Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges

We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coefficients and their uncertainties for the major gas-phase processes -- ion-neutral reactions, neutral-neutral reactions, radiative association, and dissociative recombination -- is reviewed. Emphasis is placed on those reactions that have been identified, by sensitivity analyses, as 'crucial' in determining the predicted abundances of the species observed in the interstellar medium. These sensitivity analyses have been carried out for gas-phase models of three representative, molecule-rich, astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the expanding circumstellar envelope IRC +10216. Our review has led to the proposal of new values and uncertainties for the rate coefficients of many of the key reactions. The impact of these new data on the predicted abundances in TMC-1 and L134N is reported. Interstellar dust particles also influence the observed abundances of molecules in the interstellar medium. Their role is included in gas-grain, as distinct from gas-phase only, models. We review the methods for incorporating both accretion onto, and reactions on, the surfaces of grains in such models, as well as describing some recent experimental efforts to simulate and examine relevant processes in the laboratory. These efforts include experiments on the surface-catalysed recombination of hydrogen atoms, on chemical processing on and in the ices that are known to exist on the surface of interstellar grains, and on desorption processes, which may enable species formed on grains to return to the gas-phase.Comment: Accepted for publication in Space Science Review

Lorenz function of Bi2_{2}Te3_{3}/Sb2_{2}Te3_{3} superlattices

Combining first principles density functional theory and semi-classical Boltzmann transport, the anisotropic Lorenz function was studied for thermoelectric Bi$_{2}$Te$_{3}$/Sb$_{2}$Te$_{3}$ superlattices and their bulk constituents. It was found that already for the bulk materials Bi$_{2}$Te$_{3}$ and Sb$_{2}$Te$_{3}$, the Lorenz function is not a pellucid function on charge carrier concentration and temperature. For electron-doped Bi$_{2}$Te$_{3}$/Sb$_{2}$Te$_{3}$ superlattices large oscillatory deviations for the Lorenz function from the metallic limit were found even at high charge carrier concentrations. The latter can be referred to quantum well effects, which occur at distinct superlattice periods

Potential barrier heights at metal on oxygen-terminated diamond interfaces

International audienceElectrical properties of metal-semiconductor (M/SC) and metal/oxide/SC structures built with Zr or ZrO_2 deposited on oxygen-terminated surfaces of (001)-oriented diamond films, comprising a stack of lightly p-doped diamond on a heavily doped layer itself homoepitaxially grown on a Ib substrate, are investigated experimentally and compared to different models. In Schottky barrier diodes, the interfacial oxide layer evidenced by high resolution transmission electron microscopy and electron energy losses spectroscopy before and after annealing, and barrier height inhomogeneities accounts for the measured electrical characteristics until flat bands are reached, in accordance with a model which generalizes that of R.T. Tung [Phys. Rev. B 45, 13509 (1992)] and permits to extract physically meaningful parameters of the three kinds of interface: (a) unannealed ones; (b) annealed at 350°C; (c) annealed at 450°C, with characteristic barrier heights of 2.2-2.5 V in case (a) while as low as 0.96 V in case (c). Possible models of potential barriers for several metals deposited on well defined oxygen-terminated diamond surfaces are discussed and compared to experimental data. It is concluded that interface dipoles of several kinds present at these compound interfaces and their chemical evolution due to annealing are the suitable ingredients able to account for the Mott-Schottky behavior when the effect of the metal work function is ignored, and to justify the reverted slope observed regarding metal work function, in contrast to the trend always reported for all other metal-semiconductor interfaces.Les propriétés électriques et structurales d'interfaces métal/diamant et métal/oxyde/diamant où le métal est le Zirconium et le semi-conducteur comporte un empilement de couches faiblement et fortement dopées au bore sur substrat Ib, sont étudiées expérimentalement et comparées à différents modèles. Dans le barrière de Schottky, une inter-couche d'oxyde d'environ 2 couches atomiques, mise en évidence par diverses techniques de microscopie électronique à transmission, est présente et ajoutée à la présence d'inhomogénéités de barrière de potentiel, est corrélée aux propriétés électriques simulées par un modèle qui généralise celui de R. T. Tung [Phys. Rev. B 45, 13509 (1992)] . Les paramètres physiquement caractéristiques des interfaces (a) non recuites, (b) recuite à 350°C et (c) recuite à 450°C peuvent ainsi être extraits, en particulier des hauteurs de barrière de 2.2-2.5 V dans le cas (a) et aussi basses que 0.96 V dans le cas (c). Les modèles possibles de fixation du niveau de Fermi aux interfaces métal/diamant sont examinés et confrontés aux données récemment publiées pour différents métaux sur la surface oxygénée du diamant. On conclue que les quantités physiques judicieuses sont l'affinité électronique du diamant, fonction de son état de surface, pour justifier l'allure générale conforme au modèle de Mott-Schottky et la force du dipole d'interface, dépendante des liaisons chimiques à l'interface, pour expliquer la pente de la variation de la barrière en fonction du travail de sortie du métal, qui est inversée par rapport à tous les autres semi-conducteurs

Brachytherapy of stage II mobile tongue carcinoma. Prediction of local control and QOL

BACKGROUND: There is no consensus as to the prognostic model for brachytherapy of tongue carcinoma. This study was designed to evaluate the prognostic factors for local control based on a large population under a unified treatment policy. RESULTS: Between 1970 and 1998, 433 patients with stage II tongue squamous cell carcinoma were treated by low-dose-rate brachytherapy. This series included 277 patients treated with a linear source with a minimum follow-up of 3 years. A spacer was introduced in 1987. The primary local control rates were 85.6%. CONCLUSION: In the multivariate analysis, an invasive growth pattern was a significant factor for local recurrence. The disease-related survival was influenced by old age and an invasive growth pattern. A spacer lowered mandibular bone complications. The growth pattern was the most important factor for recurrence. Brachytherapy was associated with a high cure rate and the use of spacers brought about good quality of life (QOL)

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Performance and Operation of the CMS Electromagnetic Calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N

Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria. Like some other intrinsically disordered proteins in the solution state of the protein, ColN-T shows dual recognition, initially interacting with other domains of the same colicin N molecule and later, during cell killing, binding to two different receptors, OmpF and TolA, in the target bacterium. ColN-T is invisible in the high-resolution x-ray model and yet accounts for 90 of the toxin’s 387 amino acid residues. To reveal its solution structure that underlies such a dynamic and complex system, we carried out mutagenic, biochemical, hydrodynamic and structural studies using analytical ultracentrifugation, NMR, and small-angle x-ray scattering on full-length ColN and its fragments. The structure was accurately modeled from small-angle x-ray scattering data by treating ColN as a flexible system, namely by the ensemble optimization method, which enables a distribution of conformations to be included in the final model. The results reveal, to our knowledge, for the first time the dynamic structure of a colicin T-domain. ColN-T is in dynamic equilibrium between a compact form, showing specific self-recognition and resistance to proteolysis, and an extended form, which most likely allows for effective receptor binding

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers

Molecular Dynamics Simulation of the Complex PBP-2x with Drug Cefuroxime to Explore the Drug Resistance Mechanism of Streptococcus suis R61

Drug resistance of Streptococcus suis strains is a worldwide problem for both humans and pigs. Previous studies have noted that penicillin-binding protein (PBPs) mutation is one important cause of β-lactam antibiotic resistance. In this study, we used the molecular dynamics (MD) method to study the interaction differences between cefuroxime (CES) and PBP2x within two newly sequenced Streptococcus suis: drug-sensitive strain A7, and drug-resistant strain R61. The MM-PBSA results proved that the drug bound much more tightly to PBP2x in A7 (PBP2x-A7) than to PBP2x in R61 (PBP2x-R61). This is consistent with the evidently different resistances of the two strains to cefuroxime. Hydrogen bond analysis indicated that PBP2x-A7 preferred to bind to cefuroxime rather than to PBP2x-R61. Three stable hydrogen bonds were formed by the drug and PBP2x-A7, while only one unstable bond existed between the drug and PBP2x-R61. Further, we found that the Gln569, Tyr594, and Gly596 residues were the key mutant residues contributing directly to the different binding by pair wise energy decomposition comparison. By investigating the binding mode of the drug, we found that mutant residues Ala320, Gln553, and Thr595 indirectly affected the final phenomenon by topological conformation alteration. Above all, our results revealed some details about the specific interaction between the two PBP2x proteins and the drug cefuroxime. To some degree, this explained the drug resistance mechanism of Streptococcus suis and as a result could be helpful for further drug design or improvement

Simulation of Postsynaptic Glutamate Receptors Reveals Critical Features of Glutamatergic Transmission

Activation of several subtypes of glutamate receptors contributes to changes in postsynaptic calcium concentration at hippocampal synapses, resulting in various types of changes in synaptic strength. Thus, while activation of NMDA receptors has been shown to be critical for long-term potentiation (LTP) and long term depression (LTD) of synaptic transmission, activation of metabotropic glutamate receptors (mGluRs) has been linked to either LTP or LTD. While it is generally admitted that dynamic changes in postsynaptic calcium concentration represent the critical elements to determine the direction and amplitude of the changes in synaptic strength, it has been difficult to quantitatively estimate the relative contribution of the different types of glutamate receptors to these changes under different experimental conditions. Here we present a detailed model of a postsynaptic glutamatergic synapse that incorporates ionotropic and mGluR type I receptors, and we use this model to determine the role of the different receptors to the dynamics of postsynaptic calcium with different patterns of presynaptic activation. Our modeling framework includes glutamate vesicular release and diffusion in the cleft and a glutamate transporter that modulates extracellular glutamate concentration. Our results indicate that the contribution of mGluRs to changes in postsynaptic calcium concentration is minimal under basal stimulation conditions and becomes apparent only at high frequency of stimulation. Furthermore, the location of mGluRs in the postsynaptic membrane is also a critical factor, as activation of distant receptors contributes significantly less to calcium dynamics than more centrally located ones. These results confirm the important role of glutamate transporters and of the localization of mGluRs in postsynaptic sites in their signaling properties, and further strengthen the notion that mGluR activation significantly contributes to postsynaptic calcium dynamics only following high-frequency stimulation. They also provide a new tool to analyze the interactions between metabotropic and ionotropic glutamate receptors