Electron Impact Ionization Close to the Threshold: Classical Calculations

In this paper we present Classical Trajectory Monte Carlo (CTMC) calculations for single and multiple electron ionization of Argon atoms and ions in the threshold region. We are able to recover the Wannier exponents a for the power-law behavior of the cross section s versus excess energy: the exact value of the exponent as well as the existence of its saturation for multiple ionization appear to be related to how the total binding energy is shared between target electrons.Comment: 9 pages. To be published in Journal of Physics

A Proposal for an Environmental Decision Support System at the Regional Level: Concepts, Support Methodology, Tools and their Terminology

One of the goals of IIASA's research activities in the area of environmental quality modeling is the integration of data and models in a unified framework to assist decision makers with the management of complex environmental systems. Building on IIASA's work undertaken within the WELMM (Water, Energy, Land, Materials and Manpower) project of the former Resources and Environment Area and the work on Decision Support Systems of the former Management and Technology Area, a conceptual framework for an environmental decision support system (EDSS) has been developed and is presented in this paper. The proposed EDSS has been developed with the interest and the financial support of the CSI, the Center for Information Systems of the Regional Government of Piemonte, Italy. The main issue addressed by this paper is to devise a system assisting decision makers in tackling environmental problems at the regional level. These decisions are typically characterized by a combination of both structured (formalizable, described in a quantitative model) and unstructured elements (incomplete information, undefined cause-effect relationships, influence of political objectives, public perception, consideration of aesthetics, etc.). The proposed EDSS enables the user to use models and data, of relevance to a particular task, which are embedded in the EDSS in the form of a process information system. The specific feature of this process information system is that it contains processes of anthropogenic nature (the socio-economic activities being the cause of environmental impacts like power plants, industrial production units, etc.) as well as natural processes determining the spatial/temporal distribution and the extent of environmental quality changes (like the dispersion and deposition of air pollutants and their effect on human population, vegetation and wildlife). The system ensures that the data and models, which have been developed in the context of specific EDSS applications are documented right from the outset and become thus equally available for further use. This becomes especially important in view of the long-term effort to be put into the development of data and models dealing with the large number of environmental problems that governments, industry and academic institutions are confronted with at the regional level

Two-Dimensional Molecular Patterning by Surface-Enhanced Zn-Porphyrin Coordination

In this contribution, we show how zinc-5,10,15,20-meso-tetradodecylporphyrins (Zn-TDPs) self-assemble into stable organized arrays on the surface of graphite, thus positioning their metal center at regular distances from each other, creating a molecular pattern, while retaining the possibility to coordinate additional ligands. We also demonstrate that Zn-TDPs coordinated to 3-nitropyridine display a higher tendency to be adsorbed at the surface of highly oriented pyrolytic graphite (HOPG) than noncoordinated ones. In order to investigate the two-dimensional (2D) self-assembly of coordinated Zn-TDPs, solutions with different relative concentrations of 3-nitropyridine and Zn-TDP were prepared and deposited on the surface of HOPG. STM measurements at the liquid-solid interface reveal that the ratio of coordinated Zn-TDPs over noncoordinated Zn-TDPs is higher at the n-tetradecane/HOPG interface than in n-tetradecane solution. This enhanced binding of the axial ligand at the liquid/solid interface is likely related to the fact that physisorbed Zn-TDPs are better binding sites for nitropyridines.

Stabilizing single atom contacts by molecular bridge formation

Gold-molecule-gold junctions can be formed by carefully breaking a gold wire in a solution containing dithiolated molecules. Surprisingly, there is little understanding on the mechanical details of the bridge formation process and specifically on the role that the dithiol molecules play themselves. We propose that alkanedithiol molecules have already formed bridges between the gold electrodes before the atomic gold-gold junction is broken. This leads to stabilization of the single atomic gold junction, as observed experimentally. Our data can be understood within a simple spring model.Comment: 14 pages, 3 figures, 1 tabl

Photochromism and Electrochemistry of a Dithienylcyclopentene Electroactive Polymer

A bifunctional substituted dithienylcyclopentene photochromic switch bearing electropolymerisable methoxystyryl units, which enable immobilization of the photochromic unit on conducting substrates, is reported. The spectroscopic, electrochemical, and photochemical properties of a monomer in solution are compared with those of the polymer formed through oxidative electropolymerization. The electroactive polymer films prepared on gold, platinum, glassy carbon, and indium titanium oxide (ITO) electrodes were characterized by cyclic voltammetry, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). The thickness of the films formed is found to be limited to several monolayer equivalents. The photochromic properties and stability of the polymer films have been investigated by UV/vis spectroscopy, electrochemistry, and XPS. Although the films are electrochemically and photochemically stable, their mechanical stability with respect to adhesion to the electrode was found to be sensitive to both the solvent and the electrode material employed, with more apolar solvents, glassy carbon, and ITO electrodes providing good adhesion of the polymer film. The polymer film is formed consistently as a thin film and can be switched both optically and electrochemically between the open and closed state of the photochromic dithienylethene moiety.

Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites

RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods