The DOE E3SM Coupled Model Version 1: Overview and Evaluation at Standard Resolution

This work documents the first version of the U.S. Department of Energy (DOE) new Energy Exascale Earth System Model (E3SMv1). We focus on the standard resolution of the fully coupled physical model designed to address DOE mission-relevant water cycle questions. Its components include atmosphere and land (110-km grid spacing), ocean and sea ice (60 km in the midlatitudes and 30 km at the equator and poles), and river transport (55 km) models. This base configuration will also serve as a foundation for additional configurations exploring higher horizontal resolution as well as augmented capabilities in the form of biogeochemistry and cryosphere configurations. The performance of E3SMv1 is evaluated by means of a standard set of Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima simulations consisting of a long preindustrial control, historical simulations (ensembles of fully coupled and prescribed SSTs) as well as idealized CO2 forcing simulations. The model performs well overall with biases typical of other CMIP-class models, although the simulated Atlantic Meridional Overturning Circulation is weaker than many CMIP-class models. While the E3SMv1 historical ensemble captures the bulk of the observed warming between preindustrial (1850) and present day, the trajectory of the warming diverges from observations in the second half of the twentieth century with a period of delayed warming followed by an excessive warming trend. Using a two-layer energy balance model, we attribute this divergence to the model’s strong aerosol-related effective radiative forcing (ERFari+aci = -1.65 W/m2) and high equilibrium climate sensitivity (ECS = 5.3 K).Plain Language SummaryThe U.S. Department of Energy funded the development of a new state-of-the-art Earth system model for research and applications relevant to its mission. The Energy Exascale Earth System Model version 1 (E3SMv1) consists of five interacting components for the global atmosphere, land surface, ocean, sea ice, and rivers. Three of these components (ocean, sea ice, and river) are new and have not been coupled into an Earth system model previously. The atmosphere and land surface components were created by extending existing components part of the Community Earth System Model, Version 1. E3SMv1’s capabilities are demonstrated by performing a set of standardized simulation experiments described by the Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima protocol at standard horizontal spatial resolution of approximately 1° latitude and longitude. The model reproduces global and regional climate features well compared to observations. Simulated warming between 1850 and 2015 matches observations, but the model is too cold by about 0.5 °C between 1960 and 1990 and later warms at a rate greater than observed. A thermodynamic analysis of the model’s response to greenhouse gas and aerosol radiative affects may explain the reasons for the discrepancy.Key PointsThis work documents E3SMv1, the first version of the U.S. DOE Energy Exascale Earth System ModelThe performance of E3SMv1 is documented with a set of standard CMIP6 DECK and historical simulations comprising nearly 3,000 yearsE3SMv1 has a high equilibrium climate sensitivity (5.3 K) and strong aerosol-related effective radiative forcing (-1.65 W/m2)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151288/1/jame20860_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151288/2/jame20860.pd

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Reduced-order representation of stratified wakes by proper orthogonal decomposition utilizing translational symmetry

Visualizations of reduced-order representations of stratified wakes of Reynolds number Re∈{5,25,100}×103 are presented at a fixed internal Froude number. The reduced-order representations are constructed by applying proper orthogonal decomposition (POD) to numerical datasets that are high-resolution, three-dimensional and time-dependent. Due to the transient nature of the flow, the dynamics to be represented are highly non-stationary, posing a challenge for the effectiveness of POD. The translational symmetry inherent in the computational configuration is utilized for the POD analysis. This technique turns out to be effective in terms of improving the convergence of energy content represented by the POD modes and enhancing the interpretability of the temporal dynamics. Individual POD modes representing distinct dynamics of various scales are visualized. In the turbulent region, visualizations of the reconstructed vertical vorticity fields suggest that the dominant length scale of flow structures decreases with the modal index. For internal wave motions, visualizations of the reconstructed vertical velocity fields show the opposite trend, as the wavelength of internal waves observed in the wake’s ambient increases with the modal index. The temporal coefficients for a given mode are observed to vary minimally between Re=2.5×104 and 105, suggesting a potential asymptote of the large-scale temporal dynamics in terms of Reynolds number.Natural Sciences and Engineering Research Council (NSERC

Pore formation study in porous nanocrystalline silicon membrane

Thesis (Ph. D.)--University of Rochester. Materials Science Program, 2014Porous nanocrystalline silicon (pnc-Si) membrane is a new class of materials that is promising for a wide range of applications from biofiltration to cell culture substrate. Nano-size pores are spontaneously formed in a silicon film sandwiched between two silicon dioxide layers during rapid thermal annealing. Previous research has shown that pore formation in the pnc-Si membrane is thermally driven and closely connected to silicon crystallization, however, the process by which pore are formed is still not well understood. In this thesis, the fabrication and characterization process of pnc-Si membranes is first introduced to understand their basic structure and properties, followed next by a study on the effects silicon dioxide capping films have on pore formation. The results show that both the top and bottom silicon dioxide films are essential to pore formation in pnc-Si membranes. The top oxide layer prevents the silicon film from agglomerating while the bottom oxide layer acts as a barrier layer to prevent homoepitaxy of the silicon film during annealing. To study the effects of capping materials on pore formation, silicon nitride, is incorporated into the sandwich structure to replace the capping silicon dioxide layers. From this study, it was found for the first time that nanopores can still be formed in silicon films sandwiched between two silicon nitride layers during rapid thermal annealing. Pore formation in these new silicon nitride capped structures is then discussed, along with the resulting pore characteristics. In the final part of this thesis, ex-situ and in-situ annealing studies of pore formation in pnc-Si membranes are discussed. The ex-situ study shows that both the silicon crystallization and associated pore formation are enhanced in the silicon film in the nitride/silicon/nitride (NSN) stack compared to that in the oxide/silicon/oxide (OSO) stack. The in-situ heating studies demonstrate that pore growth in the NSN stack follows a pearl-necklace pattern while no clear pattern is observed from the OSO stack. The energy-dispersive X-ray spectroscopy (EDS) study shows that Ar atoms embedded during sputtering move together, forming Ar bubbles to occupy the porous areas in the silicon film during the heating process. These Ar bubbles are held in the pores of the silicon film when silicon nitride is used to cap the membrane, but when silicon dioxide is used as the capping layer the Ar diffuses out of the structure. This may lead to the different pore growth patterns between the NSN and OSO stacks. Finally, pore formation process can be understood in two stages which are void nucleation and pore growth. Nano-voids are nucleated in the silicon film near interface with the oxide or nitride layer, and grow in both the vertical and lateral directions during crystallization process. This process is attributed to the diffusion of silicon atoms during the transition from amorphous silicon to nanocrystalline silicon. These voids become through pores when their growth spans the entire silicon film in the vertical direction. The pore growth is strongly affected by the silicon thickness, temperature ramp rate and capping layers

Identifying Intimacy of Self-Disclosure: A Design Based on Social Penetration Theory and Deep Learning

Research on the peer-to-peer (P2P) platforms, privacy, and digitalized business environment has overwhelmingly treated the intimacy of self-disclosure as a survey-based, subjective, and cognitive construct. A few studies have conducted topic analysis using objective data, but are still limited by the difficulty of capturing the degree of intimacy, which hinders the development of the transaction antecedents of P2P platforms. Building upon social penetration theory, we propose an innovative approach to identifying the intimacy of self-disclosure using a deep learning algorithm and an expert-compiled intimacy corpus in the context of P2P platforms. Adopting a sample dataset of 10,000 hosts’ self-descriptions in Airbnb, we introduce the computational and verification process of operationalizing the intimacy of self-disclosure. Through an empirical study, we demonstrate the theoretical feasibility of our quantification method of intimacy and show the potential of using deep learning to measure self-disclosure, expanding the theoretical development of social penetration theory and self-disclosure

Effects of Seasonal Ice Coverage on the Physical Oceanographic Conditions of the Kitikmeot Sea in the Canadian Arctic Archipelago

The Kitikmeot Sea is a semi-enclosed, east–west waterway in the southern Canadian Arctic Archipelago (CAA). In the present work, the ice conditions, stratification, and circulation of the Kitikmeot Sea are diagnosed using numerical simulations with a 1/12° resolution. The physical oceanographic conditions of the Kitikmeot Sea are different from channels in the northern CAA due to the existence of a substantial ice-free period each year. The consequences of such ice conditions are twofold. First, through fluctuations of external forcings, such as solar radiation and wind stress, acting directly or indirectly on the sea surface, the seasonal ice coverage leads to significant seasonal variations in both stratification and circulation. Our simulation results suggest that such variations include freshening and deepening of the surface layer, in which salinity can reach as low as 15 during the peak runoff season, and significantly stronger along-shore currents driven directly by the wind stress during the ice-free season. The second consequence is that the sea ice is not landfast but can move freely during the melting season. By analyzing the relative importance of thermodynamic (freezing and/or melting) and dynamic (ice movement) processes to the ice dynamics, our simulation results suggest that there is a net inflow of sea ice into the Kitikmeot Sea, which melts locally each summer. The movement of sea ice thus provides a significant freshwater pathway, which contributes approximately 14 km3 yr−1 of fresh water to the Kitikmeot Sea, on average, equivalent to a third of freshwater input from runoff from the land

Influence of silicon dioxide capping layers on pore characteristics in nanocrystalline silicon membranes

Abstract Porous nanocrystalline silicon (pnc-Si) membranes are a new class of membrane material with promising applications in biological separations. Pores are formed in a silicon film sandwiched between nm thick silicon dioxide layers during rapid thermal annealing. Controlling pore size is critical in the size-dependent separation applications. In this work, we systematically studied the influence of the silicon dioxide capping layers on pnc-Si membranes. Even a single nm thick top oxide layer is enough to switch from agglomeration to pore formation after annealing. Both the pore size and porosity increase with the thickness of the top oxide, but quickly reach a plateau after 10 nm of oxide. The bottom oxide layer acts as a barrier layer to prevent the a-Si film from undergoing homo-epitaxial growth during annealing. Both the pore size and porosity decrease as the thickness of the bottom oxide layer increases to 100 nm. The decrease of the pore size and porosity is correlated with the increased roughness of the bottom oxide layer, which hinders nanocrystal nucleation and nanopore formation