Stability and Electronic Properties of TiO2 Nanostructures With and Without B and N Doping

We address one of the main challenges to TiO2-photocatalysis, namely band gap narrowing, by combining nanostructural changes with doping. With this aim we compare TiO2's electronic properties for small 0D clusters, 1D nanorods and nanotubes, 2D layers, and 3D surface and bulk phases using different approximations within density functional theory and GW calculations. In particular, we propose very small (R < 0.5 nm) but surprisingly stable nanotubes with promising properties. The nanotubes are initially formed from TiO2 layers with the PtO2 structure, with the smallest (2,2) nanotube relaxing to a rutile nanorod structure. We find that quantum confinement effects - as expected - generally lead to a widening of the energy gap. However, substitutional doping with boron or nitrogen is found to give rise to (meta-)stable structures and the introduction of dopant and mid-gap states which effectively reduce the band gap. Boron is seen to always give rise to n-type doping while depending on the local bonding geometry, nitrogen may give rise to n-type or p-type doping. For under coordinated TiO2 surface structures found in clusters, nanorods, nanotubes, layers and surfaces nitrogen gives rise to acceptor states while for larger clusters and bulk structures donor states are introduced

Trends in Metal Oxide Stability for Nanorods, Nanotubes, and Surfaces

The formation energies of nanostructures play an important role in determining their properties, including the catalytic activity. For the case of 15 different rutile and 8 different perovskite metal oxides, we find that the density functional theory (DFT) calculated formation energies of (2,2) nanorods, (3,3) nanotubes, and the (110) and (100) surfaces may be described semi-quantitatively by the fraction of metal--oxygen bonds broken and the bonding band centers in the bulk metal oxide

Improving phylogeny reconstruction at the strain level using peptidome datasets

Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.This research was funded by Grant AGL2013-44039-R from the Spanish “Plan Estatal de I+D+I”, and by Grant EM2014/046 from the “Plan Galego de investigación, innovación e crecemento 2011-2015”. BS was recipient of a Ramón y Cajal postdoctoral contractfrom the Spanish Ministry of Economyand Competitiveness. This work was also partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273).The research leading to these results has also received funding from the European Union’s Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement n˚ 316265, BIOCAPS. This document reflects only the authors’ views and the European Union is not liable for any use that may be made of the information contained herein. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Phylogeny in Aid of the Present and Novel Microbial Lineages: Diversity in Bacillus

Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed

Toxicological Effects of Weapons of Mass Destruction and Noxious Agents in Modern Warfare and Terorrism

Oružja za masovno uništavanje najbolji su primjer uporabe civilizacijskih tehnoloških dostignuća u štetne svrhe i protiv ljudske civilizacije. Unatoč nastojanjima oko kontrole i smanjenja njihove količine, rizik zbog samoga postojanja pa čak i širenja zahtijeva da se o njihovoj uporabi i dalje vodi računa i da se povećaju obrambene mjere – nuklearno-biološko-kemijske obrane (NBKO). Osim suvremenog vojnika koji je u vojnim i mirovnim operacijama diljem svijeta izložen raznim noksama kemijskog, biološkog i radiološkog podrijetla, nezaštićeno i uglavnom slabo educirano civilno stanovništvo može biti izloženo terorističkim napadima. Oružja za masovno uništavanje i nokse kemijskog, biološkog i radiološkog podrijetla uzrokuju razne toksikološke posljedice, a bez obzira na njihovo podrijetlo, imaju zajednički nazivnik djelovanja – poremećaj fi ziološkog stanja u organizmu. Poremećaji proizašli nakon izlaganja tim noksama nerijetko se teško determiniraju, dijagnosticiraju i liječe. U ovome su radu s biomedicinskog aspekta obrađene važnije nokse kemijskog, biološkog i radiološkog podrijetla na temelju odabranih primjera iz terorizma i suvremenog ratovanja: polonij-210, osiromašeni uran, salmonela, bedrenica (antraks), genetički modifi cirane bakterije, polimerno predivo “paučina” i bojni otrovi sarin i iperit.Weapons of mass destruction (WMD) best portray the twisted use of technological achievements against the human species. Despite arm control efforts, WMD threat continues to exist and even proliferate. This in turn calls for improvement in defensive measures against this threat. The modern soldier is exposed to a number of chemical, biological, and radiological agents in military and peace operations, while civilians are mainly exposed to terrorist attacks. Regardless of origin or mode of action, WMDs and other noxious agents aim for the same – to make an organism dysfunctional. Because their effects are often delayed, these agents are hard to spot on time and treat. This review presents a biomedical aspect of agents used in warfare and terrorism, including polonium-210, depleted uranium, salmonella, anthrax, genetically modifi ed bacteria, cobweb-like polymer fi bre, sarin, and mustard gas