Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

BackgroundTo reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.ResultsLog::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research

Pauli-Limited Superconductivity in Small Grains

We report on an exploration of the mean-field phase diagram for Pauli-limited superconductivity in small metallic grains. Emphasis is placed on the crossover from the ultra-small grain limit where superconductivity disappears to the bulk thin-film limit as the single-particle level spacing in the grain decreases. We find that the maximum Zeeman coupling strength compatible with superconductivity increases with decreasing grain size, in spite of a monotonically decreasing condensation energy per unit volume.Comment: 4 pages of text, 6 figure

Potential impact of climate change on improved and unimproved water supplies in Africa

With significant climate change predicted in Africa over the next century, this chapter explores a key question: how will rural water supplies in Africa be affected? Approximately 550 million people in Africa live in rural communities and are reliant on water resources within walking distance of their community for drinking water. Less than half have access to improved sources (generally large diameter wells, springs, or boreholes equipped with handpumps); the majority rely on unimproved sources, such as open water and shallow wells. Major climate modelling uncertainties, combined with rapid socio-economic change, make predicting the future state of African water resources difficult; an appropriate response to climate change is to assume much greater uncertainty in climate and intensification of past climate variability. Based on this assumption the following should be considered: 1. Those relying on unimproved water sources (300 million in rural Africa) are likely to be most affected by climate change because unimproved sources often use highly vulnerable water resources. 2. Improved rural water supplies in Africa are overwhelmingly dependent on groundwater, due to the unreliability of other sources. 3. Climate change is unlikely to lead to continent-wide failure of improved rural water sources that access deeper groundwater (generally over 20 metres below ground surface) through boreholes or deep wells. This is because groundwater-based domestic supply requires little recharge, and the groundwater resources at depth will generally be of sufficient storage capacity to remain a secure water resource. However, a significant minority of people could be affected if the frequency and length of drought increases – particularly those in areas with limited groundwater storage. 4. In most areas, the key determinants of water security will continue to be driven by access to water rather than absolute water availability. Extending access, and ensuring that targeting and technology decisions are informed by an understanding of groundwater conditions, will become increasingly important. 5. Accelerating groundwater development for irrigation could increase food production, raise farm incomes and reduce overall vulnerability. However, ad hoc development could threaten domestic supplies and, in some areas, lead to groundwater depletion. Although climate change will undoubtedly be important in determining future water security, other drivers (such as population growth and rising food demands) are likely to provide greater pressure on rural water supplies

Magnetization orientation dependence of the quasiparticle spectrum and hysteresis in ferromagnetic metal nanoparticles

We use a microscopic Slater-Koster tight-binding model with short-range exchange and atomic spin-orbit interactions that realistically captures generic features of ferromagnetic metal nanoparticles to address the mesoscopic physics of magnetocrystalline anisotropy and hysteresis in nanoparticle quasiparticle excitation spectra. Our analysis is based on qualitative arguments supported by self-consistent Hartree-Fock calculations for nanoparticles containing up to 260 atoms. Calculations of the total energy as a function of magnetization direction demonstrate that the magnetic anisotropy per atom fluctuates by several percents when the number of electrons in the particle changes by one, even for the largest particles we consider. Contributions of individual orbitals to the magnetic anisotropy are characterized by a broad distribution with a mean more than two orders of magnitude smaller than its variance and with no detectable correlations between anisotropy contribution and quasiparticle energy. We find that the discrete quasiparticle excitation spectrum of a nanoparticle displays a complex non-monotonic dependence on an external magnetic field, with abrupt jumps when the magnetization direction is reversed by the field, explaining recent spectroscopic studies of magnetic nanoparticles. Our results suggests the existence of a broad cross-over from a weak spin-orbit coupling to a strong spin-orbit coupling regime, occurring over the range from approximately 200- to 1000-atom nanoparticles.Comment: 39 pages, 18 figures, to be published in Physical Review

Thin films of a three-dimensional topological insulator in a strong magnetic field: a microscopic study

The response of thin films of Bi$_2$Se$_3$ to a strong perpendicular magnetic field is investigated by performing magnetic bandstructure calculations for a realistic multi-band tight-binding model. Several crucial features of Landau quantization in a realistic three-dimensional topological insulator are revealed. The $n=0$ Landau level is absent in ultra-thin films, in agreement with experiment. In films with a crossover thickness of five quintuple layers, there is a signature of the $n=0$ level, whose overall trend as a function of magnetic field matches the established low-energy effective-model result. Importantly, we find a field-dependent splitting and a strong spin-polarization of the $n=0$ level which can be measured experimentally at reasonable field strengths. Our calculations show mixing between the surface and bulk Landau levels which causes the character of levels to evolve with magnetic field.Comment: 5 pages, 4 figure

Design Patterns for Fusion-Based Object Retrieval

We address the task of ranking objects (such as people, blogs, or verticals) that, unlike documents, do not have direct term-based representations. To be able to match them against keyword queries, evidence needs to be amassed from documents that are associated with the given object. We present two design patterns, i.e., general reusable retrieval strategies, which are able to encompass most existing approaches from the past. One strategy combines evidence on the term level (early fusion), while the other does it on the document level (late fusion). We demonstrate the generality of these patterns by applying them to three different object retrieval tasks: expert finding, blog distillation, and vertical ranking.Comment: Proceedings of the 39th European conference on Advances in Information Retrieval (ECIR '17), 201

Elementary Excitations of Ferromagnetic Metal Nanoparticles

We present a theory of the elementary spin excitations in transition metal ferromagnet nanoparticles which achieves a unified and consistent quantum description of both collective and quasiparticle physics. The theory starts by recognizing the essential role played by spin-orbit interactions in determining the energies of ferromagnetic resonances in the collective excitation spectrum and the strength of their coupling to low-energy particle-hole excitations. We argue that a crossover between Landau-damped ferromagnetic resonance and pure-state collective magnetic excitations occurs as the number of atoms in typical transition metal ferromagnet nanoparticles drops below approximately $10^4$, approximately where the single-particle level spacing, $\delta$, becomes larger than, $\sqrt{\alpha} E_{\rm res}$, where $E_{\rm res}$ is the ferromagnetic resonance frequency and $\alpha$ is the Gilbert damping parameter. We illustrate our ideas by studying the properties of semi-realistic model Hamiltonians, which we solve numerically for nanoparticles containing several hundred atoms. For small nanoparticles, we find one isolated ferromagnetic resonance collective mode below the lowest particle-hole excitation energy, at $E_{\rm res} \approx 0.1$ meV. The spectral weight of this pure excitation nearly exhausts the transverse dynamical susceptibility spectral weight. As $\delta$ approaches $\sqrt{\alpha} E_{\rm res}$, the ferromagnetic collective excitation is more likely to couple strongly with discrete particle-hole excitations. In this regime the distinction between the two types of excitations blurs. We discuss the significance of this picture for the interpretation of recent single-electron tunneling experiments.Comment: 19 pages, 13 figure

Current-induced torques due to compensated antiferromagnets

We analyse the influence of current induced torques on the magnetization configuration of a ferromagnet in a circuit containing a compensated antiferromagnet. We argue that these torques are generically non-zero and support this conclusion with a microscopic NEGF calculation for a circuit containing antiferromagnetic NiMn and ferromagnetic Co layers. Because of symmetry dictated differences in the form of the current-induced torque, the phase diagram which expresses the dependence of ferromagnet configuration on current and external magnetic field differs qualitatively from its ferromagnet-only counterpart.Comment: 4 pages, 5 figure

A new code for parameter estimation in searches for gravitational waves from known pulsars

We describe the consistency testing of a new code for gravitational wave signal parameter estimation in known pulsar searches. The code uses an implementation of nested sampling to explore the likelihood volume. Using fake signals and simulated noise we compare this to a previous code that calculated the signal parameter posterior distributions on both a grid and using a crude Markov chain Monte Carlo (MCMC) method. We define a new parameterisation of two orientation angles of neutron stars used in the signal model (the initial phase and polarisation angle), which breaks a degeneracy between them and allows more efficient exploration of those parameters. Finally, we briefly describe potential areas for further study and the uses of this code in the future.Comment: Accepted for proceedings of Amaldi 9 meetin