Three-dimensional direct numerical simulations of autoignition in turbulent non-premixed flows with simple and complex chemistry

3D Direct Numerical Simulations (DNS) of autoignition in turbulent non-premixed flows between fuel and hotter air have been carried out using both 1-step and complex chemistry consisting of a 22 species n-heptane mechanism to investigate spontaneous ignition timing and location. The simple chemistry results showed that the previous findings from 2D DNS that ignition occurred at the most reactive mixture fraction (ξMR) and at small values of the conditional scalar dissipation rate (N|ξMR) are valid also for 3D turbulent mixing fields. Performing the same simulation many times with different realizations of the initial velocity field resulted in a very narrow statistical distribution of ignition delay time, consistent with a previous conjecture that the first appearance of ignition is correlated with the low-N content of the conditional probability density function of N. The simulations with complex chemistry for conditions outside the Negative Temperature Coefficient (NTC) regime show behaviour similar to the single-step chemistry simulations. However, in the NTC regime, the most reactive mixture fraction is very rich and ignition seems to occur at high values of scalar dissipation. Copyright © 2006 by ASME.

Shock / boundary-layer interaction control using three-dimensional bumps for transonic wings

Three-dimensional bumps have been developed and investigated, aiming at the two major objectives of shock-wave / boundary-layer interaction control, i.e. drag reduction and suppression of separation, simultaneously. An experimental investigation has been conducted for a default rounded bump in channel now at University of Cambridge and a computational study has been performed for a spanwise series of rounded bumps mounted on a transonic aerofoil at University of Stuttgart. Observed in both cases are wave drag reduction owing to A-shock structures produced by three-dimensional surface bumps and mild control effects on the boundary layer. The effects of rough surface and tall extension have been investigated as well as several geometric variations and multiple bump configurations. A double configuration of narrow rounded bumps has been found to best perform amongst the tested, considerably reducing wave drag through a well-established A-shock structure with little viscous penalty and thus achieving substantial overall drag reduction. Counter-rotating streamwise vortex pairs have been produced by some configurations as a result of local flow separation, but they have been observed to be confined in relatively narrow wake regions, expected to be beneficial in suppressing large-scale separation under off-design condition despite increase of viscous drag. On the whole a large potential of three-dimensional control with discrete rounded bumps has been demonstrated both experimentally and numerically, and experimental investigation of bumps fitted on a transonic aerofoil or wing is suggested toward practical application.

Behaviour of unsteady transonic shock / boundary layer interactions with three-dimensional effects

An experimental investigation into the response of transonic SBLIs to periodic down-stream pressure perturbations in a parallel walled duct has been conducted. Tests have been carried out with a shock strength of M ∞ = 1.5 for pressure perturbation frequencies in the range 16-90 Hz. Analysis of the steady interaction at M∞ = 1.5 has also been made. The principle measurement techniques were high speed schlieren photography and laser Doppler anemometry. The structure of the steady SBLI was found to be highly three-dimensional, with large corner flows and sidewall SBLIs. These aspects are thought to influence the upstream transmission of pressure information through the interaction by affecting the post-shock flow field, including the extent of regions of secondary supersonic flow. At low frequency, the dynamics of shock motion can be predicted using an inviscid analytical model. At increased frequencies, viscous effects become significant and the shock exhibits unexpected dynamic behaviour, due to a phase lag between the upstream transmission of pressure information in the core flow and in the viscous boundary layers. Flow control in the form of micro-vane vortex generators was found to have a small impact on shock dynamics, due to the effect it had on the post-shock flow field outside the viscous boundary layer region. The relationship between inviscid and viscous effects is developed and potential destabilising mechanisms for SBLIs in practical applications are suggested. Copyright © 2009 by Paul Bruce and Holger Babinsky.

Three-dimensional effects on sliding and waving wings

Like large insects, micro air vehicles operate at low Reynolds numbers O(1; 000 - 10; 000) in a regime characterized by separated flow and strong vortices. The leading-edge vortex has been identified as a significant source of high lift on insect wings, but the conditions required for the formation of a stably attached leading-edge vortex are not yet known. The waving wing is designed to model the translational phase of an insect wing stroke by preserving the unsteady starting and stopping motion as well as three-dimensionality in both wing geometry (via a finite-span wing) and kinematics (via wing rotation). The current study examines the effect of the spanwise velocity gradient on the development of the leading-edge vortex along the wing as well as the effects of increasing threedimensionalityby decreasing wing aspect ratio from four to two. Dye flow visualization and particle image velocimetry reveal that the leading-edge vortices that form on a sliding or waving wing have a very high aspect ratio. The structure of the flow is largely two-dimensional on both sliding and waving wings and there is minimal interaction between the leading-edge vortices and the tip vortex. Significant spanwise flow was observed on the waving wing but not on the sliding wing. Despite the increased three-dimensionality on the aspect ratio 2 waving wing, there is no evidence of an attached leading-edge vortex and the structure of the flow is very similar to that on the higher-aspect-ratio wing and sliding wing. © Copyright 2010.

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

High order schemes on three-dimensional general polyhedral meshes - Application to the level set method

In this article, we detail the methodology developed to construct arbitrarily high order schemes - linear and WENO - on 3D mixed-element unstructured meshes made up of general convex polyhedral elements. The approach is tailored specifically for the solution of scalar level set equations for application to incompressible two-phase flow problems. The construction of WENO schemes on 3D unstructured meshes is notoriously difficult, as it involves a much higher level of complexity than 2D approaches. This due to the multiplicity of geometrical considerations introduced by the extra dimension, especially on mixed-element meshes. Therefore, we have specifically developed a number of algorithms to handle mixed-element meshes composed of convex polyhedra with convex polygonal faces. The contribution of this work concerns several areas of interest: the formulation of an improved methodology in 3D, the minimisation of computational runtime in the implementation through the maximum use of pre-processing operations, the generation of novel methods to handle complex 3D mixed-element meshes and finally the application of the method to the transport of a scalar level set. © 2012 Global-Science Press.

The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

Is there a genetic relationship between mRNA and the encoded protein at three-dimensional level?

A comparative study on the structures of some mRNAs and their encoded proteins shows an intriguing correlation between the two foldings. Non-random distribution of codons in the secondary structures of mRNAs is also shown, which appears to be in accordance with the conformational properties of amino acids in protein structures to some extent. These results seem to suggest that there may be a kind of genetic relationship between mRNA and protein at three-dimensional level.