Formulation structure of the mass-flux convection parameterization

AbstractStructure of the mass-flux convection parameterization formulation is re-examined. Many of the equations associated with this formulation are derived in systematic manner with various intermediate steps explicitly presented. The nonhydrostatic anelastic model (NAM) is taken as a starting point of all the derivations.Segmentally constant approximation (SCA) is a basic geometrical constraint imposed on a full system (e.g., NAM) as a first step for deriving the mass-flux formulation. The standard mass-flux convection parameterization, as originally formulated by Ooyama, Fraedrich, Arakawa and Schubert, is re-derived under the two additional hypotheses concerning entrainment–detrainment and environment, and an asymptotic limit of vanishing areas occupied by convection.A model derived at each step of the deduction constitutes a stand-alone subgrid-scale representation by itself, leading to a hierarchy of subgrid-scale schemes. A backward tracing of this deduction process provides paths for generalizing mass-flux convection parameterization. Issues of the high-resolution limit for parameterization are also understood as those of relaxing various traditional constraints. The generalization presented herein can include various other subgrid-scale processes under a mass-flux framework

Why does Arakawa and Schubert's convective quasi-equilibrium closure not work? Mathematical analysis and implications

Arakawa and Schubert (1974) proposed convective quasi-equilibrium as a guiding principle for the closure of convection parameterization. However, empirical experiences from operational implementation efforts suggest that its strict application does not work well. The purpose of the present paper is to explain mathematically why this closure does not work in practice, and to suggest that problems stem from physically unrealistic assumptions. For this purpose, the closure hypothesis is examined in its original form, and without imposing a condition of a positiveness to the convective mass fluxes. The Jordan sounding with idealized large-scale forcing is used for diagnosis purposes. The question is addressed from several perspectives including the completeness of the entraining plume spectrum, and a singular vector decomposition of the interaction kernel matrix. The main problems with the quasi–equilibrium closure are traced to: (i) the relatively slow response of shallower convective modes to large-scale forcing; and, (ii) detrainment at convection top producing strong cooling and moistening. A strict application of the convective quasi-equilibrium principle leads to a singular response of shallow convection. An explicit coupling of convection with stratiform clouds would be crucial for preventing this unrealistic behavior, recognizing that the re-evaporation of detrained cloudy-air is a relatively slow process

Dynamics of the outer planets : 1992 Summer Study Program in Geophysical Fluid Dynamics

The topic this summer was "The Dynamics of the Outer Planets." Andrew Ingersoll gave an excellent review of the current understanding of the strcture of the atmospheres of Jupiter, Neptune, Saturn, and Uranus. He presented the flow structures inferred from the information gathered by the Voyager probes and other observations. The models of the circulations of the interior and of the weather layer - the jets and vortices that we see in the images - were discussed. Jun-Ichi Yano gave further discussions on vortex dynamics in the lab, analytical, and numerical models as applied to the outer planets. Finally, Andy returned with a discussion of thin atmospheres (some so thin that they disappear at night) and new approaches to the dynamics of the interiors. These lectures provided a thorough background in both the data and the theory. As usual, we had talks (or what are sometimes called interactive seminars!) from many visitors during the summer, some directly related to the main topic and others covering other new research in geophysical fluid dynamics. From these, the fellows and staff found new aras for collaborative research and new ideas which they may explore after the summer. Finally, the summer was completed with talks from the fellows on their individual research during the summer. These reports reflect the thought and energy that went into learning new topics and formulating new problems. We look forward to seeing fuller versions of these in journal articles. We gratefully acknowledge the support of the National Science Foundation and the Office of Naval Research. The assistance of Jake Peirson and Barbara Ewing-DeRemer, made the summer, once again, pleasant and easy for all.Funding was provided by the National Science Foundation under Grant No. OCE8901012

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

<p>Abstract</p> <p>Background</p> <p>To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.</p> <p>Results</p> <p>The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity</p> <p>Conclusions</p> <p>Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.</p

Interactions between shallow and deep convection under a finite departure from convective quasi–equilibrium

The present paper presents a simple theory for the transformation of non-precipitating, shallow convection into precipitating, deep convective clouds. In order to make the pertinent point a much idealized system is considered, consisting only of shallow and deep convection without large–scale forcing. The transformation is described by an explicit coupling between these two types of convection. Shallow convection moistens and cools the atmosphere, whereas deep convection dries and warms, leading to destabilization and stabilization respectively. Consequently, in their own stand–alone modes, shallow convection perpetually grows, whereas deep convection simply damps: the former never reaches equilibrium, and the latter is never spontaneously generated. Coupling the modes together is the only way to reconcile these undesirable separate tendencies so that the convective system as a whole can remain in a stable periodic state under this idealized setting. Such coupling is a key missing element in current global atmospheric models. The energy–cycle description as originally formulated by Arakawa and Schubert, and presented herein is suitable for direct implementation into models using a mass–flux parameterization, and would alleviate the current problems with the representation of these two types of convection in numerical models. The present theory also provides a pertinent framework for analyzing large–eddy simulations and cloud–resolving modelling

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars

BACKGROUND: High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield. RESULTS: An informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta. CONCLUSIONS: Introgression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-346) contains supplementary material, which is available to authorized users

Basic concepts for convection parameterization in weather forecast and climate models: COST Action ES0905 final report

The research network “Basic Concepts for Convection Parameterization in Weather Forecast and Climate Models” was organized with European funding (COST Action ES0905) for the period of 2010–2014. Its extensive brainstorming suggests how the subgrid-scale parameterization problem in atmospheric modeling, especially for convection, can be examined and developed from the point of view of a robust theoretical basis. Our main cautions are current emphasis on massive observational data analyses and process studies. The closure and the entrainment–detrainment problems are identified as the two highest priorities for convection parameterization under the mass–flux formulation. The need for a drastic change of the current European research culture as concerns policies and funding in order not to further deplete the visions of the European researchers focusing on those basic issues is emphasized