Electronic structure changes of Si(001)-(2x1) from subsurface Mn observed by STM

The deposition of Mn atoms onto the Si(001)-(2x1) reconstructed surface has been studied using scanning tunneling microscopy (STM) and first-principles electronic structure calculations. Room-temperature deposition of 0.1 ML (monolayer) of Mn gives rise to a disordered surface structure. After in situ annealing between 300 and 700 °C, most of the Mn is incorporated into three-dimensional manganese silicide islands, and Si dimer rows reappear in the STM images on most of the substrate surface. At the same time, rowlike structures are visible in the atomic-scale STM images. A comparison with calculated STM images provides evidence that Mn atoms are incorporated into the row structures in subsurface interstitial sites, which are the lowest-energy position for Mn on Si(001). The subsurface Mn alters the height and local density of states of the Si dimer atoms, causing them to appear 0.6 Å higher than a neighboring Si dimer with no Mn below. This height difference that allows the detection the subsurface Mn results from a subtle interplay of geometrical and electronic effects

Non-relativistic quantum systems on topological defects space-times

We study the behavior of non-relativistic quantum particles interacting with different potentials in the space-times generated by a cosmic string and a global monopole. We find the energy spectra in the presence of these topological defects and show how they differ from their free space-time values.Comment: 17 pages, LATEX fil

Carbohydrate‐Based Polymer Brushes Prevent Viral Adsorption on Electrostatically Heterogeneous Interfaces

Chemical heterogeneity on biomaterial surfaces can transform its interfacial properties, rendering nanoscale heterogeneity profoundly consequential during bioadhesion. To examine the role played by chemical heterogeneity in the adsorption of viruses on synthetic surfaces, a range of novel coatings is developed wherein a tunable mixture of electrostatic tethers for viral binding, and carbohydrate brushes, bearing pendant α‐mannose, β‐galactose, or β‐glucose groups, is incorporated. The effects of binding site density, brush composition, and brush architecture on viral adsorption, with the goal of formulating design specifications for virus‐resistant coatings are experimentally evaluated. It is concluded that virus‐coating interactions are shaped by the interplay between brush architecture and binding site density, after quantifying the adsorption of adenoviruses, influenza, and fibrinogen on a library of carbohydrate brushes co‐immobilized with different ratios of binding sites. These insights will be of utility in guiding the design of polymer coatings in realistic settings where they will be populated with defects.A tunable coating comprising nonfouling carbohydrate brushes and electrostatic binding sites for viruses is employed to study the relationship between surface design parameters and viral adsorption. Ultimately, brush architecture determines whether the binding sites are exposed to, or shielded from viruses. These insights will guide the design of polymer coatings that can resist viral binding despite being populated with defects.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147118/1/marc201800530-sup-0001-SuppMat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147118/2/marc201800530_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147118/3/marc201800530.pd

Highly site-specific H2 adsorption on vicinal Si(001) surfaces

Experimental and theoretical results for the dissociative adsorption of H_2 on vicinal Si(001) surfaces are presented. Using optical second-harmonic generation, sticking probabilities at the step sites are found to exceed those on the terraces by up to six orders of magnitude. Density functional theory calculations indicate the presence of direct adsorption pathways for monohydride formation but with a dramatically lowered barrier for step adsorption due to an efficient rehybridization of dangling orbitals.Comment: 5 pages, 4 figures, submitted to Phys. Rev. Lett. (1998). Other related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification

Influence of the substrate lattice structure on the formation of Quantum Well States in thin In and Pb films on silicon

The substrate lattice structure may have a considerable influence on the formation of quantum well states in a metal overlayer material. Here we study three model systems using angle resolved photoemission and low energy electron diffraction: indium films on Si(111) and indium and lead on Si(100). Data are compared with theoretical predictions based on density functional theory. We find that the interaction between the substrate and the overlayer strongly influences the formation of quantum well states; indium layers only exhibit well defined quantum well states when the layer relaxes from an initial face-centered cubic to the bulk body-centered tetragonal lattice structure. For Pb layers on Si(100) a change in growth orientation inhibits the formations of quantum well states in films thicker than 2 ML.Comment: 16 pages, 7 figure

Lef1 regulates caveolin expression and caveolin dependent endocytosis, a process necessary for Wnt5a/Ror2 signaling during Xenopus gastrulation

The activation of distinct branches of the Wnt signaling network is essential for regulating early vertebrate development. Activation of the canonical Wnt/β-catenin pathway stimulates expression of β-catenin-Lef/Tcf regulated Wnt target genes and a regulatory network giving rise to the formation of the Spemann organizer. Non-canonical pathways, by contrast, mainly regulate cell polarization and migration, in particular convergent extension movements of the trunk mesoderm during gastrulation. By transcriptome analyses, we found caveolin1, caveolin3 and cavin1 to be regulated by Lef1 in the involuting mesoderm of Xenopus embryos at gastrula stages. We show that caveolins and caveolin dependent endocytosis are necessary for proper gastrulation, most likely by interfering with Wnt5a/Ror2 signaling. Wnt5a regulates the subcellular localization of receptor complexes, including Ror2 homodimers, Ror2/Fzd7 and Ror2/dsh heterodimers in an endocytosis dependent manner. Live-cell imaging revealed endocytosis of Ror2/caveolin1 complexes. In Xenopus explants, in the presence of Wnt5a, these receptor clusters remain stable exclusively at the basolateral side, suggesting that endocytosis of non-canonical Wnt/receptor complexes preferentially takes place at the apical membrane. In support of this blocking endocytosis with inhibitors prevents the effects of Wnt5a. Thus, target genes of Lef1 interfere with Wnt5a/Ror2 signaling to coordinate gastrulation movements

Understanding Shale Gas: Recent Progress and Remaining Challenges

Because of a number of technological advancements, unconventional hydrocarbons, and in particular shale gas, have transformed the US economy. Much is being learned, as demonstrated by the reduced cost of extracting shale gas in the US over the past five years. However, a number of challenges still need to be addressed. Many of these challenges represent grand scientific and technological tasks, overcoming which will have a number of positive impacts, ranging from the reduction of the environmental footprint of shale gas production to improvements and leaps forward in diverse sectors, including chemical manufacturing and catalytic transformations. This review addresses recent advancements in computational and experimental approaches, which led to improved understanding of, in particular, structure and transport of fluids, including hydrocarbons, electrolytes, water, and CO2 in heterogeneous subsurface rocks such as those typically found in shale formations. The narrative is concluded with a suggestion of a few research directions that, by synergistically combining computational and experimental advances, could allow us to overcome some of the hurdles that currently hinder the production of hydrocarbons from shale formations

STRoe deer: a validated forensic STR profiling system for the European roe deer (Capreolus capreolus)

European roe deer (Capreolus capreolus L.) are the most common game species in Europe, hunted for meat and trophies. Forensic investigations involving roe deer poaching may often benefit from an individual identification method to link a suspect to a specific incident. The current paper presents a forensically validated DNA profiling system for European roe deer called “STRoe deer”. This DNA profiling system consists of 12 novel unlinked tetra-nucleotide short tandem repeat (STR) loci and two sexing markers, with an allelic ladder to facilitate accurate genotyping. Validation results using 513 European roe deer samples collected from a single population from the Swiss Plateau demonstrated successful amplification of all 14 loci with as little as 0.05 ng of European roe deer DNA. Species-specificity tests showed that other members of the Cervidae family exhibited partial profiles and non-specific peaks, whereas most members of the Bovidae family showed just non-specific cross-species amplification products. Three different methods to calculate match probabilities for randomly sampled European roe deer genotypes resulted in median match probabilities ranging from 1.4 × 10−13 to 2.5 × 10−5. These methods accounted for possible population structure, occurrence of null alleles and individual relatedness. Based on these results, we conclude that STRoe deer is a robust genotyping system that should prove a valuable tool for individual identification and sexing of European roe deer to support criminal investigations