Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Effects of flow-geometry and Damkohler number on turbulence-flame interaction

DNS of turbulent hydrogen-air premixed flame is conducted for freely propagating and V-flames, using complex chemical kinetics. The results are analysed to study the influence of flame configuration on the turbulence-scalar interaction, which is critical for the scalar gradient generation process. The result suggests that this interaction process is not influenced by the flame configuration and the flame normal is found to predominantly align with the most extensive strain in the region of intense heat release.

Effect of flow-geometry on turbulence-scalar interaction in premixed flames

Turbulent combustion of stoichiometric hydrogen-air mixture is simulated using direct numerical simulation methodology, employing complex chemical kinetics. Two flame configurations, freely propagating and V-flames stabilized behind a hot rod, are simulated. The results are analyzed to study the influence of flame configuration on the turbulence-scalar interaction, which is critical for the scalar gradient generation processes. The result suggests that this interaction process is not influenced by the flame configuration and the flame normal is found to align with the most extensive strain in the region of intense heat release. The combustion in the rod stabilized flame is found to be flamelet like in an average sense and the growth of flame-brush thickness with the downstream distance is represented well by Taylor theory of turbulent diffusion, when the flame-brushes are non-interacting. The thickness is observed to saturate when the flame-brushes interact, which is found to occur in the simulated rod stabilized flame with Taylor micro-scale Reynolds number of 97. © 2011 American Institute of Physics.

Effects of flow geometry and Damkohler number on turbulent premixed flame

DNS of planar turbulent flame and turbulent V-flame has been conducted to investigate turbulence-scalar interaction in relatively practical turbulent combustion. Several turbulence quantities are examined for the understandings of fundamental characteristics of flow field in V-flame. Due to the additional turbulence production by the hot-rod, turbulence does not simply decay in V-flame. Turbulence-scalar interaction, scalar alignments with the principal strain rate in other words, is then clarified. The competition of turbulence and dilatation can be found in the conditional PDF of flame normal alignment. The results suggests that the alignment characteristics in high Da flames are applicable to low Da flames in the region of intense heat release.

DNS of EGR-type turbulent flame in MILD condition

Three-dimensional direct numerical simulation (DNS) of exhaust gas recirculation (EGR)-type turbulent combustion operated in moderate and intense low-oxygen dilution (MILD) condition has been carried out to study the flame structure and flame interaction. In order to achieve adequate EGR-type initial/inlet mixture fields, partially premixed mixture fields which are correlated with the turbulence are carefully preprocessed. The chemical kinetics is modelled using a skeletal mechanism for methane-air combustion. The results suggest that the flame fronts have thin flame structure and the direct link between the mean reaction rate and scalar dissipation rate remains valid in the EGR-type combustion with MILD condition. However, the commonly used canonical flamelet is not fully representative for MILD combustion. During the flame-flame interactions, the heat release rate increases higher than the maximum laminar flame value, while the gradient of progress variable becomes smaller than laminar value. It is also proposed that the reaction rate and the scalar gradient can be used as a marker for the flame interaction. © 2012 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Scalar gradient behaviour in MILD combustion

The results of three-dimensional Direct Numerical Simulation (DNS) of Moderate, Intense Low-oxygen Dilution (MILD) and conventional premixed turbulent combustion conducted using a skeletal mechanism including the effects of non-unity Lewis numbers and temperature dependent transport properties are analysed to investigate combustion characteristics using scalar gradient information. The DNS data is also used to synthesise laser induced fluorescence (LIF) signals of OH, CH2O, and CHO. These signals are analysed to verify if they can be used to study turbulent MILD combustion and it has been observed that at least two (OH and CH2O) LIF signals are required since the OH increase across the reaction zone is smaller in MILD combustion compared to premixed combustion. The scalar gradient PDFs conditioned on the reaction rate obtained from the DNS data and synthesised LIF signals suggests a strong gradient in the direction normal to the MILD reaction zone with moderate reaction rate implying flamelet combustion. However, the PDF of the normal gradient is as broad as for the tangential gradient when the reaction rate is high. This suggests a non-flamelet behaviour, which is due to interaction of reaction zones. The analysis of the conditional PDFs for the premixed case confirms the expected behaviour of scalar gradient in flamelet combustion. It has been shown that the LIF signals synthesised using 2D slices of DNS data also provide very similar insights. These results demonstrate that the so-called flameless combustion is not an idealised homogeneous reactive mixture but has common features of conventional combustion while containing distinctive characteristics. © 2013 The Combustion Institute.