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At least 1,729 records · Page 96

Two-Stage Conversion of Silicon to Nanostructured Carbon by the Method of Coordinated Atomic Substitution

Abstract—: A fundamentally new method of obtaining epitaxial layers of nanostructured carbon on silicon substrates has been considered. Epitaxial growth in the case of seemingly incompatible lattices has been achieved by converting the crystal by the method of coordinated substitution of atoms, in which the overall structure of the bonds between the atoms is not destroyed. In the first stage of conversion, the first half of the silicon atoms are concertedly replaced by the carbon atoms due to the reaction of silicon with CO gas, during which an epitaxial layer of SiC–3C cubic silicon carbide is obtained. In the second stage of conversion, the remaining half of silicon atoms is concertedly replaced by carbon atoms due to the reaction of SiC with CF{sub 4} gas. Carbon structures with different properties from nanodiamonds to nanotubes and carbon nanoonions have been obtained depending on the orientation of the silicon surface, pressure of the reagent gas, and temperature and growth time. A key feature of this method is that the substrate orders the resulting structures using the original chemical bonds between the atoms in silicon. The term “concertedly” means that new chemical bonds are formed simultaneously and concertedly with the destruction of old bonds. Data on electron diffraction and analysis of Raman and ellipsometric spectra of the obtained samples of nanostructured carbon on silicon substrates have been presented. Two competing growth mechanisms have been discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Interfacing of a Coordinate-Sensitive Detector Based on Charge-Coupled Devices for Recording Ions with a Portable Static Mass Spectrograph

An IDS 2030 IonCCD coordinate-sensitive detector (Analytical/CMS Field Products) is interfaced with a small-sized mass spectrograph developed at the Ioffe Physical Technical Institute, Russian Academy of Sciences. The measurement data obtained with the mass spectrograph using an IonCCD detector and a Magnum-5901-37029PS channel secondary electron multiplier (Photonics USA Inc., United States) are compared. The results of measurements are discussed, and the prospects for using the IonCCD coupled with a microchannel plate are assessed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Generalizable coordination of large multiscale workflows: challenges and learnings at scale

The advancement of machine learning techniques and the heterogeneous architectures of most current supercomputers are propelling the demand for large multiscale simulations that can automatically and autonomously couple diverse components and map them to relevant resources to solve complex problems at multiple scales. Nevertheless, despite the recent progress in workflow technologies, current capabilities are limited to coupling two scales. In the first-ever demonstration of using three scales of resolution, we present a scalable and generalizable framework that couples pairs of models using machine learning and in situ feedback. We expand upon the massively parallel Multiscale Machine-Learned Modeling Infrastructure (MuMMI), a recent, award-winning workflow, and generalize the framework beyond its original design. We discuss the challenges and learnings in executing a massive multiscale simulation campaign that utilized over 600,000 node hours on Summit and achieved more than 98% GPU occupancy for more than 83% of the time. We present innovations to enable several orders of magnitude scaling, including simultaneously coordinating 24,000 jobs, and managing several TBs of new data per day and over a billion files in total. Finally, we describe the generalizability of our framework and, with an upcoming open-source release, discuss how the presented framework may be used for new applications.

Bhatia, Harsh↗

Umpire: Application-Focused Management and Coordination of Complex Hierarchical Memory

Advanced architectures like Sierra provide a wide range of memory resources that must often be carefully controlled by the user. These resources have varying capacities, access timing rules, and visibility to different compute resources. Applications must intelligently allocate data in these spaces, and depending on the total amount of memory required, applications may also be forced to move data between different parts of the memory hierarchy. Finally, applications using multiple packages must coordinate effectively to ensure that each package can use the memory resources it needs. To address these challenges, we present Umpire, an application-oriented library for managing memory resources. Specifically, Umpire provides support for querying memory resources, provisioning and allocating memory, and memory introspection. It allows computer scientists and computational physicists to efficiently program the memory hierarchies of current and future high-performance computing architectures, without tying their application to specific hardware or software. In this paper, we describe the design and implementation of Umpire and present case studies from the integration of Umpire into applications that are currently running on Sierra.

97 MATHEMATICS AND COMPUTING↗

High-Platinum-Content Catalysts on Atomically Dispersed and Nitrogen Coordinated Single Manganese Site Carbons for Heavy-Duty Fuel Cells

Fuel cells for heavy-duty vehicles (HDVs) have attracted considerable attention because of their unique scalability, better fuel economy, the less demand for hydrogen refilling infrastructure. However, the potential application requires more stringent fuel cell durability up to 25,000 h. Membrane electrode assemblies (MEAs) made from platinum group metal (PGM) catalyst with relatively high loading 0.3 mgPt cm –2 play a crucial role in ensuring high-power and long-term durability. Integrating fine PGM nanoparticles and robust carbon support with strengthened interactions is critical for improving MEA performance and durability. Herein, a unique atomically dispersed and nitrogen coordinated single Mn site-rich carbon (M–N–C) support was developed for high content (40 wt%) platinum catalysts for the oxygen reduction reaction (ORR) cathode with reduced thickness. Compared with two controls studied in this work (e.g., a porous graphitic carbon-supported Pt and a commercial TKK Pt/C catalysts), the Pt (40 wt%)/Mn–N–C catalyst exhibited much enhanced catalytic activity and stability for the ORR in both aqueous acidic electrolyte and polymer electrolyte-based MEA. Here, we carefully elucidated the—role of the Mn–N–C support in promoting Pt catalyst concerning its high surface area, partially graphitic structure, and nitrogen dopants, providing better Pt nanoparticle dispersion, and strengthened interactions between Pt and carbon. Consequently, the MEA from the Pt (40 wt%)/Mn–N–C catalyst generated a 1.61 A cm –2 at 0.7 V based on HDV conditions (0.2 mgPt cm –2 and 250 kPa air). More importantly, the MEA is highly durable and can retain 1.31 A cm –2 at 0.7 V after 30,000 voltage cycles (~19% loss), surpassing the commercial Pt/C catalyst (loss of ~56%). Therefore, the Mn–N–C carbon-supported Pt catalyst holds a great promise to meet the challenging DOE target (1.07 A cm –2 at 0.7 V after 150,000 cycles) for HDVs.

25 ENERGY STORAGE↗

Transport of Ligand Coordinated Iron and Chromium through Cation-Exchange Membranes

Fluxes of negatively charged ligand-coordinated iron, Fe(CN) 6 3/4- , and chromium, CrPDTA 1/2− , through two promising commercial cation-exchange membranes, Aquivion E87–05S and Fumasep E-620(K), were measured as functions of current density. The magnitude of the partial current density reached a maximum of − 43 μ A cm −2 at the maximum applied current density magnitude of − 43 mA cm −2 for Fe(CN) 6 3/4− transport through Aquivion, or 0.1% of the total current density. Fumasep E-620(K) blocks practically all crossover of both compounds. Both membranes sorb more Fe(CN) 6 3/4− and CrPDTA 1/2− than predicted by Donnan equilibrium, and low crossover rates can be attributed mainly to slow diffusion, not charge-based rejection of co-ions. The magnitude of the diffusion coefficient appears to correlate with hydraulic permeability. Although Aquivion E87–05S and Fumasep E-620(K) have significant and observable differences in membrane crossover rates, cells built with the DI-soaked membranes offer similarly high coulombic efficiency, indicating the relatively small contribution that crossover makes to inefficiency over a single cycle.

25 ENERGY STORAGE↗

Genetic Background Modulates lncRNA-Coordinated Tissue Response to Low Dose Ionizing Radiation

Long noncoding RNAs (lncRNAs) are emerging as key regulators of diverse cell functions and processes. However, the relevance of lncRNAs in the cell and tissue response to ionizing radiation has not yet been characterized. Here we used microarray profiling to determine lncRNA and mRNA expression in mammary glands of BALB/c and SPRET/EiJ mice after low-dose ionizing radiation (LDIR) exposure. We found that unirradiated mammary tissues of these strains differed significantly in baseline expressions of 290 lncRNAs. LDIR exposure (10 cGy) induced a significant change in the expression of many lncRNAs. The vast majority of lncRNAs identified to be differentially expressed after LDIR in either BALB/c or SPRET/EiJ had a significantly correlated expression pattern with at least one LDIR responsive mRNA. Functional analysis revealed that the response to LDIR in BALB/c mice is highly dynamic with enrichment for genes involved in tissue injury, inflammatory responses, and mammary gland development at 2, 4, and 8 weeks after LDIR, respectively. Our study demonstrates that genetic background strongly influences the expression of lncRNAs and their response to radiation and that lncRNAs may coordinate the tissue response to LDIR exposure via regulation of coding mRNAs.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

EMC3 coordinates surfactant protein and lipid homeostasis required for respiration

Adaptation to respiration at birth is dependent upon the synthesis of pulmonary surfactant, a lipid-protein complex that reduces surface tension at the air-liquid interface in the alveoli, preventing lung collapse during the ventilatory cycle. Herein, we demonstrate that Emc3/Tmem111, the gene encoding a subunit of endoplasmic reticulum membrane complex, was required for pulmonary surfactant synthesis and lung function at birth. Conditional deletion of Emc3 in embryonic lung epithelial cells disrupted the synthesis and packaging of surfactant lipids and proteins, impaired the formation of lamellar bodies and induced the unfolded protein response in alveolar type 2 (AT2) cells. EMC3 was essential for the processing and routing of surfactant proteins, SP-B and SP-C, and the biogenesis of the phospholipid transport protein ABCA3. Transcriptomic, lipidomic, and proteomic analyses demonstrated that EMC3 coordinates the assembly of lipids and proteins in AT2 cells that are necessary for surfactant synthesis and function at birth.

Tang, Xiaofang↗

Multi-scale Analysis of Surface Heterogeneity Induced Convection on Isentropic Coordinates

This research uses semi-idealized simulations to investigate multi-scale processes induced by the heterogeneity of soil moisture observed during the 2016 Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) field campaign. The semi-idealized simulations have realistic land heterogeneity, but large-scale winds are removed. Analysis on isentropic coordinates enables the tracking of circulation that transports energy vertically and facilitates the identification of the primary convective processes induced by realistic land heterogeneity. The isentropes associated with upward motion are found to connect the ground characterized by high latent heat flux to cloud bases directly over the ground with high sensible heat flux, while isentropes associated with downward motion connect precipitation to the ground characterized by high sensible heat fluxes. The mixing of dry, warm parcels ascending from the ground with high sensible heat fluxes and moist parcels from high latent heat regions leads to cloud formation. This new mechanism explains how soil moisture heterogeneity provides the key ingredients such as buoyancy and moisture for shallow cloud formation. We also found that the sub-mesoscale dominates upward energy transport in the boundary layer, while mesoscale circulations contribute to vertical energy transport above the boundary layer. Our novel method better illustrates and elucidates the nature of land atmospheric interactions under irregular and realistic soil moisture patterns.

54 ENVIRONMENTAL SCIENCES↗

Coordinated Abrupt Weakening of the Eurasian and North African Monsoons in the 1960s and Links to Extratropical North Atlantic Cooling

Previous modeling and paleoclimate studies have suggested that cooling originating from the extratropical North Atlantic can abruptly weaken the Eurasian and North African monsoons. The climatic signature includes a widespread cooling over the Eurasian and North African continents and an associated increase to surface pressure. It is explored whether such coordinated changes are similarly exhibited in the observed twentieth-century climate, in particular with the well-documented shift of Sahel rainfall during the 1960s. Surface temperature, sea level pressure, and precipitation changes are analyzed using combined principal component analysis (CPCA). The leading mode exhibits a monotonic shift in the 1960s, and the transition is associated with a relative cooling and pressure increase over the interior Eurasia and North Africa, and rainfall reduction over the Sahel, South Asia, and East Asia. The local circulation changes suggest that the rainfall shift results from the regional response of the summer monsoons to these continental- wide changes. A similar CPCA analysis of atmospheric general circulation model (AGCM) simulations forced by twentieth-century-observed forcings shows similar results, suggesting that origins of the climate shift reside in the sea surface temperature changes, specifically over the extratropical North Atlantic. Finally, an AGCM forced with extratropical North Atlantic cooling appears to simulate these climate impacts, at least qualitatively. The result herein shows that the observed climate signature of the 1960s abrupt shift in Eurasian and North African climate is consistent with the influence of the abrupt highlatitudeNorthAtlantic cooling that occurred in the late 1960s.Adefinitive causal relationship remains to be shown, and mechanisms elucidated.

Climate change↗

An Analysis of Coordinated Observations from NOAA’s Ronald H. Brown Ship and G-IV Aircraft in a Landfalling Atmospheric River over the North Pacific during CalWater-2015

Using a diverse suite of mobile observing platforms deployed on NOAA’s Ronald H. Brown (RHB) research vessel and G-IV research aircraft during the CalWater-2015 field campaign, this study describes the structure and evolution of a long-lived atmospheric river (AR) modulated by six frontal waves over the northeastern Pacific on 20-25 January 2015. Satellite observations and reanalysis diagnostics provided synoptic-scale context, illustrating the warm, moist southwesterly airstream within the quasi-stationary AR situated between an upper-level trough and ridge. The AR remained offshore of the U.S. West Coast but made landfall across British Columbia where heavy precipitation and high melting levels occurred, resulting in flooding. Forty-seven rawinsondes launched from the RHB provided a comprehensive thermodynamic and kinematic depiction of the AR, including an upward intrusion of strong water-vapor transport in the low-level moist southwesterly flow during the passage of frontal waves 2 through 6. A collocated 1290-MHz wind profiler showed an abrupt frontal transition from southwesterly to northerly flow below 1 km MSL coinciding with the tail-end of AR conditions. Shipborne radar and disdrometer observations in the AR uniquely captured key microphysical characteristics of shallow warm rain, convection, and deep mixed-phase precipitation. Continuous and novel observations of sea-surface fluxes documented persistent ocean-surface evaporation into the AR and sensible-heat transfer from the AR into the ocean. The G-IV aircraft coordinated with the RHB and flew directly over the ship. Dropsonde and radar spatial analyses complemented the temporal depictions of the AR from the RHB. The AR characteristics varied, depending on the location of the cross section through the frontal waves.

54 ENVIRONMENTAL SCIENCES↗

Leading-process actomyosin coordinates organelle positioning and adhesion receptor dynamics in radially migrating cerebellar granule neurons

During brain development, neurons migrate from germinal zones to their final positions to assemble neural circuits. A unique saltatory cadence involving cyclical organelle movement (e.g., centrosome motility) and leading-process actomyosin enrichment prior to nucleokinesis organizes neuronal migration. While functional evidence suggests that leading-process actomyosin is essential for centrosome motility, the role of the actin-enriched leading process in globally organizing organelle transport or traction forces remains unexplored. Our results show that myosin ii motors and F-actin dynamics are required for Golgi apparatus positioning before nucleokinesis in cerebellar granule neurons (CGNs) migrating along glial fibers. Moreover, we show that primary cilia are motile organelles, localized to the leading-process F-actin-rich domain and immobilized by pharmacological inhibition of myosin ii and F-actin dynamics. Finally, leading process adhesion dynamics are dependent on myosin ii and F-actin. In conclusion, we propose that actomyosin coordinates the overall polarity of migrating CGNs by controlling asymmetric organelle positioning and cell-cell contacts as these cells move along their glial guides.

59 BASIC BIOLOGICAL SCIENCES↗

Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas

Abstract Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii , to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.

09 BIOMASS FUELS↗

Septins coordinate cell wall integrity and lipid metabolism in a sphingolipid-dependent process

ABSTRACT Septins colocalize with membrane sterol-rich regions and facilitate recruitment of cell wall synthases during wall remodeling. We show that null mutants missing an Aspergillus nidulans core septin present in hexamers and octamers (ΔaspAcdc11, ΔaspBcdc3 or ΔaspCcdc12) are sensitive to multiple cell wall-disturbing agents that activate the cell wall integrity MAPK pathway. The null mutant missing the octamer-exclusive core septin (ΔaspDcdc10) showed similar sensitivity, but only to a single cell wall-disturbing agent and the null mutant missing the noncore septin (ΔaspE) showed only very mild sensitivity to a different single agent. Core septin mutants showed changes in wall polysaccharide composition and chitin synthase localization. Mutants missing any of the five septins resisted ergosterol-disrupting agents. Hexamer mutants showed increased sensitivity to sphingolipid-disrupting agents. Core septins mislocalized after treatment with sphingolipid-disrupting agents, but not after ergosterol-disrupting agents. Our data suggest that the core septins are involved in cell wall integrity signaling, that all five septins are involved in monitoring ergosterol metabolism, that the hexamer septins are required for sphingolipid metabolism and that septins require sphingolipids to coordinate the cell wall integrity response.

59 BASIC BIOLOGICAL SCIENCES↗

Δ133p53 coordinates ECM-driven morphogenesis and gene expression in 3-dimensional mammary epithelial acini

Growing evidence indicates that p53 has a crucial role in normal tissue development. The role of the canonical p53 (p53α) and its 12± isoforms in development and homeostasis of healthy tissue remains poorly understood. Here we demonstrate that Δ133p53, three short isoforms of p53 isoform, responds specifically to laminin-111 and plays an important regulatory role in formation of mammary organoids in concert with p53α. We demonstrate that down-modulation of Δ133p53 isoforms leads to changes in gene expression of extracellular matrix molecules: fibronectin (FN), EDA+-FN, laminin α5, and laminin α3 in human breast epithelial cells. These changes resulted in increased actin stress fibers and enhanced migratory behavior of cells in 2-dimensional culture. We found that α5β1-integrin coupled with the extracellularly deposited EDA+-FN activates Akt signaling pathway in 3-dimensional (3D) culture when Δ133p53 is dysregulated. Cells that do not express detectable Δ133p53 isoforms or express low levels of these isoforms failed to form polarized structures in 3D. These results uncover that Δ133p53 isoforms coordinate expression and deposition of organ-specific ECM molecules that are critical for maintenance of tissue architecture and function.

Lee, Sun-Young (ORCID:000000034970241X)↗

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

Coordination of the Ser2056 and Thr2609 Clusters of DNA-PKcs in Regulating Gamma Rays and Extremely Low Fluencies of Alpha-Particle Irradiation to G 0 /G 1 Phase Cells

The catalytic subunit of DNA dependent protein kinase (DNA-PKcs) and its kinase activity are critical for mediation of non-homologous end-joining (NHEJ) of DNA double-strand breaks (DSB) in mammalian cells after gamma-ray irradiation. Additionally, DNA-PKcs phosphorylations at the T2609 cluster and the S2056 cluster also affect DSB repair and cellular sensitivity to gamma radiation. Previously we reported that phosphorylations within these two regions affect not only NHEJ but also homologous recombination repair (HRR) dependent DSB repair. In this study, we further examine phenotypic effects on cells bearing various combinations of mutations within either or both regions. Effects studied included cell killing as well as chromosomal aberration induction after 0.5–8 Gy gamma-ray irradiation delivered to synchronized cells during the G0/G1 phase of the cell cycle. Blocking phosphorylation within the T2609 cluster was most critical regarding sensitization and depended on the number of available phosphorylation sites. It was also especially interesting that only one substitution of alanine in each of the two clusters separately abolished the restoration of wild-type sensitivity by DNA-PKcs. Similar patterns were seen for induction of chromosomal aberrations, reflecting their connection to cell killing. To study possible change in coordination between HRR and NHEJ directed repair in these DNA-PKcs mutant cell lines, we compared the induction of sister chromatid exchanges (SCEs) by very low fluencies of alpha particles with mutant cells defective in the HRR pathway that is required for induction of SCEs. Finally, levels of true SCEs induced by very low fluence of alpha-particle irradiation normally seen in wild-type cells were only slightly decreased in the S2056 cluster mutants, but were completely abolished in the T2609 cluster mutants and were indistinguishable from levels seen in HRR deficient cells. Again, a single substitution in the S2056 together with a single substitution in the T2609 cluster abolished SCE formation and thus also effectively interferes with HRR.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis of Allison Scanner Phase Portraits Using Action-Phase Coordinates

Allison scanners provide detailed information on the beam transverse phase space. An effective way for analyzing the beam distribution from these measurements is to use action-phase coordinates, where beam propagation in a linear lattice is reduced to advancing the phase. This report presents such analysis for measurements performed with a 2.1 MeV, 5 mA H⁻ beam in the MEBT of the PIP2IT test accelerator at Fermilab. In part, with the choice of calculating the Twiss parameters over the high intensity portion of the beam, the beam core is found to be phase-independent with intensity decreasing exponentially with action, while the beam tails exhibit a clear phase dependence that is stable over the beam line.

43 PARTICLE ACCELERATORS↗