Para to Ortho transition of metallic dimers on Si(001)

Extensive electronic structure calculations are performed to obtain the stable geometries of metals like Al, Ga and In on the Si(001) surface at 0.5 ML and 1 ML coverages. Our results coupled with previous theoretical findings explain the recent experimental data in a comprehensive fashion. At low coverages, as shown by previous works, `Para' dimers give the lowest energy structure. With increasing coverage beyond 0.5 ML, `Ortho' dimers become part of low energy configurations leading toward a `Para' to `Ortho' transition at 1 ML coverage. For In mixed staggered dimers (`Ortho' and `Para') give the lowest energy configuration. For Ga, mixed dimers are non-staggered, while for Al `Para' to `Ortho' transition of dimers is complete. Thus at intermediate coverages between 0.5 and 1 ML, the `Ortho' and `Para' dimers may coexist on the surface. Consequently, this may be an explanation of the fact that the experimental observations can be successfully interpreted using either orientation. A supported zigzag structure at 0.5 ML, which resembles ${\rm (CH)_x}$, does not undergo a dimerization transition, and hence stays semi-metallic. Also, unlike ${\rm (CH)_x}$ the soliton formation is ruled out for this structure.Comment: 8 pages, 6 figure

Density functional theories and self-energy approaches

A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to investigate the changes in gene expression within the liver of rainbow trout during exposure to a prolonged period of confinement. Tissue and blood samples were collected from trout at intervals up to 648 h after transfer to a standardised confinement stressor, together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, glucose and lactate were analysed to confirm that the neuroendocrine response to confinement was consistent with previous findings and to provide a phenotypic context to assist interpretation of gene expression data. Liver samples for suppression subtractive hybridisation (SSH) library construction were selected from within the experimental groups comprising “early” stress (2–48 h) and “late” stress (96–504 h). In order to reduce redundancy within the four SSH libraries and yield a higher number of unique clones an additional subtraction was carried out. After printing of the arrays a series of 55 hybridisations were executed to cover 6 time points. At 2 h, 6 h, 24 h, 168 h and 504 h 5 individual confined fish and 5 individual control fish were used with control fish only at 0 h. A preliminary list of 314 clones considered differentially regulated over the complete time course was generated by a combination of data analysis approaches and the most significant gene expression changes were found to occur during the 24 h to 168 h time period with a general approach to control levels by 504 h. Few changes in expression were apparent over the first 6 h. The list of genes whose expression was significantly altered comprised predominantly genes belonging to the biological process category (response to stimulus) and one cellular component category (extracellular region) and were dominated by so-called acute phase proteins. Analysis of the gene expression profile in liver tissue during confinement revealed a number of significant clusters. The major patterns comprised genes that were up-regulated at 24 h and beyond, the primary examples being haptoglobin, β-fibrinogen and EST10729. Two representative genes from each of the six k-means clusters were validated by qPCR. Correlations between microarray and qPCR expression patterns were significant for most of the genes tested. qPCR analysis revealed that haptoglobin expression was up-regulated approximately 8-fold at 24 h and over 13-fold by 168 h.This project was part funded by the European Commission (Q5RS-2001-02211), Enterprise Ireland and the Natural Environment Research Council of the United Kingdom