Local dynamics and primitive path analysis for a model polymer melt near a surface

By applying local primitive path and Rouse modes analysis we study the chains conformations, local dynamics and viscosity of a model polymer melt in a polymer-wall interface. We establish that the presence of a repulsive wall leads to acceleration of the dynamics both for unentangled and weakly entangled melts and to a depletion in the entanglement density in the wall vicinity. When the surface bears some grafted chains, we show that the melt chains are accelerated in the unentangled regime and slowed down in the entangled regime. By analyzing the primitive paths we attribute the observed slowdown to an increase in the entanglement density in the interfacial layer. The presence of a relatively small density of grafting sites thus leads to improved mechanical properties (reinforcement) and decreases locally the entanglement length even if the surface is repulsive

Modeling transient absorption and thermal conductivity in a simple nanofluid

Molecular dynamics simulations are used to simulate the thermal properties of a model fluid containing nanoparticles (nanofluid). By modelling transient absorption experiments, we show that they provide a reliable determination of interfacial resistance between the particle and the fluid. The flexibility of molecular simulation allows us to consider separately the effect of confinement, particle mass and Brownian motion on the thermal transfer between fluid and particle. Finally, we show that in the absence of collective effects, the heat conductivity of the nanofluid is well described by the classical Maxwell Garnet equation model

Defining bacterial species in the genomic era : insights from the genus Acinetobacter

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical

Linear and nonlinear viscoelasticity of a model polymer melt: Molecular Dynamics and Rouse Modes analysis

Using molecular dynamics simulations, we determine the linear and nonlinear viscoelastic properties of a model polymer melt in the unentangled regime. Several approaches are compared for the computation of linear moduli, including Green-Kubo and non equilibrium molecular dynamics (NEMD). An alternative approach, based on the use of the Rouse modes, is also discussed. This approach could be used to assess local viscoelastic properties in inhomogeneous systems. We also focus on the contributions of different interactions to the viscoelastic moduli and explain the microscopic mechanisms involved in the mechanical response of the melt to external sollicitation

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice.

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15-1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing

Lattice fence and hedge barriers around an apiary increase honey bee flight height and decrease stings to people nearby

Urban beekeeping is becoming more popular in the UK. One of the challenges faced by urban beekeepers is finding a suitable apiary location. Honey bees are often perceived as a nuisance, mainly due to their stinging behaviour. Here, we experimentally test the assumption that barriers around an apiary such as walls or fences, force the bees to fly above human height, thereby reducing collisions with people and, consequently, stinging. The experiment was conducted in two apiaries using two common types of barrier: a lattice fence (trellis) and hedge. Barriers were 2 m high, which is taller than > 99% of humans and is also the maximum height allowed by UK planning regulations for garden fences or walls. We found that barriers were effective at both raising the mean honey bee flight height and reducing stinging. However, the effects were only seen when the barrier had been in place for a few days, not immediately after the barrier was put in place. Although this raises interesting questions regarding honey bee navigation and memory, it is not a problem for beekeepers, as any barrier placed around an apiary will be permanent. The effect of the barriers on raising bee flight height to a mean of c. 2.2-2.5 m was somewhat weak and inconsistent, probably because the bees flew high, mean of c. 1.6-2.0 m, even in the absence of a barrier. As barriers can also reduce wind exposure, improve security and are inexpensive, we recommend their use around urban apiaries in places such as private gardens or allotments, where nuisance to humans is likely to be a problem

Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server). Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a “divide and conquer” approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available at http://www.xbase.ac.uk/

Junctions of anyonic Luttinger wires

We present an extended study of anyonic Luttinger liquids wires jointing at a single point. The model on the full line is solved with bosonization and the junction of an arbitrary number of wires is treated imposing boundary conditions that preserve exact solvability in the bosonic language. This allows to reach, in the low momentum regime, some of the critical fixed points found with the electronic boundary conditions. The stability of all the fixed points is discussed.Comment: 16 pages, 2 figures, typos corrected, Refs adde

Electrochemical detection of Nitrofural in the presence of sodium amminepentacyanoferrate (II)

The present study deals with the development of a new qualitative electrochemical analytic test for detecting the chemotherapeutic agent Nitrofural. The combination of sodium amminepentacyanoferrate(II) and electric power, provided by a 9V battery, was successfully implemented for the analysis of the medicine in question