Resonant Excitonic Optical Stark Effect In Gase

The time-resolved nonlinear transmission of bulk ε-GaSe has been studied in the femtosecond regime when resonantly exciting the material in the vicinity of the exciton at room temperature. Two regimes are evidenced. At early time delay, a blue shift of the exciton with no linewidth broadening can be related to optical Stark effect, while at longer time delay the usual exciton screening and band-gap renormalization due to real electronic transitions is observed. At resonance, a dependence of the Stark shift with the amplitude of the exciting field is obtained, as predicted by a simple "dressed- atom" model.55222307230

Approximation of excitonic absorption in disordered systems using a compositional component weighted CPA

Employing a recently developed technique of component weighted two particle Green's functions in the CPA of a binary substitutional alloy $A_cB_{1-c}$ we extend the existing theory of excitons in such media using a contact potential model for the interaction between electrons and holes to an approximation which interpolates correctly between the limits of weak and strong disorder. With our approach we are also able to treat the case where the contact interaction between carriers varies between sites of different types, thus introducing further disorder into the system. Based on this approach we study numerically how the formation of exciton bound states changes as the strengths of the contact potentials associated with either of the two site types are varied through a large range of parameter values.Comment: 27 pages RevTeX (preprint format), 13 Postscript figure file

Metabolomic profiling of Drosophila using liquid chromatography Fourier transform mass spectrometry

Hydrophilic interaction chromatography (HILIC) interfaced with an Orbitrap Fourier transform mass spectrometer (FT-MS) was used to carry out metabolomic profiling of the classical Drosophila mutation, rosy (ry). This gene encodes a xanthine oxidase/dehydrogenase. In addition to validating the technology by detecting the same changes in xanthine, hypoxanthine, urate and allantoin that have been reported classically, completely unsuspected changes were detected in each of the tryptophan, arginine, pyrimidine and glycerophospholipid metabolism pathways. The rosy mutation thus ramifies far more widely than previously detected

Translation from the quantified implicit process flow abstraction in SBGN-PD diagrams to Bio-PEPA illustrated on the cholesterol pathway

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the way in which such graphical maps are drawn in order to facilitate the exchange of information. Its qualitative Process Description (SBGN-PD) diagrams are based on an implicit Process Flow Abstraction (PFA) that can also be used to construct quantitative representations, which facilitate automated analyses of the system. Here we explicitly describe the PFA that underpins SBGN-PD and define attributes for SBGN-PD glyphs that make it possible to capture the quantitative details of a biochemical reaction network. Such quantitative details can be used to automatically generate an executable model. To facilitate this, we developed a textual representation for SBGN-PD called “SBGNtext” and implemented SBGNtext2BioPEPA, a tool that demonstrates how Bio-PEPA models can be generated automatically from SBGNtext. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. The scheme developed here is general and can be easily adapted to other output formalisms. To illustrate the intended workflow, we model the metabolic pathway of the cholesterol synthesis. We use this to compute the statin dosage response of the flux through the cholesterol pathway for different concentrations of the enzyme HMGCR that is inhibited by statin

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

The transcriptional regulatory structure of plant genomes is still relatively unexplored and little is known about factors that influence expression variation in plants. We used a genetic system consisting of 10 heterozygous grape varieties with high consanguinity and high haplotypic diversity to: (i) identify regions of haplotype sharing through whole genome resequencing and SNP genotyping; (ii) analyse gene expression through RNA-seq in four stages of berry development; (iii) associate gene expression variation with genetic and epigenetic properties. We found that haplotype sharing in and around genes was positively correlated with similarity in expression and negatively correlated with the fraction of differentially expressed genes. Genetic and epigenetic properties of the gene and the surrounding region showed significant effects on the extent of expression variation, with negative associations for the level of gene body methylation and the mean expression level and positive ones for nucleotide diversity, structural diversity and ratio of non-synonymous to synonymous nucleotide diversity. We also observed a spatial dependency of covariation of gene expression among varieties. These results highlight relevant roles for cis-acting factors, selective constraints and epigenetic features of the gene and the regional context in which the gene is located in the determination of expression variation. This article is protected by copyright. All rights reserved