The silent base flow and the sound sources in a laminar jet.

An algorithm to compute the silent base flow sources of sound in a jet is introduced. The algorithm is based on spatiotemporal filtering of the flow field and is applicable to multifrequency sources. It is applied to an axisymmetric laminar jet and the resulting sources are validated successfully. The sources are compared to those obtained from two classical acoustic analogies, based on quiescent and time-averaged base flows. The comparison demonstrates how the silent base flow sources shed light on the sound generation process. It is shown that the dominant source mechanism in the axisymmetric laminar jet is "shear-noise," which is a linear mechanism. The algorithm presented here could be applied to fully turbulent flows to understand the aerodynamic noise-generation mechanism.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

PNA(T).DNA(AT) triplexes with Hoogsteen base pairing are more favorable

Peptide nucleic acids (PNAs) are nucleic acid analogs with the deoxyribose phosphate backbone replaced by pseudo-peptide polymers to which the nucleobases are linked. The achiral, uncharged and rather flexible properties of the peptide backbone permit peptide nucleic acids more potential than oligonucleotides in application to antisence and antigenic reagents. The process of PNA binding to DNA duplex and forming triplex is the first step of PNA interacting with PNA. But there are no PNA.2DNA triplex crystal data up to date and little has been reported on the structure features and the force of the PNA.2DNA triplex. In this work, PNA(T).DNA(AT) triplexes are successfully built and the structures and forces to stabilize the triplex after optimizations and molecule dynamics are systematically examined, which are expected to aid in the application of PNAs as anticense and antigene agents.

Biofluid behaviour in 3D microchannel systems: Numerical analysis and design development of 3D microchannel biochip separators

This paper describes the design and development cycle of a 3D biochip separator and the modelling analysis of flow behaviour in the biochip microchannel features. The focus is on identifying the difference between 2D and 3D implementations as well as developing basic forms of 3D microfluidic separators. Five variants, based around the device are proposed and analysed. These include three variations of the branch channels (circular, rectangular, disc) and two variations of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming steady state flow has been established, the efficiencies of the flow between the main and side channels for the different designs are analysed and compared with regard to relevant biomicrofluidic laws or effects (bifurcation law, Fahraeus effect, cell-free phenomenon, bending channel effect and laminar flow behaviour). The modelling results identify flow features in microchannels, a constriction and bifurcations and show detailed differences in flow fields between the various designs. The manufacturing process using injection moulding for the initial base case design is also presented and discussed. The work reported here is supported as part of the UK funded 3D-MINTEGRATION project. © 2010 IEEE.

Growth and shape control of disks by bending and extension

Differential growth of thin elastic bodies furnishes a surprisingly simple explanation of the complex and intriguing shapes of many biological systems, such as plant leaves and organs. Similarly, inelastic strains induced by thermal effects or active materials in layered plates are extensively used to control the curvature of thin engineering structures. Such behaviour inspires us to distinguish and to compare two possible modes of differential growth not normally compared to each other, in order to reveal the full range of out-of-plane shapes of an initially flat disk. The first growth mode, frequently employed by engineers, is characterised by direct bending strains through the thickness, and the second mode, mainly apparent in biological systems, is driven by extensional strains of the middle surface. When each mode is considered separately, it is shown that buckling is common to both modes, leading to bistable shapes: growth from bending strains results in a double-curvature limit at buckling, followed by almost developable deformation in which the Gaussian curvature at buckling is conserved; during extensional growth, out-of-plane distortions occur only when the buckling condition is reached, and the Gaussian curvature continues to increase. When both growth modes are present, it is shown that, generally, larger displacements are obtained under in-plane growth when the disk is relatively thick and growth strains are small, and vice versa. It is also shown that shapes can be mono-, bi-, tri- or neutrally stable, depending on the growth strain levels and the material properties: furthermore, it is shown that certain combinations of growth modes result in a free, or natural, response in which the doubly curved shape of disk exactly matches the imposed strains. Such diverse behaviour, in general, may help to realise more effective actuation schemes for engineering structures. © 2012 Elsevier Ltd. All rights reserved.

Linear multiscale analysis and finite element validation of stretching and bending dominated lattice materials

The paper presents a multiscale procedure for the linear analysis of components made of lattice materials. The method allows the analysis of both pin-jointed and rigid-jointed microtruss materials with arbitrary topology of the unit cell. At the macroscopic level, the procedure enables to determine the lattice stiffness, while at the microscopic level the internal forces in the lattice elements are expressed in terms of the macroscopic strain applied to the lattice component. A numeric validation of the method is described. The procedure is completely automated and can be easily used within an optimization framework to find the optimal geometric parameters of a given lattice material. © 2011 Elsevier Ltd. All rights reserved.

Capillary bending of Janus carbon nanotube micropillars.

We present a scalable process for the fabrication of slanted carbon nanotube micropillar arrays by inclined metal deposition and capillary self-assembly. Local control of the micropillar angle from vertical to nearly horizontal is achieved, and is explained using a finite element model. These structures may be useful for microscale contacts and anisotropic smart surfaces.