Solid solution decomposition and Guinier-Preston zone formation in Al-Cu alloys: A kinetic theory with anisotropic interactions

Using methods of statistical kinetic theory parametrized with first-principles interatomic interactions that include chemical and strain contributions, we investigated the kinetics of decomposition and microstructure formation in Al-Cu alloys as a function of temperature and alloy concentration. We show that the decomposition of the solid solution forming platelets of copper, known as Guinier-Preston (GP) zones, includes several stages and that the transition from GP1 to GP2 zones is determined mainly by kinetic factors. With increasing temperature, the model predicts a gradual transition from platelet-like precipitates to equiaxial ones and at intermediate temperatures both precipitate morphologies may coexist.Comment: 9 pages, 8 figure

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

<p>Abstract</p> <p>Background</p> <p>The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrated workings of the cell. However, translating this amount of data into biological insight remains a daunting task. An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes).</p> <p>Results</p> <p>We developed Nearest Neighbor Networks (NNN), a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated, and requiring mutual nearest neighbors allows genes with no sufficiently similar partners to remain unclustered. We compared the clusters generated by NNN with those generated by eight other clustering methods. NNN was particularly successful at generating functionally coherent clusters with high precision, and these clusters generally represented a much broader selection of biological processes than those recovered by other methods.</p> <p>Conclusion</p> <p>The Nearest Neighbor Networks algorithm is a valuable clustering method that effectively groups genes that are likely to be functionally related. It is particularly attractive due to its simplicity, its success in the analysis of large datasets, and its ability to span a wide range of biological functions with high precision.</p

Ground state laser cooling using electromagnetically induced transparency

A laser cooling method for trapped atoms is described which achieves ground state cooling by exploiting quantum interference in a driven Lambda-shaped arrangement of atomic levels. The scheme is technically simpler than existing methods of sideband cooling, yet it can be significantly more efficient, in particular when several motional modes are involved, and it does not impose restrictions on the transition linewidth. We study the full quantum mechanical model of the cooling process for one motional degree of freedom and show that a rate equation provides a good approximation.Comment: 4 pages, 3 figures; v2: minor modifications to abstract, text and figure captions; v3: few references added and rearranged; v4: One part significantly changed, 1 figure removed, new equations; v5: typos corrected, to appear in PR

Mitigating the impact of Bats in historic churches: The response of Natterer's Bats Myotis nattereri to artificial roosts and deterrence

© 2016 Zeale et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Bats frequently roost in historic churches, and these colonies are of considerable conservation value. Inside churches, bat droppings and urine can cause damage to the historic fabric of the building and to items of cultural significance. In extreme cases, large quantities of droppings can restrict the use of a church for worship and/or other community functions. In the United Kingdom, bats and their roosts are protected by law, and striking a balance between conserving the natural and cultural heritage can be a significant challenge. We investigated mitigation strategies that could be employed in churches and other historic buildings to alleviate problems caused by bats without adversely affecting their welfare or conservation status. We used a combination of artificial roost provision and deterrence at churches in Norfolk, England, where significant maternity colonies of Natterer's bats Myotis nattereri damage church features. Radio-tracking data and population modelling showed that excluding M. nattereri from churches is likely to have a negative impact on their welfare and conservation status, but that judicious use of deterrents, especially high intensity ultrasound, can mitigate problems caused by bats. We show that deterrence can be used to move bats humanely from specific roosting sites within a church and limit the spread of droppings and urine so that problems to congregations and damage to cultural heritage can be much reduced. In addition, construction of bespoke roost spaces within churches can allow bats to continue to roost within the fabric of the building without flying in the church interior. We highlight that deterrence has the potential to cause serious harm toM. nattereri populations if not used judiciously, and so the effects of deterrents will need careful monitoring, and their use needs strict regulation

Destabilization of dark states and optical spectroscopy in Zeeman-degenerate atomic systems

We present a general discussion of the techniques of destabilizing dark states in laser-driven atoms with either a magnetic field or modulated laser polarization. We show that the photon scattering rate is maximized at a particular evolution rate of the dark state. We also find that the atomic resonance curve is significantly broadened when the evolution rate is far from this optimum value. These results are illustrated with detailed examples of destabilizing dark states in some commonly-trapped ions and supported by insights derived from numerical calculations and simple theoretical models.Comment: 14 pages, 10 figure

Quantum Coherence in a Single Ion due to strong Excitation of a metastable Transition

We consider pump-probe spectroscopy of a single ion with a highly metastable (probe) clock transition which is monitored by using the quantum jump technique. For a weak clock laser we obtain the well known Autler-Townes splitting. For stronger powers of the clock laser we demonstrate the transition to a new regime. The two regimes are distinguished by the transition of two complex eigenvalues to purely imaginary ones which can be very different in magnitude. The transition is controlled by the power of the clock laser. For pump on resonance we present simple analytical expressions for various linewidths and line positions.Comment: 6 figures. accepted for publication in PR

Did tool-use evolve with enhanced physical cognitive abilities?

The use and manufacture of tools have been considered to be cognitively demanding and thus a possible driving factor in the evolution of intelligence. In this study, we tested the hypothesis that enhanced physical cognitive abilities evolved in conjunction with the use of tools, by comparing the performance of naturally tool-using and non-tool-using species in a suite of physical and general learning tasks. We predicted that the habitually tool-using species, New Caledonian crows and Galápagos woodpecker finches, should outperform their non-tool-using relatives, the small tree finches and the carrion crows in a physical problem but not in general learning tasks. We only found a divergence in the predicted direction for corvids. That only one of our comparisons supports the predictions under this hypothesis might be attributable to different complexities of tool-use in the two tool-using species. A critical evaluation is offered of the conceptual and methodological problems inherent in comparative studies on tool-related cognitive abilities

Background-free detection of trapped ions

We demonstrate a Doppler cooling and detection scheme for ions with low-lying D levels which almost entirely suppresses scattered laser light background, while retaining a high fluorescence signal and efficient cooling. We cool a single ion with a laser on the 2S1/2 to 2P1/2 transition as usual, but repump via the 2P3/2 level. By filtering out light on the cooling transition and detecting only the fluorescence from the 2P_3/2 to 2S1/2 decays, we suppress the scattered laser light background count rate to 1 per second while maintaining a signal of 29000 per second with moderate saturation of the cooling transition. This scheme will be particularly useful for experiments where ions are trapped in close proximity to surfaces, such as the trap electrodes in microfabricated ion traps, which leads to high background scatter from the cooling beam

Fabrication and heating rate study of microscopic surface electrode ion traps

We report heating rate measurements in a microfabricated gold-on-sapphire surface electrode ion trap with trapping height of approximately 240 micron. Using the Doppler recooling method, we characterize the trap heating rates over an extended region of the trap. The noise spectral density of the trap falls in the range of noise spectra reported in ion traps at room temperature. We find that during the first months of operation the heating rates increase by approximately one order of magnitude. The increase in heating rates is largest in the ion loading region of the trap, providing a strong hint that surface contamination plays a major role for excessive heating rates. We discuss data found in the literature and possible relation of anomalous heating to sources of noise and dissipation in other systems, namely impurity atoms adsorbed on metal surfaces and amorphous dielectrics.Comment: 17 pages, 5 figure

Ensemble Composition and Activity Levels of Insectivorous Bats in Response to Management Intensification in Coffee Agroforestry Systems

Shade coffee plantations have received attention for their role in biodiversity conservation. Bats are among the most diverse mammalian taxa in these systems; however, previous studies of bats in coffee plantations have focused on the largely herbivorous leaf-nosed bats (Phyllostomidae). In contrast, we have virtually no information on how ensembles of aerial insectivorous bats – nearly half the Neotropical bat species – change in response to habitat modification. To evaluate the effects of agroecosystem management on insectivorous bats, we studied their diversity and activity in southern Chiapas, Mexico, a landscape dominated by coffee agroforestry. We used acoustic monitoring and live captures to characterize the insectivorous bat ensemble in forest fragments and coffee plantations differing in the structural and taxonomic complexity of shade trees. We captured bats of 12 non-phyllostomid species; acoustic monitoring revealed the presence of at least 12 more species of aerial insectivores. Richness of forest bats was the same across all land-use types; in contrast, species richness of open-space bats increased in low shade, intensively managed coffee plantations. Conversely, only forest bats demonstrated significant differences in ensemble structure (as measured by similarity indices) across land-use types. Both overall activity and feeding activity of forest bats declined significantly with increasing management intensity, while the overall activity, but not feeding activity, of open-space bats increased. We conclude that diverse shade coffee plantations in our study area serve as valuable foraging and commuting habitat for aerial insectivorous bats, and several species also commute through or forage in low shade coffee monocultures