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At least 343 records · Page 19

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DOE OSTI2023

A new efficient grain growth model using a random Gaussian-sampled mode filter

This paper presents the use of a Gaussian neighborhood mode filter for predicting grain growth in a manner similar to the solutions obtained by a Monte Carlo Potts model. This flexible grain growth model can quickly utilize modern, computationally optimized data science strategies on graphics processing units to simulate grain growth up to 100 times faster than the state-of-the-art, publicly available Monte Carlo Potts model. We show that, given the correct neighborhood, the mode filter can replicate normal grain growth in two or three dimensions. In addition, the paper briefly demonstrates the ability to model limited anisotropic in grain boundary energy and mobility. Anisotropic grain boundary energy is modeled by defining a weighted mode filter operation. Anisotropic grain boundary mobility is modeled by scaling and orienting the Gaussian neighborhood in a particular direction.

Anisotropy↗

DOE OSTI2022

Effects of warming on bacterial growth rates in a peat soil under ambient and elevated CO 2

Boreal peatlands are important global carbon reservoirs that are particularly vulnerable to predicted climate changes such as increasing CO 2 and temperature. Since microbial activities regulate the balance of carbon sequestered into soil organic matter or remineralized to CO 2 , characterizing their response to these environmental factors is critical to predicting how peatland ecosystems will affect climate-carbon cycle feedbacks. Here we examined in-situ taxon-specific variation in microbial growth under long-term elevated CO 2 and across a gradient of warming treatments in a northern Minnesota peat bog using quantitative stable isotope probing with 18 O-water. Across temperatures, bacterial taxa were grouped according to the excess atom fraction 18 O (EAF) of their genomes, a proxy for DNA replication and hence, growth. Taxon-specific growth across CO 2 and temperature treatments clustered into relatively few response patterns. While a large portion of taxa showed little to no growth under ambient CO 2 , many of the same taxa grew rapidly under elevated CO 2 . We found support for phylogenetic conservation of response patterns among Acidobacteria and Proteobacteria, the two most abundant phyla in our data. Our results suggest certain taxa may be primed for new climate conditions and have a greater influence on carbon cycling with implications for future climate mitigation strategies.

16S amplicon sequencing, Carbon Dioxide (CO2), pea↗

DOE OSTI2026

Rewiring the unfolded protein response for plant growth recovery after stress

The unfolded protein response (UPR) is a highly coordinated signaling network that alleviates endoplasmic reticulum (ER) stress, a condition induced by diverse environmental challenges in plants. Over the past two decades, substantial progress has been made in elucidating the genetic and molecular mechanisms of ER stress sensing and signal transduction in plants, largely through studies in the model plant Arabidopsis thaliana . These advances have established the UPR as a central regulator of proteostasis and underscored its broader relevance to plant growth and development and crop productivity under stress conditions. Despite this progress, critical knowledge gaps remain, particularly concerning the downstream biological processes required for growth recovery once ER stress has subsided and how these processes are coordinated by UPR regulators. Recent systems-level and integrative studies have begun to reveal critical roles of UPR signaling in pathways governing growth re-establishment and homeostasis of nutrient allocation and energy metabolism. In this review, we highlight recent findings on the functional roles of the plant UPR in recovery from ER stress, with a focus on mechanisms mediated by UPR regulators and downstream biological pathways that enable the transition from stress mitigation to growth restoration. Although this research area is still emerging, accumulating evidence supports a model in which the UPR functions as a dynamic regulatory network that actively coordinates post-stress physiological recovery to support plant fitness.

ER stress↗

DOE OSTI2020

Moisture-Driven Formation and Growth of Quasi-2-D Organolead Halide Perovskite Crystallites

Ruddlesden–Popper phase quasi-2-D organolead halide perovskites like n-butylammonium methylammonium lead iodide (nBA-MAPI) exhibit improved moisture stability over typical 3-D perovskite materials, making them exciting for use in a variety of applications such as photovoltaic (PV) devices. This improved stability is the result of a unique disproportionation-based degradation mechanism that protects the bulk of the nBA-MAPI from extensive damage through the formation of a protective, low-n surface layer. In addition to this surface layer, nBA-MAPI films also exhibit the dynamic growth of micrometer-scale crystallites and cracks at the surface of the film, unique and potentially important byproducts of quasi-2-D perovskite disproportionation. Here, we present a detailed study of these crystallites using several analytical techniques including photoluminescence spectroscopy (PL), confocal fluorescence microscopy (CFM), atomic force microscopy (AFM) combined with time-of-flight-secondary ion mass spectrometry (ToF-SIMS), and others in an effort to better understand the relationship between material disproportionation and crystallite growth. Our results show that the crystallites form after exposure to humid air and confirm that they are composed of low-n phases of nBA-MAPI. The crystallites are found to extend into the interior of the film and exhibit continued growth while exposed to moisture over 72 h. This growth is accompanied by both a decrease in the bulk 2-D phase and an increase in a 3-D-like phase in the surface PL spectra, indicating that the crystallites are likely a product of moisture-driven disproportionation. Importantly, similar crystallites are also observed to form within model PV devices, indicating that such processes must be accounted for when designing future devices containing materials like nBA-MAPI.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The ‘photosynthetic C 1 pathway’ links carbon assimilation and growth in California poplar

Although primarily studied in relation to photorespiration, serine metabolism in chloroplasts may play a key role in plant CO 2 fertilization responses by linking CO 2 assimilation with growth. Here, we show that the phosphorylated serine pathway is part of a 'photosynthetic C 1 pathway' and demonstrate its high activity in foliage of a C 3 tree where it rapidly integrates photosynthesis and C 1 metabolism contributing to new biomass via methyl transfer reactions, imparting a large natural 13 C-depleted signature. Using 13 CO 2 -labelling, we show that leaf serine, the S-methyl group of leaf methionine, pectin methyl esters, and the associated methanol released during cell wall expansion during growth, are directly produced from photosynthetically-linked C 1 metabolism, within minutes of light exposure. We speculate that the photosynthetic C 1 pathway is highly conserved across the photosynthetic tree of life, is responsible for synthesis of the greenhouse gas methane, and may have evolved with oxygenic photosynthesis by providing a mechanism of directly linking carbon and ammonia assimilation with growth. Although the rise in atmospheric CO 2 inhibits major metabolic pathways like photorespiration, our results suggest that the photosynthetic C 1 pathway may accelerate and represents a missing link between enhanced photosynthesis and plant growth rates during CO 2 fertilization under a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nucleation and growth of blue phase liquid crystals on chemically-patterned surfaces: a surface anchoring assisted blue phase correlation length

In condensed matter, the correlation length is an essential parameter which describes the distance over which a material maintains its structural properties. In liquid crystals, for the orientational order parameter this characteristic length is of the order of nanometers, while in solid crystals it can extend to macroscopic length scales. Here, we report the measurement of the correlation length, or persistence length, of the crystallographic orientation of blue phases (BPs)—chiral liquid crystals with long-range 3D-crystalline structures and submicron-sized lattice-parameters. These materials exhibit phase transformations that have been identified as the liquid analog of crystal-crystal martensitic transformations. In this work, we use liquid epitaxial growth to achieve spontaneous BP-crystal nucleation and subsequent growth. Specifically, we design patterned substrates made of a binary array of regions with different liquid crystal anchoring, which facilitate a uniform nucleation and growth of BP-crystals with (100)-lattice orientation and a simple cubic symmetry. Furthermore, our results indicate that this simple cubic BP, the so-called blue phase II (BPII), forms first on the patterned surface, thereby propagating the growth of domains in directions parallel or perpendicular to the patterned regions. These results are used to understand the emergence of a surface anchoring assisted BPII-correlation length, taken as the distance over which the BP preserves its lattice orientation, as a function of time and pattern characteristics. We found that BPII single crystals can be achieved on patterned regions whose lateral dimensions are equal to or larger than 10 μm, consistent with our measurements of the BPII-correlation length. This newly acquired understanding of the role of surfaces on the formation of BPs is then used to design processes that permit formation of macroscopically large mono-domain, single-crystal BPs by relying on significantly reduced patterned areas (only part of the area is patterned), a feature that could benefit the applications of this intriguing class of materials.

correlation length↗

DOE OSTI2020

GaAs growth rates of 528 μm/h using dynamic-hydride vapor phase epitaxy with a nitrogen carrier gas

Herein we demonstrate record GaAs growth rates approaching 530 μm/h using nitrogen carrier gas and 400 μm/h using hydrogen carrier gas in a dynamic-hydride vapor phase epitaxy reactor. We measured root mean square surface roughness below 1 nm using a 1 μm × 1 μm atomic force microscopy scan for GaAs growth rates up to 483 μm/h using a nitrogen carrier gas and 400 μm/h using a hydrogen carrier gas. We performed computational fluid dynamics modeling to study the effect of the carrier gas choice on the thermal profile within the reactor and how that influences the degree of AsH 3 decomposition. The modeling suggests that the lower thermal conductivity of the nitrogen carrier gas minimizes the amount of AsH 3 that thermally decomposes before reaching the wafer surface and the heavier atomic mass decreases the likelihood that AsH 3 will reach the heated reactor walls, leading to a growth rate enhancement relative to the hydrogen carrier case in a hydride-enhanced growth regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Temperature-dependent growth of hexagonal and monoclinic gallium sulfide films by pulsed-laser deposition

We demonstrate the selective, pulsed-laser deposition of hexagonal GaS and monoclinic Ga2S3 films on sapphire substrates from a single Ga 2 S 3 target in high-vacuum conditions. Growth at substrate temperatures below 550 °C causes GaS film formation, which indicates non-stoichiometric transfer from the target to the film. Surprisingly, stoichiometric transfer occurs at substrate temperatures above 650 °C with monoclinic Ga 2 S 3 as the preferred, higher S-content phase. Through a series of growth and annealing experiments, we show that GaS nucleation under S-deficient conditions leads to the preferred growth of this layered, hexagonal phase below 550 °C. Furthermore, GaS films annealed above 650 °C under high vacuum are transformed to Ga 2 S 3 , reflecting the greater stability of the monoclinic phase. By first growing Ga 2 S 3 at a higher temperature and subsequently growing GaS at a lower temperature, we can fabricate GaS/Ga 2 S 3 heterostructures in a single growth process.

36 MATERIALS SCIENCE↗

DOE OSTI2021

How production networks amplify economic growth

Technological improvement is the most important cause of long-term economic growth. In standard growth models, technology is treated in the aggregate, but an economy can also be viewed as a network in which producers buy goods, convert them to new goods, and sell the production to households or other producers. We develop predictions for how this network amplifies the effects of technological improvements as they propagate along chains of production, showing that longer production chains for an industry bias it toward faster price reduction and that longer production chains for a country bias it toward faster growth. These predictions are in good agreement with data from the World Input Output Database and improve with the passage of time. The results show that production chains play a major role in shaping the long-term evolution of prices, output growth, and structural change.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

A molecular view of peptoid-induced acceleration of calcite growth

The extensive deposits of calcium carbonate (CaCO 3 ) generated by marine organisms constitute the largest and oldest carbon dioxide (CO 2 ) reservoir. These organisms utilize macromolecules like peptides and proteins to facilitate the nucleation and growth of carbonate minerals, serving as an effective method for CO 2 sequestration. However, the precise mechanisms behind this process remain elusive. In this study, we report the use of sequence-defined peptoids, a class of peptidomimetics, to achieve the accelerated calcite step growth kinetics with the molecular level mechanistic understanding. By designing peptoids with hydrophilic and hydrophobic blocks, we systematically investigated the acceleration in step growth rate of calcite crystals using in situ atomic force microscopy (AFM), varying peptoid sequences and concentrations, CaCO 3 supersaturations, and the ratio of Ca 2+ / HCO 3 − . Mechanistic studies using NMR, three-dimensional fast force mapping (3D FFM), and isothermal titration calorimetry (ITC) were conducted to reveal the interactions of peptoids with Ca 2+ and HCO 3 − ions in solution, as well as the effect of peptoids on solvation and energetics of calcite crystal surface. Our results indicate the multiple roles of peptoid in facilitating HCO 3 − deprotonation, Ca 2+ desolvation, and the disruption of interfacial hydration layers of the calcite surface, which collectively contribute to a peptoid-induced acceleration of calcite growth. These findings provide guidelines for future design of sequence-specific biomimetic polymers as crystallization promoters, offering potential applications in environmental remediation (such as CO 2 sequestration), biomedical engineering, and energy storage where fast crystallization is preferred.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Urban morphology and urban water demand: a case study in the land constrained Los Angeles region using urban growth modeling

The interactions between population growth, urban morphology, and water demand have important implications for water resources and supply in urban regions. Water use for irrigation comprises a significant fraction of urban water demand, and is potentially influenced by long-term changes in urban morphology. To investigate this, we used spatially explicit projections of urban land development intensity (fraction impervious area) generated from a 30 m resolution urban growth model for the Los Angeles (LA) region. Recent historical data on water use and high resolution landcover were used to establish relationships between green area, urban development intensity, and outdoor water demand. These relationships were then used to project outdoor and total water demand in 2100 using the urban growth model outputs. We considered two different population scenarios informed by the shared socioeconomic pathway (SSP) projections for the region (SSP3 and SSP5), and three scenarios of urban development intensification. Our analysis is resolved for over 80 water providers in the region, from the urban core to suburban fringe, and highlights diverse demand responses influenced by initial urban form and water demand attributes. Assumptions about outdoor water use factors based on recent water supply data were found to be nearly as influential on future outdoor demand as the urban growth scenario settings. Compared to previous studies, our work is unique in coherently linking high resolution SSP population scenarios, urban land cover evolution, and urban water demand projections, demonstrating the approach for the LA region—the largest population center in the western United States.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress

Biofilms aid bacterial adhesion to surfaces via direct and indirect mechanisms, and formation of biofilms is considered as an important strategy for adaptation and survival in suboptimal environmental conditions. However, the molecular underpinnings of biofilm formation in subsurface sediment/groundwater ecosystems where microorganisms often experience fluctuations in nutrient input, pH, and nitrate or metal concentrations are underexplored. Here, we examined biofilm formation under different nutrient, pH, metal, and nitrate regimens of 16 Rhodanobacter strains isolated from subsurface groundwater wells spanning diverse levels of pH (3.5 to 5) and nitrates (13.7 to 146 mM). Eight Rhodanobacter strains demonstrated significant biofilm growth under low pH, suggesting adaptations for survival and growth at low pH. Biofilms were intensified under aluminum stress, particularly in strains possessing fewer genetic traits associated with biofilm formation, findings warranting further investigation. Through random barcode transposon-site sequencing (RB-TnSeq), proteomics, use of specific mutants, and transmission electron microscopy analysis, we discovered flagellar loss under aluminum stress, indicating a potential relationship between motility, metal tolerance, and biofilm growth. Comparative genomic analyses revealed the absence of flagella and chemotaxis genes and the presence of a putative type VI secretion system in the highly biofilm-forming strain FW021-MT20. In this study we identified genetic determinants associated with biofilm growth under metal stress in a predominant environmental genus, Rhodanobacter, and identified traits aiding survival and adaptation to contaminated subsurface environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Statistical mechanical model for crack growth

Analytic relations that describe crack growth are vital for modeling experiments and building a theoretical understanding of fracture. Upon constructing an idealized model system for the crack and applying the principles of statistical thermodynamics, it is possible to formulate the rate of thermally activated crack growth as a function of load, but the result is analytically intractable. In this report an asymptotically correct theory is used to obtain analytic approximations of the crack growth rate from the fundamental theoretical formulation. These crack growth rate relations are compared to those that exist in the literature and are validated with respect to Monte Carlo calculations and experiments. The success of this approach is encouraging for future modeling endeavors that might consider more complicated fracture mechanisms, such as inhomogeneity or a reactive environment.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Self-selecting vapor growth of transition-metal-halide single crystals

Transition-metal halides can host a large variety of novel phenomena, such as magnetism in the monolayer limit, quantum spin liquid and spiral spin liquid states, topological magnons, and chiral phonons. Sizable high-quality single crystals are necessary for investigations of magnetic and lattice excitations by, for example, inelastic neutron scattering. In this paper, we review a less well-known vapor transport technique, self-selecting vapor growth, and report our growths of transition-metal halides using this technique. We report the growth and characterizations of sizable single crystals of α–RuCl 3 , CrCl 3 , Ru 1–x Cr x Cl 3 , and CrBr 3 . In order to expedite the conversion of starting powder to single crystals, we modified the technique by cooling the growth ampoule through an appropriate temperature range. Our work shows that the self-selecting vapor transport technique can provide large single crystals of transition-metal halides, demonstrating its potential for providing high-quality single crystals of quantum materials.

2-dimensional systems↗

DOE OSTI2021

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Abstract Background Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. Results We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. Conclusions The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The importance of long-timescale simulations for driven systems: An example of He bubble growth at a W GB

Accelerated Molecular Dynamics (AMD) is used to study complex systems under realistic conditions by extending the timescales accessible by Molecular Dynamics. However, some studies rely instead on driving atomic systems harder with higher temperature, faster growth, etc. Here, we study He bubble growth at a W grain boundary as an illustration of harnessing AMD methods to avoid consequences of over-driving the system. The growth mechanisms observed for a He bubble grown under realistic conditions are compared to bubbles-grown orders of magnitude faster, at rates typical of conventional molecular dynamics simulations. We find that progressive growth mechanisms and bubble structures depend on the rate at which the bubble is grown providing further evidence that care must be taken when simulating the dynamics of driven systems such as this one.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Hydrothermal Growth of Magnetically Frustrated Crystals: Lanthanide Stannate Pyrochlores as a Prototype

One important test bed system for frustrated magnetism is the pyrochlore lattice with the formula A2B2O7 in the cubic space group Fd3(-)m. Both the A and B sites occupy crystallographic trigonal sites and both sites possess a tetrahedral relationship with the other similar metal ion sites. These symmetry relationships generate a 3 D frustrated structure. In frustrated magnetic systems, typically a trivalent lanthanide ion occupies the A site and a magnetically silent tetravalent ion (Ti, Zr, Sn, etc.) occupies the B site. A classical problem related to the crystal growth of these compounds is sample quality. As refractory oxides, the traditional synthesis and crystal growth techniques require high temperatures, which creates two problems that are quite common and endemic to the pyrochlores. One is oxide lattice defects and the other is A/B site disorder. Both issues often occur in the same crystals at the same time and can have a significant impact on the study of physical properties. A hydrothermal approach can be applied to this problem. The relatively low crystal growth temperatures (600-720˚C) greatly minimize nonstoichiometry, lattice defects and A/B site disorder. The reduction of these pervasive imperfections significantly increases the quality of the observed physical property data. This talk will focus on the lanthanide stannates Ln2Sn2O7 as a prototype test bed of these systems. The stannates are among the few building blocks that can stabilize the pyrochlore structure type for all the lanthanides and they serve as an excellent proving ground for a wide range of physical properties. The synthesis and crystal growth of the lanthanide stannates will be reviewed, along with a discussion of some of the physical properties that result from the frustrated magnetic states of these low defect crystals.

Hydrothermal, crystal growth↗

DOE OSTI2022

Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development

The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO 4 ), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.

36 MATERIALS SCIENCE↗