Heavy ion ranges from first-principles electron dynamics

The effects of incident energetic particles, and the modification of materials under irradiation, are governed by the mechanisms of energy losses of ions in matter. The complex processes affecting projectiles spanning many orders of magnitude in energy depend on both ion and electron interactions. Developing multi-scale modeling methods that correctly capture the relevant processes is crucial for predicting radiation effects in diverse conditions. In this work, we obtain channeling ion ranges for tungsten, a prototypical heavy ion, by explicitly simulating ion trajectories with a method that takes into account both the nuclear and the electronic stopping power. The electronic stopping power of self-ion irradiated tungsten is obtained from first-principles time-dependent density functional theory (TDDFT). Although the TDDFT calculations predict a lower stopping power than SRIM by a factor of three, our result shows very good agreement in a direct comparison with ion range experiments. These results demonstrate the validity of the TDDFT method for determining electronic energy losses of heavy projectiles, and in turn its viability for the study of radiation damage.Peer reviewe

Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1.

One third of inherited genetic diseases are caused by mRNAs harboring premature termination codons as a result of nonsense mutations. These aberrant mRNAs are degraded by the Nonsense-Mediated mRNA Decay (NMD) pathway. A central component of the NMD pathway is Upf1, an RNA-dependent ATPase and helicase. Upf1 is a known phosphorylated protein, but only portions of this large protein have been examined for phosphorylation sites and the functional relevance of its phosphorylation has not been elucidated in Saccharomyces cerevisiae. Using tandem mass spectrometry analyses, we report the identification of 11 putative phosphorylated sites in S. cerevisiae Upf1. Five of these phosphorylated residues are located within the ATPase and helicase domains and are conserved in higher eukaryotes, suggesting a biological significance for their phosphorylation. Indeed, functional analysis demonstrated that a small carboxy-terminal motif harboring at least three phosphorylated amino acids is important for three Upf1 functions: ATPase activity, NMD activity and the ability to promote translation termination efficiency. We provide evidence that two tyrosines within this phospho-motif (Y-738 and Y-742) act redundantly to promote ATP hydrolysis, NMD efficiency and translation termination fidelity

Multiphase equation of state for carbon addressing high pressures and temperatures

We present a 5-phase equation of state for elemental carbon which addresses a wide range of density and temperature conditions: 3g/cc 100 000K (both for ρ between 3 and 12 g/cc, with select higher-ρ DFT calculations as well). The liquid free energy model includes an atom-in-jellium approach to account for the effects of ionization due to temperature and pressure in the plasma state, and an ion-thermal model which includes the approach to the ideal gas limit. The precise manner in which the ideal gas limit is reached is greatly constrained by both the highest-temperature DFT data and the path integral data, forcing us to discard an ion-thermal model we had used previously in favor of a new one. Predictions are made for the principal Hugoniot and the room-temperature isotherm, and comparisons are made to recent experimental results.United States. Dept. of Energy (Contract DE-AC52-07NA27344