Short‐term time step convergence in a climate model

This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities.Key Points:Convergence is slow in CAM5Stratiform cloud parameterizations have large errorsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111268/1/jame20146.pd

Multimodality imaging: Bird’s eye view from The European Society of Cardiology Congress 2015 London, August 29-September 2, 2015

Cardiolog

DCMIP2016: a review of non-hydrostatic dynamical core design and intercomparison of participating models

Atmospheric dynamical cores are a fundamental component of global atmospheric modeling systems and are responsible for capturing the dynamical behavior of the Earth's atmosphere via numerical integration of the Navier-Stokes equations. These systems have existed in one form or another for over half of a century, with the earliest discretizations having now evolved into a complex ecosystem of algorithms and computational strategies. In essence, no two dynamical cores are alike, and their individual successes suggest that no perfect model exists. To better understand modern dynamical cores, this paper aims to provide a comprehensive review of 11 non-hydrostatic dynamical cores, drawn from modeling centers and groups that participated in the 2016 Dynamical Core Model Intercomparison Project (DCMIP) workshop and summer school. This review includes a choice of model grid, variable placement, vertical coordinate, prognostic equations, temporal discretization, and the diffusion, stabilization, filters, and fixers employed by each syste

Hurricanes and Climate: the U.S. CLIVAR Working Group on Hurricanes

While a quantitative climate theory of tropical cyclone formation remains elusive, considerable progress has been made recently in our ability to simulate tropical cyclone climatologies and understand the relationship between climate and tropical cyclone formation. Climate models are now able to simulate a realistic rate of global tropical cyclone formation, although simulation of the Atlantic tropical cyclone climatology remains challenging unless horizontal resolutions finer than 50 km are employed. The idealized experiments of the Hurricane Working Group of U.S. CLIVAR, combined with results from other model simulations, have suggested relationships between tropical cyclone formation rates and climate variables such as mid-tropospheric vertical velocity. Systematic differences are shown between experiments in which only sea surface temperature is increases versus experiments where only atmospheric carbon dioxide is increased, with the carbon dioxide experiments more likely to demonstrate a decrease in numbers. Further experiments are proposed that may improve our understanding of the relationship between climate and tropical cyclone formation, including experiments with two-way interaction between the ocean and the atmosphere and variations in atmospheric aerosols

A New Fluorescence-Based Method Identifies Protein Phosphatases Regulating Lipid Droplet Metabolism

In virtually every cell, neutral lipids are stored in cytoplasmic structures called lipid droplets (LDs) and also referred to as lipid bodies or lipid particles. We developed a rapid high-throughput assay based on the recovery of quenched BODIPY-fluorescence that allows to quantify lipid droplets. The method was validated by monitoring lipid droplet turnover during growth of a yeast culture and by screening a group of strains deleted in genes known to be involved in lipid metabolism. In both tests, the fluorimetric assay showed high sensitivity and good agreement with previously reported data using microscopy. We used this method for high-throughput identification of protein phosphatases involved in lipid droplet metabolism. From 65 yeast knockout strains encoding protein phosphatases and its regulatory subunits, 13 strains revealed to have abnormal levels of lipid droplets, 10 of them having high lipid droplet content. Strains deleted for type I protein phosphatases and related regulators (ppz2, gac1, bni4), type 2A phosphatase and its related regulator (pph21 and sap185), type 2C protein phosphatases (ptc1, ptc4, ptc7) and dual phosphatases (pps1, msg5) were catalogued as high-lipid droplet content strains. Only reg1, a targeting subunit of the type 1 phosphatase Glc7p, and members of the nutrient-sensitive TOR pathway (sit4 and the regulatory subunit sap190) were catalogued as low-lipid droplet content strains, which were studied further. We show that Snf1, the homologue of the mammalian AMP-activated kinase, is constitutively phosphorylated (hyperactive) in sit4 and sap190 strains leading to a reduction of acetyl-CoA carboxylase activity. In conclusion, our fast and highly sensitive method permitted us to catalogue protein phosphatases involved in the regulation of LD metabolism and present evidence indicating that the TOR pathway and the SNF1/AMPK pathway are connected through the Sit4p-Sap190p pair in the control of lipid droplet biogenesis

Plasma–liquid interactions: a review and roadmap

Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas

DCMIP2016: the tropical cyclone test case

This paper describes and analyzes the Reed–Jablonowski (RJ) tropical cyclone (TC) test case used in the 2016 Dynamical Core Model Intercomparison Project (DCMIP2016). This intermediate-complexity test case analyzes the evolution of a weak vortex into a TC in an idealized tropical environment. Reference solutions from nine general circulation models (GCMs) with identical simplified physics parameterization packages that participated in DCMIP2016 are analyzed in this study at 50 km horizontal grid spacing, with five of these models also providing solutions at 25 km grid spacing. Evolution of minimum surface pressure (MSP) and maximum 1 km azimuthally averaged wind speed (MWS), the wind–pressure relationship, radial profiles of wind speed and surface pressure, and wind composites are presented for all participating GCMs at both horizontal grid spacings. While all TCs undergo a similar evolution process, some reach significantly higher intensities than others, ultimately impacting their horizontal and vertical structures. TCs simulated at 25 km grid spacings retain these differences but reach higher intensities and are more compact than their 50 km counterparts. These results indicate that dynamical core choice is an essential factor in GCM development, and future work should be conducted to explore how specific differences within the dynamical core affect TC behavior in GCMs.</p

DCMIP2016: the splitting supercell test case

This paper describes the splitting supercell idealized test case used in the 2016 Dynamical Core Model Intercomparison Project (DCMIP2016). These storms are useful test beds for global atmospheric models because the horizontal scale of convective plumes is O(1&thinsp;km), emphasizing non-hydrostatic dynamics. The test case simulates a supercell on a reduced-radius sphere with nominal resolutions ranging from 4 to 0.5&thinsp;km and is based on the work of Klemp et al. (2015). Models are initialized with an atmospheric environment conducive to supercell formation and forced with a small thermal perturbation. A simplified Kessler microphysics scheme is coupled to the dynamical core to represent moist processes. Reference solutions for DCMIP2016 models are presented. Storm evolution is broadly similar between models, although differences in the final solution exist. These differences are hypothesized to result from different numerical discretizations, physics–dynamics coupling, and numerical diffusion. Intramodel solutions generally converge as models approach 0.5&thinsp;km resolution, although exploratory simulations at 0.25&thinsp;km imply some dynamical cores require more refinement to fully converge. These results can be used as a reference for future dynamical core evaluation, particularly with the development of non-hydrostatic global models intended to be used in convective-permitting regimes.</p

Defects in tRNA Modification Associated with Neurological and Developmental Dysfunctions in Caenorhabditis elegans Elongator Mutants

Elongator is a six subunit protein complex, conserved from yeast to humans. Mutations in the human Elongator homologue, hELP1, are associated with the neurological disease familial dysautonomia. However, how Elongator functions in metazoans, and how the human mutations affect neural functions is incompletely understood. Here we show that in Caenorhabditis elegans, ELPC-1 and ELPC-3, components of the Elongator complex, are required for the formation of the 5-carbamoylmethyl and 5-methylcarboxymethyl side chains of wobble uridines in tRNA. The lack of these modifications leads to defects in translation in C. elegans. ELPC-1::GFP and ELPC-3::GFP reporters are strongly expressed in a subset of chemosensory neurons required for salt chemotaxis learning. elpc-1 or elpc-3 gene inactivation causes a defect in this process, associated with a posttranscriptional reduction of neuropeptide and a decreased accumulation of acetylcholine in the synaptic cleft. elpc-1 and elpc-3 mutations are synthetic lethal together with those in tuc-1, which is required for thiolation of tRNAs having the 5′methylcarboxymethyl side chain. elpc-1; tuc-1 and elpc-3; tuc-1 double mutants display developmental defects. Our results suggest that, by its effect on tRNA modification, Elongator promotes both neural function and development