Gallium self-interstitial relaxation in Gallium Arsenide: an {ab initio} characterization

Ga interstitials in GaAs ($I_{Ga}$) are studied using the local-orbital {ab-initio} code SIESTA in a supercell of {216+1} atoms. Starting from eight different initial configurations, we find five metastable structures: the two tetrahedral sites in addition to the 110-split$\mathrm{_{[Ga-As]}}$, 111-split$\mathrm{_{[Ga-As]}}$, and 100-split$\mathrm{_{[Ga-Ga]}}$. Studying the competition between various configuration and charges of $I_{Ga}$, we find that predominant gallium interstitials in GaAs are charged +1, neutral or at most -1 depending on doping conditions and prefer to occupy the tetrahedral configuration where it is surrounded by Ga atoms. Our results are in excellent agreement with recent experimental results concerning the dominant charge of $I_{Ga}$, underlining the importance of finite size effects in the calculation of defects.Comment: v1) 18 pages, 5 figures, submitted to PRB (Latex preprint version) v2) 9 pages, 5 figures, reviewed version resubmitted to PRB (correction to equation 1, some changes and reformulations, minor grammatical and typo corrections, added reference

Explosive Nucleosynthesis: What we learned and what we still do not understand

This review touches on historical aspects, going back to the early days of nuclear astrophysics, initiated by B$^2$FH and Cameron, discusses (i) the required nuclear input from reaction rates and decay properties up to the nuclear equation of state, continues (ii) with the tools to perform nucleosynthesis calculations and (iii) early parametrized nucleosynthesis studies, before (iv) reliable stellar models became available for the late stages of stellar evolution. It passes then through (v) explosive environments from core-collapse supernovae to explosive events in binary systems (including type Ia supernovae and compact binary mergers), and finally (vi) discusses the role of all these nucleosynthesis production sites in the evolution of galaxies. The focus is put on the comparison of early ideas and present, very recent, understanding.Comment: 11 pages, to appear in Springer Proceedings in Physics (Proc. of Intl. Conf. "Nuclei in the Cosmos XV", LNGS Assergi, Italy, June 2018

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation

Have Superheavy Elements been Produced in Nature?

We discuss the possibility whether superheavy elements can be produced in Nature by the astrophysical rapid neutron capture process. To this end we have performed fully dynamical network r-process calculations assuming an environment with neutron-to-seed ratio large enough to produce superheavy nuclei. Our calculations include two sets of nuclear masses and fission barriers and include all possible fission channels and the associated fission yield distributions. Our calculations produce superheavy nuclei with A ~ 300 that however decay on timescales of days.Comment: 12 pages, 11 figure

Anaerobically controlled expression system derived from the arcDABC operon of Pseudomonas aeruginosa: application to lipase production.

The anaerobically inducible arcDABC operon encodes the enzymes of the arginine deiminase pathway in Pseudomonas aeruginosa. Upon induction, the arcAB mRNAs and proteins reach high intracellular levels, because of a strong anaerobically controlled promoter and mRNA processing in arcD, leading to stable downstream transcripts. We explored the usefulness of this system for the construction of expression vectors. The lacZ gene of Escherichia coli was expressed to the highest levels when fused close to the arc promoter. Insertion of lacZ further downstream into arcA or arcB did not stabilize the intrinsically unstable lacZ mRNA. On the contrary, lacZ mRNA appeared to be a vulnerable endonuclease target destabilizing arcAB mRNAs in the 5'-to-3' direction in P. aeruginosa. The native arc promoter was modified for optional expression in the -10 sequence and in the -40 region, which is a binding site for the anaerobic regulator ANR. In P. aeruginosa grown either anaerobically or with oxygen limitation in unshaken cultures, this promoter was stronger than the induced tac promoter. The P. aeruginosa lipAH genes, which encode extracellular lipase and lipase foldase, respectively, were fused directly to the modified arc promoter in an IncQ vector plasmid. Semianaerobic static cultures of P. aeruginosa PAO1 carrying this recombinant plasmid overproduced extracellular lipase 30-fold during stationary phase compared with the production by strain PAO1 without the plasmid. Severe oxygen limitation, in contrast, resulted in poor lipase productivity despite effective induction of the ANR-dependent promoter, suggesting that secretion of active lipase is blocked by the absence of oxygen. In conclusion, the modified arc promoter is useful for driving the expression of cloned genes in P. aeruginosa during oxygen-limited growth and stationary phase