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

Chaotic features in classical scattering processes between ions and atoms

A numerical study has been done of collisions between protons and hydrogen atoms, treated as classical particles, at low impact velocities. The presence of chaos has been looked for by investigating the processes with standard techniques of the chaotic--scattering theory. The evidence of a sharp transition from nearly regular scattering to fully developed chaos has been found at the lower velocities.Comment: 10 pages, Latex, 3 figures (available upon request to the authors), submitted to Journal of Physics

Argon 4 s

Evaluated atomic data concerning the 4s and 4p configurations of Ar I are averaged in order to simplify their use in various cases of Ar plasma modeling and diagnostics. These data are used here to model a low-power arcjet, running with Argon at low pressure. In so doing, they are explicitly introduced in the chemical processes included in a fluid Navier-Stokes type code, allowing for evaluation of the spectroscopically measurable level populations and of the electronic temperatures. The characteristics of the model are described and the main processes are discussed in view of the results of the calculations

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.

Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016

The NAGLU challenge of the fourth edition of the Critical Assessment of Genome Interpretation experiment (CAGI4) in 2016, invited participants to predict the impact of variants of unknown significance (VUS) on the enzymatic activity of the lysosomal hydrolase α‐N‐acetylglucosaminidase (NAGLU). Deficiencies in NAGLU activity lead to a rare, monogenic, recessive lysosomal storage disorder, Sanfilippo syndrome type B (MPS type IIIB). This challenge attracted 17 submissions from 10 groups. We observed that top models were able to predict the impact of missense mutations on enzymatic activity with Pearson's correlation coefficients of up to .61. We also observed that top methods were significantly more correlated with each other than they were with observed enzymatic activity values, which we believe speaks to the importance of sequence conservation across the different methods. Improved functional predictions on the VUS will help population‐scale analysis of disease epidemiology and rare variant association analysis

MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer

Upregulation of MYC is a hallmark of cancer, wherein MYC drives oncogenic gene expression and elevates total RNA synthesis across cancer cell transcriptomes. Although this transcriptional anabolism fuels cancer growth and survival, the consequences and metabolic stresses induced by excess cellular RNA are poorly understood. Herein, we discover that RNA degradation and downstream ribonucleotide catabolism is a novel mechanism of MYC-induced cancer cell death. Combining genetics and metabolomics, we find that MYC increases RNA decay through the cytoplasmic exosome, resulting in the accumulation of cytotoxic RNA catabolites and reactive oxygen species. Notably, tumor-derived exosome mutations abrogate MYC-induced cell death, suggesting excess RNA decay may be toxic to human cancers. In agreement, purine salvage acts as a compensatory pathway that mitigates MYC-induced ribonucleotide catabolism, and inhibitors of purine salvage impair MYC+ tumor progression. Together, these data suggest that MYC-induced RNA decay is an oncogenic stress that can be exploited therapeutically. Significance: MYC is the most common oncogenic driver of poor-prognosis cancers but has been recalcitrant to therapeutic inhibition. We discovered a new vulnerability in MYC+ cancer where MYC induces cell death through excess RNA decay. Therapeutics that exacerbate downstream ribonucleotide catabolism provide a therapeutically tractable approach to TNBC (Triple-negative Breast Cancer) and other MYC-driven cancers

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