Shifting atomic patterns: on the origin of the different atomic-scale patterns of graphite as observed using scanning tunnelling microscopy.

We present an in-depth study of the myriad atomically resolved patterns observed on graphite using the scanning tunnelling microscope (STM) over the past three decades. Through the use of highly resolved atomic resolution images, we demonstrate how the interactions between the different graphene layers comprising graphite affect the local surface atomic charge density and its resulting symmetry orientation, with particular emphasis on interactions that are thermodynamically unstable. Moreover, the interlayer graphene coupling is controlled experimentally by varying the tip-surface interaction, leading to associated changes in the atomic patterns. The images are corroborated by first-principles calculations, further validating our claim that surface graphene displacement, coming both from lateral and vertical displacement of the top graphene layer, forms the basis of the rich variety of atomic patterns observed in STM experiments on graphite.

Oscillatory sensitivity patterns for global modes in wakes

Globally unstable wakes with co-flow at intermediate Reynolds numbers are studied, to quantify important spatial regions for the development and control of the global instability. One region of high structural sensitivity is found close to the inlet for all wakes, in agreement with previous findings for cylinder wakes. A second, elongated region of high structural sensitivity is seen downstream of the first one for unconfined wakes at Re = 400. When base flow modifications are considered, a spatially oscillating sensitivity pattern is found inside the downstream high structural sensitivity region. This implies that the same change in the base flow can either destabilize or stabilize the flow, depending on the exact position where it is applied. It is shown that the sensitivity pattern remains unchanged for different choices of streamwise boundary conditions and numerical resolution. Actual base flow modifications are applied in selected configurations, and the linear global modes recomputed. It is confirmed that the linear global eigenvalues move according to the predicted sensitivity pattern for small amplitude base flow modifications, for which the theory applies. We also look at the implications of a small control cylinder on the flow. Only the upstream high sensitivity region proves to be robust in terms of control, but one should be careful not to disturb the flow in the downstream high sensitivity region, in order to achieve control. The findings can have direct implications on the numerical resolution requirements for wakes at higher Reynolds numbers. Furthermore, they provide one more possible explanation to why confined wakes have a more narrow frequency spectrum than unconfined wakes.

Microfabrication of electrode patterns for high-frequency ultrasound transducer arrays.

High-frequency ultrasound is needed for medical imaging with high spatial resolution. A key issue in the development of ultrasound imaging arrays to operate at high frequencies (≥30 MHz) is the need for photolithographic patterning of array electrodes. To achieve this directly on 1-3 piezocomposite, the material requires not only planar, parallel, and smooth surfaces, but also an epoxy composite filler that is resistant to chemicals, heat, and vacuum. This paper reports, first, on the surface finishing of 1-3 piezocomposite materials by lapping and polishing. Excellent surface flatness has been obtained, with an average surface roughness of materials as low as 3 nm and step heights between ceramic/polymer of ∼80 nm. Subsequently, high-frequency array elements were patterned directly on top of these surfaces using a photolithography process. A 30-MHz linear array electrode pattern with 50-μm element pitch has been patterned on the lapped and polished surface of a high-frequency 1-3 piezocomposite. Excellent electrode edge definition and electrical contact to the composite were obtained. The composite has been lapped to a final thickness of ∼55 μm. Good adhesion of electrodes on the piezocomposite has been achieved and electrical impedance measurements have demonstrated their basic functionality. The array was then packaged, and acoustic pulse-echo measurements were performed. These results demonstrate that direct patterning of electrodes by photolithography on 1-3 piezocomposite is feasible for fabrication of high-frequency ultrasound arrays. Furthermore, this method is more conducive to mass production than other reported array fabrication techniques.

Continuous Diffraction Patterns from Circular Arrays of Carbon Nanotubes

We report the remarkable diffraction effects produced from circular patterned arrays of multiwalled carbon nanotubes (MWCNTs). Highly ordered circular arrays of multiwalled carbon nanotubes (with inter-nanotube spacings of 633 nm) display optical dispersion effects similar to compact discs. These arrays display remarkable diffraction patterns in the far field which are spatially continuous. High quality diffraction patterns were obtained experimentally which are in excellent agreement with the theoretical calculations. The achieved continuous diffraction patterns pave the way towards the utilization of engineered carbon nanotube arrays in applications like three dimensional holograms.

Effects of exhaust inlet size on the fluid flow patterns created by an Aaberg exhaust hood

The aim of this paper is to investigate the effects of the size of the exhaust inlet on the fluid flow patterns created by an Aaberg exhaust hood. Streamlines and lines of constant speed modelling those created by an Aaberg hood are used to examine the effect of the inlet size on the size and profile of the hood's effective suction area. © 1992.

Alternating spatial patterns for coordinated group motion

Motivated by recent observations of fish schools, we study coordinated group motion for individuals with oscillatory speed. Neighbors that have speed oscillations with common frequency, amplitude and average but different phases, move together in alternating spatial patterns, taking turns being towards the front, sides and back of the group. We propose a model and control laws to investigate the connections between these spatial dynamics, communication when sensing is range or direction limited, and convergence of coordinated group motions. ©2007 IEEE.

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

Population genetic structure and geographical differentiation of the Chinese catfish Hemibagrus macropterus (Siluriformes, Bagridae): Evidence for altered drainage patterns

National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Identical sequences but different expression patterns of Hira gene in gynogenetic and gonochoristic crucian carps

Hir/Hira (histone regulation) genes were first identified in yeast as negative regulators of histone gene expression. It has been confirmed that HIRA is a conserved family of proteins present in various animals and plants. In this paper, the cDNAs of the Hira homolog named CagHira and CaHira were isolated from gynogenetic gibel carp (gyno-carp) and gonochoristic color crucian carp (gono-carp) respectively. The full-length CagHira is 3,860 bp in length with an open reading frame (ORF) of 3,033 bp that encodes 1,011 amino acids, while the full-length CaHira is 3,748 bp in length and also has an ORF of 3,033 bp. The deduced amino acid sequences of both Hira homologs contain seven WD domains and show high identity with other HIRA family members. RT-PCR analyses revealed strong expression of Hira in the ovaries, whereas no expression was detected in the testes of either of the fishes. Hira transcription was not detected in the liver of gyno-carp, but a high level of Hira mRNA was observed in gono-carp. The temporal expression pattern showed that the Hira mRNA is consistently expressed during all embryonic development stages in gyno-carp. However, the abundance of CaHira mRNA significantly decreased (P < 0.05) shortly after fertilization and then increased again and remained stable from gastrula till hatching. The varying spatiotemporal expression patterns of Hira genes in gyno-carp and gono-carp may be associated with the differing reproductive modes used by these two closely related fishes. Our results suggest that Hira may play a role not only in the decondensation of sperm nucleus and the formation of pronucleus during fertilization, but also in gastrulation and the subsequent development of embryos.