THEORETICAL STUDIES OF BILIPROTEIN CHROMOPHORES AND RELATED BILE PIGMENTS BY MOLECULAR ORBITAL AND RAMACHANDRAN TYPE CALCULATIONS

Ramachandran calculations have been used to gain insight into steric hindrance in bile pigments related to biliprotein chromophores. The high optical activity of denatured phycocyanin, as compared to phycoerythrin, has been related to the asymmetric substitution at ring A, which shifts the equilibrium towards the P-helical form of the chromophore. Geometric effects on the electronic structures and transitions have then been studied by molecular orbital calculations for several conjugation systems including the chromophores of phycocyanin. phytochrome P,, cations, cation radicals and tautomeric forms. For these different chromophores some general trends can be deduced. For instance, for a given change in the gross shape (e.g. either unfolding of the molecule from a cyclic-helical to a fully extended geometry, or upon out-of-plane twists of the pyrrole ring A) of the molecules under study, the predicted absorption spectra all change in a simikar way. Nonetheless, there are characteristic distinctions between the different n-systems, both in the transition energies and the charge distribution, which can be related to their known differences in spectroscopic properties and their reactivity

A Glial Variant of the Vesicular Monoamine Transporter Is Required To Store Histamine in the Drosophila Visual System

Unlike other monoamine neurotransmitters, the mechanism by which the brain's histamine content is regulated remains unclear. In mammals, vesicular monoamine transporters (VMATs) are expressed exclusively in neurons and mediate the storage of histamine and other monoamines. We have studied the visual system of Drosophila melanogaster in which histamine is the primary neurotransmitter released from photoreceptor cells. We report here that a novel mRNA splice variant of Drosophila VMAT (DVMAT-B) is expressed not in neurons but rather in a small subset of glia in the lamina of the fly's optic lobe. Histamine contents are reduced by mutation of dVMAT, but can be partially restored by specifically expressing DVMAT-B in glia. Our results suggest a novel role for a monoamine transporter in glia that may be relevant to histamine homeostasis in other systems

De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits

Locusts exhibit remarkable density-dependent phenotype (phase) changes from the solitary to the gregarious, making them one of the most destructive agricultural pests. This phenotype polyphenism arises from a single genome and diverse transcriptomes in different conditions. Here we report a de novo transcriptome for the migratory locust and a comprehensive, representative core gene set. We carried out assembly of 21.5 Gb Illumina reads, generated 72,977 transcripts with N50 2,275 bp and identified 11,490 locust protein-coding genes. Comparative genomics analysis with eight other sequenced insects was carried out to indentify the genomic divergence between hemimetabolous and holometabolous insects for the first time and 18 genes relevant to development was found. We further utilized the quantitative feature of RNA-seq to measure and compare gene expression among libraries. We first discovered how divergence in gene expression between two phases progresses as locusts develop and identified 242 transcripts as candidates for phase marker genes. Together with the detailed analysis of deep sequencing data of the 4th instar, we discovered a phase-dependent divergence of biological investment in the molecular level. Solitary locusts have higher activity in biosynthetic pathways while gregarious locusts show higher activity in environmental interaction, in which genes and pathways associated with regulation of neurotransmitter activities, such as neurotransmitter receptors, synthetase, transporters, and GPCR signaling pathways, are strongly involved. Our study, as the largest de novo transcriptome to date, with optimization of sequencing and assembly strategy, can further facilitate the application of de novo transcriptome. The locust transcriptome enriches genetic resources for hemimetabolous insects and our understanding of the origin of insect metamorphosis. Most importantly, we identified genes and pathways that might be involved in locust development and phase change, and may thus benefit pest management

3D PIC-MC simulation of anode effects in dual magnetron discharges

Development of industrial plasma coaters regarding throughput and precision necessitate the utilization of appropriate modeling tools. Thus, a parallel computing simulation environment for gas flows and gas discharges has been implemented at Fraunhofer IST. The simulation environment, called PIC-MC is based upon the particle-in-cell Monte Carlo approach. While many PIC-MC studies reported in literature are restricted to simplified two-dimensional geometries, we put much effort in enabling three-dimensional simulation studies by optimization of the underlying field solver modules in particular. This involves the parallelization of the magnetic field solver based on the boundary element method which is now capable of handling industrial sized magnetron array arrangements. Furthermore the scaling behavior of the parallel electric field solver based on the Taylor extrapolation method has been improved. With recent software optimizations and better availability of parallel high performance computing hardware, 3D magnetron discharge simulations are now becoming feasible at low and moderate power density. In this work we present PIC-MC simulation results for a dual magnetron discharge set-up with anode bars. We especially investigate the discharge dynamic and the resulting electron flux for magnetically shielded anodes. By applying our simulation tool we can reproduce experimentally observed features such as electron flux constrictions forming local "hot spots" on the anode bars. The PIC-MC simulation allows for better understanding of this phenomenon which could severely damage the sputter equipment

Multiple scale modeling of Al2O3 thin film growth in an ion beam sputtering process

A multiple scale model approach is presented in order to investigate Al2O3 thin film growth in the framework of an existing Ion Beam Sputtering (IBS) coating process. Therefore, several simulation techniques are combined via optimized interfaces for realizing the concept of a virtual coater. Characteristic coating process parameters of the IBS coating plant are applied as input parameters to model the material transport in the chamber, the energy and angular distribution of the coating material at the substrate, the formation of structural thin film properties, and the optical as well as the electronic layer properties. The resulting thin film properties are validated to the data of an experimental IBS Al2O3 single layer prepared applying the underlying coating facility. The comparison accounts for a good agreement between the modeled layer properties using the virtual coater concept and the experimental characterization data

Numerical optimization of baffles for sputtering optical precision filters

The optimization of the coating uniformity of precision optical filters generally is a critical and time consuming procedure. The present paper demonstrates this optimization procedure on a new optical precision sputter coater "Enhanced Optical Sputtering System (EOSS)" at Fraunhofer IST. The coater concept is based on dual cylindrical sputtering sources and a rotating turn-table as sample-holder. For compensating non-uniformity introduced by the particle flux profile and the radially dependent track speed on the turntable, baffle elements have to be designed and inserted beneath the substrates. For that purpose the distribution of the particle flow from the cylindrical magnetron as well as the resulting thickness profile for different shaper designs is simulated using Direct Simulation Monte Carlo (DSMC) transport simulation. For comparison, experimentally obtained film thickness profiles are evaluated by spectrophotometry and ellipsometry. The simulation model is used for optimization of the baffle geometry as well as investigation on the role of long term drifts caused by target erosion and mechanical tolerances

Numerical shaper optimization for sputtered optical precision filters

A novel optimization procedure for optical precision sputter coaters with respect to the f ilm homogeneity is demonstrated. For a coater concept based on dual cylindrical sputtering sources and a rotating turn-table as sample-holder, the inherent radial decay of the film thickness must be compensated by shaper elements. For that purpose, a simulation model of the particle flux within such a coater is set up and validated against experimental data. Subsequently, the shaper design is optimized according to the modeled metal flux profile. The resulting film thickness deviations are minimized down to ±0.35%