Emergent quantum confinement at topological insulator surfaces

Bismuth-chalchogenides are model examples of three-dimensional topological insulators. Their ideal bulk-truncated surface hosts a single spin-helical surface state, which is the simplest possible surface electronic structure allowed by their non-trivial $\mathbb{Z}_2$ topology. They are therefore widely regarded ideal templates to realize the predicted exotic phenomena and applications of this topological surface state. However, real surfaces of such compounds, even if kept in ultra-high vacuum, rapidly develop a much more complex electronic structure whose origin and properties have proved controversial. Here, we demonstrate that a conceptually simple model, implementing a semiconductor-like band bending in a parameter-free tight-binding supercell calculation, can quantitatively explain the entire measured hierarchy of electronic states. In combination with circular dichroism in angle-resolved photoemission (ARPES) experiments, we further uncover a rich three-dimensional spin texture of this surface electronic system, resulting from the non-trivial topology of the bulk band structure. Moreover, our study reveals how the full surface-bulk connectivity in topological insulators is modified by quantum confinement.Comment: 9 pages, including supplementary information, 4+4 figures. A high resolution version is available at http://www.st-andrews.ac.uk/~pdk6/pub_files/TI_quant_conf_high_res.pd

Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research

Epigenetics is the study of all mechanisms that regulate gene transcription and genome stability that are maintained throughout the cell division, but do not include the DNA sequence itself. The best-studied epigenetic mechanism to date is DNA methylation, where methyl groups are added to the cytosine base within cytosine–guanine dinucleotides (CpG sites). CpGs are frequently clustered in high density (CpG islands (CGIs)) at the promoter of over half of all genes. Current knowledge of transcriptional regulation by DNA methylation centres on its role at the promoter where unmethylated CGIs are present at most actively transcribed genes, whereas hypermethylation of the promoter results in gene repression. Over the last 5 years, research has gradually incorporated a broader understanding that methylation patterns across the gene (so-called intragenic or gene body methylation) may have a role in transcriptional regulation and efficiency. Numerous genome-wide DNA methylation profiling studies now support this notion, although whether DNA methylation patterns are a cause or consequence of other regulatory mechanisms is not yet clear. This review will examine the evidence for the function of intragenic methylation in gene transcription, and discuss the significance of this in carcinogenesis and for the future use of therapies targeted against DNA methylation

Towards the glueball spectrum from unquenched lattice QCD

We use a variational technique to study heavy glueballs on gauge configurations generated with 2+1 flavours of ASQTAD improved staggered fermions. The variational technique includes glueball scattering states. The measurements were made using 2150 configurations at 0.092 fm with a pion mass of 360 MeV. We report masses for 10 glueball states. We discuss the prospects for unquenched lattice QCD calculations of the oddballs.Comment: 19 pages, 4 tables and 8 figures. One figure added. Now matches the published versio

Resolution of the stochastic strategy spatial prisoner's dilemma by means of particle swarm optimization

We study the evolution of cooperation among selfish individuals in the stochastic strategy spatial prisoner's dilemma game. We equip players with the particle swarm optimization technique, and find that it may lead to highly cooperative states even if the temptations to defect are strong. The concept of particle swarm optimization was originally introduced within a simple model of social dynamics that can describe the formation of a swarm, i.e., analogous to a swarm of bees searching for a food source. Essentially, particle swarm optimization foresees changes in the velocity profile of each player, such that the best locations are targeted and eventually occupied. In our case, each player keeps track of the highest payoff attained within a local topological neighborhood and its individual highest payoff. Thus, players make use of their own memory that keeps score of the most profitable strategy in previous actions, as well as use of the knowledge gained by the swarm as a whole, to find the best available strategy for themselves and the society. Following extensive simulations of this setup, we find a significant increase in the level of cooperation for a wide range of parameters, and also a full resolution of the prisoner's dilemma. We also demonstrate extreme efficiency of the optimization algorithm when dealing with environments that strongly favor the proliferation of defection, which in turn suggests that swarming could be an important phenomenon by means of which cooperation can be sustained even under highly unfavorable conditions. We thus present an alternative way of understanding the evolution of cooperative behavior and its ubiquitous presence in nature, and we hope that this study will be inspirational for future efforts aimed in this direction.Comment: 12 pages, 4 figures; accepted for publication in PLoS ON

Different atmospheric moisture divergence responses to extreme and moderate El Niños

On seasonal and inter-annual time scales, vertically integrated moisture divergence provides a useful measure of the tropical atmospheric hydrological cycle. It reflects the combined dynamical and thermodynamical effects, and is not subject to the limitations that afflict observations of evaporation minus precipitation. An empirical orthogonal function (EOF) analysis of the tropical Pacific moisture divergence fields calculated from the ERA-Interim reanalysis reveals the dominant effects of the El Niño-Southern Oscillation (ENSO) on inter-annual time scales. Two EOFs are necessary to capture the ENSO signature, and regression relationships between their Principal Components and indices of equatorial Pacific sea surface temperature (SST) demonstrate that the transition from strong La Niña through to extreme El Niño events is not a linear one. The largest deviation from linearity is for the strongest El Niños, and we interpret that this arises at least partly because the EOF analysis cannot easily separate different patterns of responses that are not orthogonal to each other. To overcome the orthogonality constraints, a self-organizing map (SOM) analysis of the same moisture divergence fields was performed. The SOM analysis captures the range of responses to ENSO, including the distinction between the moderate and strong El Niños identified by the EOF analysis. The work demonstrates the potential for the application of SOM to large scale climatic analysis, by virtue of its easier interpretation, relaxation of orthogonality constraints and its versatility for serving as an alternative classification method. Both the EOF and SOM analyses suggest a classification of “moderate” and “extreme” El Niños by their differences in the magnitudes of the hydrological cycle responses, spatial patterns and evolutionary paths. Classification from the moisture divergence point of view shows consistency with results based on other physical variables such as SST

Modelling and simulating change in reforesting mountain landscapes using a social-ecological framework

Natural reforestation of European mountain landscapes raises major environmental and societal issues. With local stakeholders in the Pyrenees National Park area (France), we studied agricultural landscape colonisation by ash (Fraxinus excelsior) to enlighten its impacts on biodiversity and other landscape functions of importance for the valley socio-economics. The study comprised an integrated assessment of land-use and land-cover change (LUCC) since the 1950s, and a scenario analysis of alternative future policy. We combined knowledge and methods from landscape ecology, land change and agricultural sciences, and a set of coordinated field studies to capture interactions and feedback in the local landscape/land-use system. Our results elicited the hierarchically-nested relationships between social and ecological processes. Agricultural change played a preeminent role in the spatial and temporal patterns of LUCC. Landscape colonisation by ash at the parcel level of organisation was merely controlled by grassland management, and in fact depended on the farmer's land management at the whole-farm level. LUCC patterns at the landscape level depended to a great extent on interactions between farm household behaviours and the spatial arrangement of landholdings within the landscape mosaic. Our results stressed the need to represent the local SES function at a fine scale to adequately capture scenarios of change in landscape functions. These findings orientated our modelling choices in the building an agent-based model for LUCC simulation (SMASH - Spatialized Multi-Agent System of landscape colonization by ASH). We discuss our method and results with reference to topical issues in interdisciplinary research into the sustainability of multifunctional landscapes

Twitter Watch: Leveraging Social Media to Monitor and Predict Collective-Efficacy of Neighborhoods

Sociologists associate the spatial variation of crime within an urban setting, with the concept of collective efficacy. The collective efficacy of a neighborhood is defined as social cohesion among neighbors combined with their willingness to intervene on behalf of the common good. Sociologists measure collective efficacy by conducting survey studies designed to measure individuals' perception of their community. In this work, we employ the curated data from a survey study (ground truth) and examine the effectiveness of substituting costly survey questionnaires with proxies derived from social media. We enrich a corpus of tweets mentioning a local venue with several linguistic and topological features. We then propose a pairwise learning to rank model with the goal of identifying a ranking of neighborhoods that is similar to the ranking obtained from the ground truth collective efficacy values. In our experiments, we find that our generated ranking of neighborhoods achieves 0.77 Kendall tau-x ranking agreement with the ground truth ranking. Overall, our results are up to 37% better than traditional baselines.Comment: 10 pages, 7 figure

A Simple and Effective Method for Construction of Escherichia coli Strains Proficient for Genome Engineering

Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the l Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.open7

Review of recent progress in nanoscratch testing

Nanoscratch testing, as an important technique for the assessment of the mechanical failure behaviour and adhesion strength of ceramic coatings and a simulation tool of single asperity contact in tribological experiments, is increasingly becoming an established nanomechanical characterisation method. This paper reviews recent work in nanoscratch testing in different engineering applications including thin ceramic films, automotive organic coatings, chemical- mechanical polishing and biomaterials. In the main part of the paper, nanoscratch results from experiments performed using NanoTest systems fitted with tangential force sensors and spherical indenters as scratch probes are presented and discussed. The types of nanoscratch tests described include constant load nanoscratches, ramped load nanoscratch tests and multipass repetitive unidirectional constant load nanoscratch tests (nanowear). The results are discussed in terms of critical load sensitivity to intrinsic and extrinsic factors, impact of scan speed and loading rate, influence of probe radius and geometry, estimation of tip contact pressure, influence of surface roughness and film stress and thickness, and finally role of ploughing on friction evolution