed, data-driven approach for efficient calibration of a 2D model for machining-induced RS through DIC analysis of in-situ characterized subsurface displacement fields.

42 ENGINEERING↗

Design Solutes to Achieve Columnar-to-Equiaxed Transition and Grain Refinement in Cast Multi-principal-element Alloys

The multi-principal-element alloys (MPEAs), also referred to as high-entropy alloys (HEAs), have attracted extensive attention during the last decade and a half due to their unique and excellent properties. However, many MPEAs show coarse and anisotropic columnar grains in the as-cast state. While constitutional supercooling (CS)-driven parameters have been widely used to evaluate and predict the effect of solutes on columnar-to-equiaxed transition (CET) and grain refinement of diluted binary alloys, similar studies are lacking on MPEAs. Due to the multiple solute elements (solutes) and their high concentrations, the CS-driven parameters for MPEAs are different from those proposed for diluted binary alloys. Here, we derived the CS-driven parameters, including undercooling parameter and growth restriction factor, for MPEAs based on their physical significances, with the help of calculated phase diagrams. The calculated CS-driven parameters were then used to predict the effect of a solute on CET and grain refinement in NiCoFeCr MPEAs. Additional alloying solutes Nb, Ti, and V in the NiCoFeCr MPEA were also evaluated for their different CS-driven characteristics. In this study, the grain size of the as-solidified microstructures of NiCoFeCr with and without Nb, Ti, and V were compared and interpreted with the predicted tendency of the CS-driven parameters.

36 MATERIALS SCIENCE↗

Data Science Techniques, Assumptions, and Challenges in Alloy Clustering and Property Prediction

Data analytics methods have been increasingly applied to understanding materials chemistry, processing due to the manufacturing approach, and uni-axial and cyclic property relationships in the highly complex space of alloy design. There are several benefits to applying data analytics to this space, including the ability to manage non-linearities in the responses of the alloy attributes and the resulting mechanical properties. However, key difficulties in applying and understanding the results of data analytics include the often lack of reported assumptions and data processing steps necessary to improve interpretation and reproducibility in derived results. In this work, the methods used to generate clustering and correlation analyses for experimental 9% Cr ferritic-martensitic steel data were investigated and the resulting implications for mechanical property predictions were assessed. This work uses principal component analysis, partitioning around medoids, t-SNE, and k-means clustering to investigate trends in composition, processing and microstructure information with creep and tensile properties, building on work done previously using a smaller version of the same dataset. The initial assumptions, preprocessing steps and methods are investigated and outlined in order to depict the fine level of detail required to convey the steps taken to process data and produce analytical results. Here, the variations in the resulting analyses are explored due to the influence of new and more varied data.

36 MATERIALS SCIENCE↗

Effectiveness of nature-based solutions to reduce flooding in Quad Cities Metro Area (QCMA) using SWMM-HEC based flood model

Nature-based solutions (NbS) have gained significant attention as strategies for addressing urban environmental challenges, particularly since the establishment of the UN Sustainable Development Goals (SDGs) for 2030. However, the current research on NbS for urban flood management lacks comprehensive methodological approaches for identifying suitable areas and evaluating their effectiveness across different urban settings. Here, this study attempts to fill this gap by proposing a methodological framework integrating multi-criteria analysis with a SWMM-HEC-based hydrologic and hydraulic (HH) model to assess the suitability of NbS for the Quad Cities Metro Area (QCMA), consisting of Davenport, Bettendorf, Moline, and Rock Island. Eight NbS options-green roofs, rain gardens, infiltration trenches, permeable pavements, vegetative swales, dry detention basins, retention ponds, and rain barrels/cisterns - were considered based on volumetric efficiency and runoff reduction efficiency. The study reveals that implementing the proposed NbS could have substantially reduced flood depths in key historical flood events by 21% in 1993, 15% in 2008, 16% in 2011, 23% in 2014, 40% in 2019, and 10% in 2023. The findings highlight a critical trade-off between peak runoff and NbS implementation: while NbS effectively reduce flood impacts, they also enhance volumetric efficiency by approximately 43%. In high-density areas of the QCMA, flood depth reductions of around 20% suggest that NbS are a viable solution for dense urban environments with limited space. This shows the potential for integrating NbS into existing infrastructure, offering a promising approach for cities facing increasing flooding risks. The proposed methodology provides a practical framework for incorporating NbS into urban stormwater management, addressing gaps in optimizing NbS performance, and offering a pathway to scale their application in other urban areas with various environmental and social contexts.

CMIP6↗

Challenges and Advances in Information Extraction from Scientific Literature: a Review

Scientific articles have long been the primary means of disseminating scientific discoveries. Over the centuries, valuable data and potentially groundbreaking insights have been collected and buried deep in the mountain of publications. In materials engineering, such data are spread across technical handbooks specification sheets, journal articles, and laboratory notebooks in myriad formats. Extracting information from papers on a large scale has been a tedious and time-consuming job to which few researchers have wanted to devote their limited time and effort, yet is an activity that is essential for modern data-driven design practices. However, in recent years, significant progress has been made by the computer science community on techniques for automated information extraction from free text. Yet, transformative application of these techniques to scientific literature remains elusive-due not to a lack of interest or effort but to technical and logistical challenges. Using the challenges in the materials science literature as a driving motivation, we review the gaps between state-of-the-art information extraction methods and the practical application of such methods to scientific texts, and offer a comprehensive overview of work that can be undertaken to close these gaps.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

The Role of Oxidation Resistance in High Temperature Alloy Selection for a Future with Green Hydrogen

Hydrogen is being considered integral to the future energy landscape but there is limited mechanistic understanding and a lack of predictive models to describe the combined effects of alloy and gas composition, temperature, thermal cycling and water vapor contents on the oxidation behavior of high-temperature materials. Experimental evaluations were combined with coupled thermodynamic-kinetic modeling to investigate the oxidation behavior of five representative Ni-based superalloys in two water vapor contents (10%, 60% H 2 O) under thermal cycling (1-h, 100-h cyles) conditions at 800°C and 1000°C. The alloy with the highest Ti content demonstrated the poorest cyclic oxidation behavior while the alloy with highest Cr and Al contents was expected to continue to support protective formation of a compact Al 2 O 3 scale. Finally, accelerated degradation of the chromia-forming alloys was observed in the higher water vapor content but the impact on transient oxidation of the alumina-forming alloys needs further investigations.

36 MATERIALS SCIENCE↗

A Phase-Field Study on Internal to External Oxidation Transition in High-Temperature Structural Alloys

Structural alloys applied at high temperatures rely on an external dense layer of oxide scale for protection. As some reactive alloy components are selectively oxidized internally, understanding how these dispersed metal oxide particles reach the surface to form a protective scale—the so-called internal to external oxidation transition—is crucial for designing these alloys. While the literature is replete with experimental studies on oxidation of alloys, there is a lack of computational studies in this realm due to the complex nature of coupled reaction and diffusion processes in multicomponent multi-phase alloy systems. In this work, we apply a recently developed phase-field model to simulate the oxidation processes under different compositions and nucleation scenarios to gain insights into how a continuous oxide scale can be established. The results show that while alloy composition is critical for internal to external oxidation transition, the oxide nuclei size, shape and distribution also have significant impact on the transition kinetics.

36 MATERIALS SCIENCE↗

The Linkage Between Electro-Chemical Mechanical Instabilities in Battery Materials

Battery chemistry must be diversified to achieve a sustainable energy landscape by effectively utilizing renewable energy sources. Alkali metal-ion, all-solid-state, metal–air batteries, and multivalent batteries offer unique cost, safety, raw material abundance, energy, and power density solutions. However, realizing these “beyond Li-ion batteries” must uncover their working principles and performance & property relationships. In this aspect, mitigating chemo-mechanical instabilities in the structure and surface of the electrodes plays a crucial role in their performance. Unfortunately, the coupling between electrochemical and mechanical interactions is often poorly understood due to a lack of operando characterization. Here, this review article explains the working principles of curvature measurement and digital image correlation for measuring stress and strain generations in battery materials. We provided specific examples of how these operando mechanical measurements shed light on instabilities in alkali metal ion electrodes, solid electrolytes, Li-O 2 batteries, and aqueous Zn-ion batteries. Operando mechanical measurements offer an effective way to map changes in the physical fingerprint of the battery materials, therefore providing crucial information to elucidate instabilities in battery materials.

25 ENERGY STORAGE↗

Scientific Foundations and Approaches for Qualification of Additively Manufactured Structural Components

Additive manufacturing (AM) maintains a wide process window that enables complex designs otherwise unattainable via conventional production technologies. However, the lack of confidence in qualifying AM parts that leverage AM process–structure–property–performance (PSPP) relationships stymies design optimization and adoption of AM. While continuing efforts to map fundamental PSPP relationships that cover the potential design space, we first need pragmatic and then long-term solutions that overcome challenges associated with qualifying AM-designed parts. Two pragmatic solutions include: (1) AM material specifications to substantiate process reproducibility, and (2) component risk categorization to associate system risk relative to part performance and required part quality. A novel qualification paradigm under development involves efficient prediction of part performance over wide-ranging PSPP relationships through targeted testing and computational simulation. Here this paper describes projects at Sandia National Laboratories on PSPP relationship discovery, these pragmatic approaches, and the novel qualification approach.

36 MATERIALS SCIENCE↗

Image-Based Fracture Surface Defect Characterization Methods for Additively Manufactured Ti-6Al-4V Tested in Fatigue

Abstract Fatigue initiation in additively manufactured samples/parts often occurs at processed-induced defects such as lack-of-fusion (LoF), keyhole, or other morphological/microstructural defects that have unique characteristics and measurable qualities. Attempts at identifying and minimizing such defects have utilized optimized processing conditions along with in situ and ex situ characterization that includes metallography and/or X-ray computed tomography (XCT). This paper highlights the benefits of using fracture surface analyses to detect and quantify defects that may not be detected by metallography/XCT due to sectioning and resolution limits. In addition to using manual quantification of fatigue initiating LoF and keyhole defects on fracture surfaces, image-based machine learning using convolutional neural networks such as U-Net were also used to automate the process. Statistical analyses were used to identify the extreme cases of defects that initiated and accelerated fatigue and to model the distribution of defect size and shape characteristics to distinguish the type of defect. Initial results show agreement between trained machine learning models and ground truth data in defect segmentation, and the distributions of defect characteristics are distinguishable to particular process-induced defect types.

Materials Science↗

Timed to save: the added value of accounting for hourly incidence of electricity savings from residential space-conditioning measures

Abstract Previous research has recognized that the value of measures that reduce electricity usage depends upon the timing of the savings generated, but the lack of hourly savings shapes has limited the demonstration of this concept. We develop empirical hourly savings shapes for residential space-conditioning measures from nearly 18,000 efficiency projects in California and show how they combine with the diurnal and seasonal variation in electricity system costs. We find that these measures (cooling replacements; windows, doors, and skylights; and other envelope measures) tend to save electricity when system costs are highest and that the hourly savings account for 1.4–1.5 times as much value as non-time-sensitive estimates of efficiency would predict. We present these impact multipliers for each measure to quantify the additional value revealed by the time-sensitive approach. We show that this additional value is similar in an evolving electricity grid with storage, rather than natural gas generation, as the marginal resource.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗