1,108 research outputs found
Turbulence and modeling in transonic flow
A review is made of the performance of a variety of turbulence models in the evaluation of a particular well documented transonic flow. This is done to supplement a previous attempt to calibrate and verify transonic airfoil codes by including many more turbulence models than used in the earlier work and applying the calculations to an experiment that did not suffer from uncertainties in angle of attack and was free of wind tunnel interference. It is found from this work, as well as in the earlier study, that the Johnson-King turbulence model is superior for transonic flows over simple aerodynamic surfaces, including moderate separation. It is also shown that some field equation models with wall function boundary conditions can be competitive with it
On the validation of a code and a turbulence model appropriate to circulation control airfoils
A computer code for calculating flow about a circulation control airfoil within a wind tunnel test section has been developed. This code is being validated for eventual use as an aid to design such airfoils. The concept of code validation being used is explained. The initial stages of the process have been accomplished. The present code has been applied to a low-subsonic, 2-D flow about a circulation control airfoil for which extensive data exist. Two basic turbulence models and variants thereof have been successfully introduced into the algorithm, the Baldwin-Lomax algebraic and the Jones-Launder two-equation models of turbulence. The variants include adding a history of the jet development for the algebraic model and adding streamwise curvature effects for both models. Numerical difficulties and difficulties in the validation process are discussed. Turbulence model and code improvements to proceed with the validation process are also discussed
Navier-Stokes calculations and turbulence modeling in the trailing edge region of a circulation control airfoil
The accurate prediction of turbulent flows over curved surfaces in general and over the trailing edge region of circulation control airfoils in particular requires the coupled efforts of turbulence modelers, numerical analysts and experimentalists. The purpose of the research program in this area is described. Then, the influence on turbulence modeling of the flow characteristics over a typical circulation control wing is discussed. Next, the scope of this effort to study turbulence in the trailing edge region of a circulation control airfoil is presented. This is followed by a brief overview of the computation scheme, including the grid, governing equations, numerical method, boundary conditions and turbulence models applied to date. Then, examples of applications of two algebraic eddy viscosity models to the trailing edge region of a circulation control airfoil is presented. The results from the calculations is summarized, and conclusions drawn based on examples. Finally, the future directions of the program is outlined
Test code for the assessment and improvement of Reynolds stress models
An existing two-dimensional, compressible flow, Navier-Stokes computer code, containing a full Reynolds stress turbulence model, was adapted for use as a test bed for assessing and improving turbulence models based on turbulence simulation experiments. To date, the results of using the code in comparison with simulated channel flow and over an oscillating flat plate have shown that the turbulence model used in the code needs improvement for these flows. It is also shown that direct simulation of turbulent flows over a range of Reynolds numbers are needed to guide subsequent improvement of turbulence models
An assessment and application of turbulence models for hypersonic flows
The current approach to the Accurate Computation of Complex high-speed flows is to solve the Reynolds averaged Navier-Stokes equations using finite difference methods. An integral part of this approach consists of development and applications of mathematical turbulence models which are necessary in predicting the aerothermodynamic loads on the vehicle and the performance of the propulsion plant. Computations of several high speed turbulent flows using various turbulence models are described and the models are evaluated by comparing computations with the results of experimental measurements. The cases investigated include flows over insulated and cooled flat plates with Mach numbers ranging from 2 to 8 and wall temperature ratios ranging from 0.2 to 1.0. The turbulence models investigated include zero-equation, two-equation, and Reynolds-stress transport models
rRNA gene activity and control of expression mediated by methylation and imprinting during embryo development in wheat x rye hybrids
Ribosomal RNA genes originating from one
parent are often suppressed in interspecific hybrids. We
show that treatments during germination with the
cytosine analogue 5-azacytidine stably reactivate the
expression of the suppressed rRNA genes of rye origin in
the wheat x rye amphiploid, triticale, by preventing
methylation of sites in the rye rDNA. When 5-azacytidine
is applied to embryos of triticale and
wheat x rye F1 hybrids nine, or more, days after fertilization,
rye rRNA gene expression is stably reactivated in
the resulting seedling. Earlier treatments have no effect
on rye rRNA gene expression, indicating that undermethylation
of DNA early in embryo development is
reversible. After 9 days, the methylation status of rRNA
genes in maintained throughout development. Since the
change in expression follows a methylation change at
particular restriction-enzyme sites, the data establish a
clear correlation between gene activity and methylation
in plants
Retrotransposons represent the most labile fraction for genomic rearrangements in polyploid plant species
Understanding how increased genome size and diversity
within polyploid genomes impacts plant evolution and
breeding continues to be challenging. Although historical
studies by McClintock suggested the importance of transposable
elements mediated by polyploidisation on genomic
changes, data from plant crosses remain scarce. Despite the
absence of a conclusive proof regarding autonomous retrotransposon
movement in synthetic allopolyploids, the
transposition of retrotransposons and their ubiquitous dispersion
in all plant species might explain the positive correlation
between the genome size of plants and the prevalence
of retrotransposons. Here, we address polyploidisationmediated
rearrangements of retrotransposon-associated sequences
and discuss a tendency for a preferential restructuring
of large ancestral genomes after polyploidisation. A
comparative analysis of the frequency of modifications of
retrotransposon-associated sequences in synthetic polyploids
with marked differences in genome sizes is presented.
Such analyses suggest the absence of a significant difference
in the rates of rearrangements despite vast dissimilarities in
the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See
also the sister article focusing on animals by Arkhipova and
Rodriguez in this themed issu
Unravelling genome dynamics in Arabidopsis synthetic auto and allopolyploid species
Polyploidization is a major genome modification that results in plant species with multiple chromosome sets. Parental
genome adjustment to co-habit a new nuclear environment results in additional innovation outcomes. We intended to
assess genomic changes in polyploid model species with small genomes using inter retrotransposons amplified
polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP). Comparative analysis
among diploid and autotetraploid A. thaliana and A. suecica lines with their parental lines revealed a marginal fraction
of novel bands in both polyploids, and a vast loss of parental bands in allopolyploids. Sequence analysis of some
remodelled bands shows that A. suecica parental band losses resulted mainly from sequence changes restricted to primer
domains. Moreover, in A. suecica, both parental genomes presented rearrangement frequencies proportional to their
sizes. Overall rates of genomic remodelling events detected in A. suecica were similar to those observed in species with
a large genome supporting the role of retrotransposons and microsatellite sequences in the evolution of most
allopolyploidsAcknowledgements: M. Bento was funded by a FCT (Fundação para a Ciência e a Tecnologia, Portugal) postdoctoral grant
(SFRH/BPD/80550/2011), Diana Tomás was funded by a FCT doctoral scholarship (SFRH/BD/93156/2013), Manuela Silva by the
FCT Investigator Programme (IF/00834/2014), and the research work was financed by FCT LEAF Unit (UID/AGR/04129/2013)
Size matters in Triticeae polyploids: larger genomes have higher remodeling
ReviewPolyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and
diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and
species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus
and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid
species are excellent models to study polyploids evolution, particularly the wheat–rye hybrid triticale, which includes
various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid
and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals
high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the
appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence
type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and
affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome
size homogenization, diploidization establishment, and stabilization of polyploid species is discussed
Differential effects of high-temperature stress on nuclear topology and transcription of repetitive noncoding and coding rye sequences
The plant stress response has been extensively characterized
at the biochemical and physiological levels. However, knowledge
concerning repetitive sequence genome fraction modulation
during extreme temperature conditions is scarce. We
studied high-temperature effects on subtelomeric repetitive
sequences (pSc200) and 45S rDNA in rye seedlings submitted
to 40 ° C during 4 h. Chromatin organization patterns were
evaluated through fluorescent in situ hybridization and transcription
levels were assessed using quantitative real-time
PCR. Additionally, the nucleolar dynamics were evaluated
through fibrillarin immunodetection in interphase nuclei.
The results obtained clearly demonstrated that the pSc200
sequence organization is not affected by high-temperature
stress (HTS) and proved for the first time that this noncoding
subtelomeric sequence is stably transcribed. Conversely, it
was demonstrated that HTS treatment induces marked rDNA
chromatin decondensation along with nucleolar enlargement
and a significant increase in ribosomal gene transcription.
The role of noncoding and coding repetitive rye sequences
in the plant stress response that are suggested by
their clearly distinct behaviors is discussed. While the hetero-chromatic conformation of pSc200 sequences seems to be
involved in the stabilization of the interphase chromatin architecture
under stress conditions, the dynamic modulation
of nucleolar and rDNA topology and transcription suggest
their role in plant stress response pathway
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