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At least 757 records · Page 42

Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time

DNA compaction is required for the condensation and resolution of chromosomes during mitosis, but the relative contribution of individual chromatin factors to this process is poorly understood. We developed a physiological, cell-free system using high-speed Xenopus egg extracts and optical tweezers to investigate real-time mitotic chromatin fiber formation and force-induced disassembly on single DNA molecules. Compared to interphase extract, which compacted DNA by ~60%, metaphase extract reduced DNA length by over 90%, reflecting differences in whole-chromosome morphology under these two conditions. Depletion of the core histone chaperone ASF1, which inhibits nucleosome assembly, decreased the final degree of metaphase fiber compaction by 29%, while depletion of linker histone H1 had a greater effect, reducing total compaction by 40%. Compared to controls, both depletions reduced the rate of compaction, led to more short periods of decompaction, and increased the speed of force-induced fiber disassembly. In contrast, depletion of condensin from metaphase extract strongly inhibited fiber assembly, resulting in transient compaction events that were rapidly reversed under high force. Altogether, these findings support a speculative model in which condensin plays the predominant role in mitotic DNA compaction, while core and linker histones act to reduce slippage during loop extrusion and modulate the degree of DNA compaction.

59 BASIC BIOLOGICAL SCIENCES↗

A rigorous framework for an improved Messinger/Myers model of ice accretion under conditions of variable property and unsteady aircraft icing

We analyse the Messinger/Myers model by critically evaluating simplifying assumptions through a rigorous formulation of the rime ice accretion process. We explore the effects of both constant and variable ice density and thermal conductivity, along with the effects of sublimation from the ice surface. The effects of key factors such as droplet impact rate, ambient temperature relative to the freezing temperature and the temperature difference between the ambient air and the airfoil surface are examined. Under these varying conditions, the present rigorous formulation is used to assess the significance of unsteady effects, variable ice properties and sublimation. We observe that the Myers model performs remarkably well in certain icing situations and analyse the reasons for this strong performance. We also show that partially relaxing the model’s assumptions can lead to poorer performance. The Myers model can lead to overprediction of ice surface temperature and correspondingly underprediction of transition time under conditions of relatively weak sublimation and surface cooling. A modified Myers model is presented, which can be used to recover near-perfect results under widely varying icing conditions of relevance. This article is part of the theme issue ‘Heat and mass transfer in frost and ice’.

Science & Technology - Other Topics↗

Study of a linear surface wave plasma source for tin removal in an extreme ultraviolet source

Tin deposition mitigation employs hydrogen radicals and ions, formed in a hydrogen plasma, to interact with tin to form tin hydride (SnH 4 ) in the gaseous state, which is then pumped away. Surface wave plasma (SWP) technology developed at Illinois generates hydrogen radicals and ions, resulting in tin etch rates that are high enough to keep extreme ultraviolet (EUV) lithographic tools clean. An advantage of an SWP antenna is the ability to generate a high density of hydrogen radicals and hydrogen ions directly at the desired etching location. In situ etching of tin enables high availability EUV tools by maintaining high reflectivity of the multilayer mirror of the collector. Additionally, the SWP is characterized with low ion energies and low electron temperature, such that the multilayer mirror does not suffer any damage from sputtering or implantation of hydrogen ions during operation. Here, experiments elucidating the fundamental processes of tin removal are conducted by varying pressure, power, surface temperature, and gas flow rate in order to observe the etch rate behavior. Our results have shown that the presence of hydrogen ions increases etch rates because ion bombardment weakens Sn–Sn bonds, which, in turn, allows for a higher rate of chemical etching by the radicals. The ion bombardment reduces the number of radicals needed to etch a single tin atom to the range of 10 2 –10 3 . The linear SWP antenna yields plasma densities on the order of 10 17 to 10 18 m -3 and radical densities on the order of 10 18 to 10 19 m -3 , allowing for greater utilization of ion etch enhancement. Etch rates of up to 200 nm/min have been achieved. The surface temperature of the samples is an important factor in the etching process such that the decrease in the surface temperature increases the etch rates and decreases the hydrogen desorption rates. In addition, a kinetic etch model is developed to explain the behavior of etch rates as a function of surface temperature. Furthermore, results from experiments performed in an Illinois NXE:3100 chamber will be discussed.

42 ENGINEERING↗

Super-swelling behavior of stacked lipid bilayer systems

Bilayer systems comprising lipid mixtures are the most well-studied model of biological membranes. While the plasma membrane of the cell is a single bilayer, many intra- and extra-cellular biomembranes comprise stacks of bilayers. Most bilayer stacks in nature are periodic, maintaining a precise water layer separation between bilayers. That equilibrium water separation is governed by multiple inter-bilayer forces and is highly responsive. Biomembranes re-configure inter-bilayer spacing in response to temperature, composition, or mass transport cues. In synthetic bilayer systems for applications in cosmetics or topical treatments, control of the hydration level is a critical design handle. Herein we investigate a binary lipid system that leverages key inter-bilayer forces leading to unprecedented levels of aqueous swelling while maintaining a coherent multilamellar form. We found that combining cationic lipids with bicontinuous cubic phase-forming lipids (lipids with positive Gaussian modulus), results in the stabilization of multilamellar phases against repulsive steric forces that typically lead to bilayer delamination at high degrees of swelling. Using ultra-small-angle X-ray scattering alongside confocal laser scanning microscopy, we characterized various super-swelled states of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and glycerol monooleate (GMO) lipids, as well as other analogous systems, at varied concentration and molar ratios. Through these experiments we established swelling profiles of various binary lipid systems that were near-linear with decreasing lipid volume fraction, showing maximum swelling with periodicity well above 200 nanometers.

42 ENGINEERING↗

Storage Futures Study: The Four Phases of Storage Deployment: A Framework for the Expanding Role of Storage in the U.S. Power System

This report is one in a series of NREL’s Storage Futures Study (SFS) publications. The SFS is a multiyear research project that explores the role and impact of energy storage in the evolution and operation of the U.S. power sector. The SFS is designed to examine the potential impact of energy storage technology advancement on the deployment of utility-scale storage and the adoption of distributed storage, and the implications for future power system infrastructure investment and operations. The research findings and supporting data will be published as a series of publications. The table on the next page lists the planned publications and specific research topics they will examine under the SFS. This report, the first in the SFS series, explores the roles and opportunities for new, cost-competitive stationary energy storage with a conceptual framework based on four phases of current and potential future storage deployment, and presents a value proposition for energy storage that could result in substantial new cost-effective deployments. This conceptual framework provides a broader context for consideration of the later reports in the series, including the detailed results of the modeling and analysis of power system evolution scenarios and their operational implications

25 ENERGY STORAGE↗

Continual learning in the presence of repetition

Continual learning (CL) provides a framework for training models in ever-evolving environments. Although re-occurrence of previously seen objects or tasks is common in real-world problems, the concept of repetition in the data stream is not often considered in standard benchmarks for CL. Unlike with the rehearsal mechanism in buffer-based strategies, where sample repetition is controlled by the strategy, repetition in the data stream naturally stems from the environment. This report provides a summary of the CLVision challenge at CVPR 2023, which focused on the topic of repetition in class-incremental learning. The report initially outlines the challenge objective and then describes three solutions proposed by finalist teams that aim to effectively exploit the repetition in the stream to learn continually. The experimental results from the challenge highlight the effectiveness of ensemble-based solutions that employ multiple versions of similar modules, each trained on different but overlapping subsets of classes. This report underscores the transformative potential of taking a different perspective in CL by employing repetition in the data stream to foster innovative strategy design.

Class-incremental learning↗

Uncertainty Quantification and Error Propagation in the Enthalpy and Entropy of Surface Reactions Arising from a Single DFT Functional

Accounting for parametric uncertainty in models is essential for quantifying the models’ predictive ability. Recently, approaches have been introduced to estimate parametric uncertainty in kinetic models while accounting for correlations among energy parameters. However, correlations have been estimated indirectly and correlations in entropies have not been accounted for. For surface-catalyzed microkinetic models of >C2 (more than two carbon-containing) molecules, which consist of thousands of reaction steps and intermediate surface species, first-principles density functional theory (DFT) is costly, and thus, estimation of thermochemistry and reaction barriers requires surrogate methods of DFT, such as group additivity and Brønsted–Evans–Polanyi relationships, respectively. For such parametrization, model uncertainty is unclear. This work develops a framework to overcome these gaps using group additivity and a single DFT functional. We estimate correlations in parameters of kinetic models and quantify uncertainty for thermochemistry, reaction barriers, reaction paths, and ultimately reaction rates, accounting also for the contribution of entropic uncertainty. Furthermore, the approach is illustrated on propane combustion and ethane oxidative dehydrogenation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High Frequency Transverse Instabilities in Low NOx Gas Turbines

This program addresses the topic of combustion instabilities under the goal of developing “Low-NOx Combustion Technology for ‘Air-Breathing’ Advanced Turbines”. With recent advances in high-temperature withstanding materials, the push towards higher efficiency has resulted in efforts to design high temperature, low NOx gas turbines. The development of such low NOx systems is often plagued with combustion instabilities. These instabilities manifest with acoustic modes that are longitudinal, transverse or both. A large body of literature and work exists addressing the underlying mechanisms and models for longitudinal instabilities and these have been successfully implemented in the design tools for low NOx gas turbines. The flame response aspect of the thermoacoustic feedback loop was often modeled in an acoustically compact framework since for low frequencies, the flame length scale was small compared to the acoustic wavelength. This enabled simplification where the modeling focused only on the overall flame response and not the local spatial distribution of the flame response. In addition, additional mechanisms such as the direct effect of pressure fluctuations on the flame response could be neglected. In contrast, high frequency instabilities which often are transverse in nature, have received relatively less attention in the literature. The flame is no longer acoustically compact and thus the local distribution of heat release must be accurately understood. The flame responds to velocity fluctuations, equivalence ratio fluctuations as before, but also to pressure fluctuations through kinetic effects. These aspects of high-frequency instabilities make it a challenging problem that requires a detailed elucidation of the underlying mechanisms and creating models for them. In this program we significantly improved the understanding of these instabilities through a combination of experiments (informed by interactions with OEMs), modeling of measured data and reduced order modeling of flame response. The results from the program can be used as basis for robust design tools that are essential for successfully developing gas turbines that operate in an environmentally acceptable manner with mitigation strategies for high-frequency instabilities.

08 HYDROGEN↗

Artificial intelligence for advanced functional materials: exploring current and future directions

This perspective addresses the topic of harnessing the tools of artificial intelligence (AI) for boosting innovation in functional materials design and engineering as well as discovering new materials for targeted applications in energy storage, biomedicine, composites, nanoelectronics or quantum technologies. It gives a current view of experts in the field, insisting on challenges and opportunities provided by the development of large materials databases, novel schemes for implementing AI into materials production and characterization as well as progress in the quest of simulating physical and chemical properties of realistic atomic models reaching the trillion atoms scale and with near ab initio accuracy.

36 MATERIALS SCIENCE↗

Solar Engineering of Thermal Processes, Photovoltaics and Wind, Fifth Edition

The updated Fifth Edition of Solar Engineering of Thermal Processes, Photovoltaics and Wind contains the fundamentals of solar energy and explains how we get energy from the sun. The authors - noted experts on the topic - provide an introduction to the technologies that harvest, store, and deliver solar energy, such as photovoltaics, solar heaters, and cells. The book also explores the applications of solar technologies and shows how they are applied in various sectors of the marketplace.

14 SOLAR ENERGY↗

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies

Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NP RBD ) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NP RBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NP RBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

59 BASIC BIOLOGICAL SCIENCES↗

Enabling Efficient and Accurate Computational Studies of MOF Reactivity via QM/MM and QM/QM Methods

Electronic structure calculations can provide unique insight into metal–organic framework (MOF) reactivity and defect formation. Such calculations can be broadly categorized as utilizing either periodic or cluster models, each with their respective advantages and disadvantages. In the present study, we demonstrate how multiscale methods can leverage the advantages of both approaches to enable high levels of accuracy and computational efficiency in studies of MOF reactivity. Using defect formation in a zeolitic imidazolate framework (ZIF) as a prototypical example, we benchmark a quantum mechanics/molecular mechanics (QM/MM) scheme that enables highly efficient cluster-based calculations on MOFs. We demonstrate the importance of correctly accounting for the influence of both dative bond cleavage in the QM cluster and long-range mechanical coupling to the bulk to achieving accurate QM/MM studies of MOFs. We subsequently leverage these cluster models in a QM/QM scheme that goes beyond standard DFT to yield “gold-standard” correlated wave function results on MOFs at modest computational cost. Crucially, we find several cases in which the incorporation of these correlated corrections yields qualitatively important corrections over conventional DFT values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Control of work functions of nanophotonic components

Work function is an essential material’s property playing important roles in electronics, photovoltaics, and more recently, in nanophotonics. We have studied effects of organic, and inorganic dielectric materials on work functions of Au films in single layered, and multilayered structures. We found that measured work function of metallic surfaces can be affected by dielectric materials situated 10–100 nm away from the metallic surface. We have found that, (i) the glass underneath ~ 50 nm gold slab reduces the work function of gold, (ii) Rh590:PMMA increases the work function of a gold film deposited on top of the polymer, and (iii) reduces it if Rh590:PMMA is deposited on top of Au. (iv) With increase of the Rh590 concentration in PMMA, n, the work function first decreases (at n < 64 g/l), and then increases (at n > 64 g/l). (v) The work function of a Fabry–Perot cavity or an MIM waveguide is almost the same as that of single Au films of comparable thickness. The experimental results can be qualitatively explained in terms of a simple model taking into account adhesion of charged molecules to a metallic surface, and formation of a double layer of charges accelerating or decelerating electrons exiting the metal and decreasing or increasing the work function.

36 MATERIALS SCIENCE↗

The shard test and nanoporomechanics reverse classical paradigm of cement hydration being contractive

Le Chatelier in 1887 and Powers in 1947 demonstrated that the volume of nanoscale C-S-H (calcium silicate hydrate) particles formed during hydration is smaller than the combined volume of the reactants—the anhydrous Portland cement and water. Hydration has thus been considered as contractive. An experiment shows that the opposite is true above the nanoscale. The porous skeleton of cement paste expands as the growing C-S-H particles push each other apart, similar to crystal growth pressure. This is significant for high-performance concretes (HPC) with low water-cement ratios (w/c ≤ 0.4), where chemical self-desiccation lowers pore relative humidity by 40%, compared to just 1% in traditional concretes (w/c ≈ 0.5). Standard American Society for Testing and Materials (ASTM) C1608 tests, using 10 mm thick water-immersed specimens, show large shrinkage because the half-time of water ingress is many decades, unable to offset shrinkage-causing self-desiccation. The present experiment, using a laser microscopy-topography technique, proves the opposite—expansion, evidenced by measuring the length changes of water-immersed HPC shards 0.5 mm thick in which the diffusion halftime, only about one hour, allows continuous resaturation of pores, canceling self-desiccation. The faster diffusion (halftime of one hour) enables continuous pore resaturation, preventing shrinkage. When sealed with paraffin oil, the shards self-desiccate and shrink. These findings align with studies since 2015, showing that models excluding hydration expansion cannot fit test data across various specimen sizes and sealing conditions. The results suggest that standardized ASTM tests for the so-called chemical shrinkage in modern concretes with very low water-cement ratios are misleading and need revision.

Science & Technology - Other Topics↗

Building a genome-based understanding of bacterial pH preferences

The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite the importance of pH as a factor structuring bacterial communities in many systems. We compiled data on bacterial distributions from five datasets spanning pH gradients in soil and freshwater systems (1470 samples), quantified the pH preferences of bacterial taxa across these datasets, and compiled genomic data from representative bacterial taxa. While taxonomic and phylogenetic information were generally poor predictors of bacterial pH preferences, we identified genes consistently associated with pH preference across environments. We then developed and validated a machine learning model to estimate bacterial pH preferences from genomic information alone, a model that could aid in the selection of microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, we demonstrate the value of combining biogeographic and genomic data to infer and predict the environmental preferences of diverse bacterial taxa.

59 BASIC BIOLOGICAL SCIENCES↗

Newly formed dust within the circumstellar environment of SN Ia-CSM 2018evt

Dust associated with various stellar sources in galaxies at all cosmic epochs remains a controversial topic, particularly whether supernovae play an important role in dust production. We report evidence of dust formation in the cold, dense shell behind the ejecta–circumstellar medium (CSM) interaction in the Type Ia-CSM supernova (SN) 2018evt three years after the explosion, characterized by a rise in mid-infrared emission accompanied by an accelerated decline in the optical radiation of the SN. Such a dust-formation picture is also corroborated by the concurrent evolution of the profiles of the Hα emission line. Our model suggests enhanced CSM dust concentration at increasing distances from the SN as compared to what can be expected from the density profile of the mass loss from a steady stellar wind. By the time of the last mid-infrared observations at day +1,041, a total amount of 1.2 ± 0.2 × 10 -2 M ⊙ of new dust has been formed by SN 2018evt, making SN 2018evt one of the most prolific dust factories among supernovae with evidence of dust formation. The unprecedented witness of the intense production procedure of dust may shed light on the perceptions of dust formation in cosmic history.

79 ASTRONOMY AND ASTROPHYSICS↗

Domain wall enabled steep slope switching in MoS2 transistors towards hysteresis-free operation

Abstract The device concept of ferroelectric-based negative capacitance (NC) transistors offers a promising route for achieving energy-efficient logic applications that can outperform the conventional semiconductor technology, while viable operation mechanisms remain a central topic of debate. In this work, we report steep slope switching in MoS 2 transistors back-gated by single-layer polycrystalline PbZr 0.35 Ti 0.65 O 3 . The devices exhibit current switching ratios up to 8 × 10 6 within an ultra-low gate voltage window of $$V_{{{\mathrm{g}}}} = \pm \! 0.5$$ V g = ± 0.5 V and subthreshold swing (SS) as low as 9.7 mV decade −1 at room temperature, transcending the 60 mV decade −1 Boltzmann limit without involving additional dielectric layers. Theoretical modeling reveals the dominant role of the metastable polar states within domain walls in enabling the NC mode, which is corroborated by the relation between SS and domain wall density. Our findings shed light on a hysteresis-free mechanism for NC operation, providing a simple yet effective material strategy for developing low-power 2D nanoelectronics.

36 MATERIALS SCIENCE↗

The rate of microtubule breaking increases exponentially with curvature

Microtubules, cylindrical assemblies of tubulin proteins with a 25 nm diameter and micrometer lengths, are a central part of the cytoskeleton and also serve as building blocks for nanobiodevices. Microtubule breaking can result from the activity of severing enzymes and mechanical stress. Breaking can lead to a loss of structural integrity, or an increase in the numbers of microtubules. We observed breaking of taxol-stabilized microtubules in a gliding motility assay where microtubules are propelled by surface-adhered kinesin-1 motor proteins. We find that over 95% of all breaking events are associated with the strong bending following pinning events (where the leading tip of the microtubule becomes stuck). Furthermore, the breaking rate increased exponentially with increasing curvature. These observations are explained by a model accounting for the complex mechanochemistry of a microtubule. The presence of severing enzymes is not required to observe breaking at rates comparable to those measured previously in cells.

42 ENGINEERING↗