DiBELLA: Distributed long read to long read alignment

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies

The magnetic exchange parameters and anisotropy of the quasi-two dimensional antiferromagnet NiPS3_3

Neutron inelastic scattering has been used to measure the magnetic excitations in powdered NiPS$_3$, a quasi-two dimensional antiferromagnet with spin $S = 1$ on a honeycomb lattice. The spectra show clear, dispersive magnons with a $\sim 7$ meV gap at the Brillouin zone center. The data were fitted using a Heisenberg Hamiltonian with a single-ion anisotropy assuming no magnetic exchange between the honeycomb planes. Magnetic exchange interactions up to the third intraplanar nearest-neighbour were required. The fits show robustly that NiPS$_3$ has an easy axis anisotropy with $\Delta = 0.3$ meV and that the third nearest-neighbour has a strong antiferromagnetic exchange of $J_3 = -6.90$ meV. The data can be fitted reasonably well with either $J_1 < 0$ or $J_1 > 0$, however the best quantitative agreement with high-resolution data indicate that the nearest-neighbour interaction is ferromagnetic with $J_1 = 1.9$ meV and that the second nearest-neighbour exchange is small and antiferromagnetic with $J_2 = -0.1$ meV. The dispersion has a minimum in the Brillouin zone corner that is slightly larger than that at the Brillouin zone center, indicating that the magnetic structure of NiPS$_3$ is close to being unstable.Comment: 21 pages, 7 figures, 33 reference

Can an ethical revival of prudence within prudential regulation tackle corporate psychopathy?

The view that corporate psychopathy played a significant role in causing the global financial crisis, although insightful, paints a reductionist picture of what we present as the broader issue. Our broader issue is the tendency for psychopathy, narcissism and Machiavellianism to cluster psychologically and culturally as ‘dark leadership’ within global financial institutions. Strong evidence for their co-intensification across society and in corporations ought to alarm financial regulators. We argue that an ‘ethical revival’ of prudence within prudential regulation ought to be included in any package of solutions. Referencing research on moral muteness and the role of language in framing thoughts and behaviours, we recommend that regulators define prudence in an explicitly normative sense, an approach that may be further strengthened by drawing upon a widely appealing ethic of intergenerational care. An ethical revival of prudence, we argue, would allow the core problems of greed and myopia highlighted by corporate psychopathy theory to be addressed in a politically sensitive manner which recognises the pitfalls of regulating directly against corporate psychopathy. Furthermore, it would provide a viable conceptual framework to guide regulators along the treacherous path to more intrusive cultural regulation

Influence of incoherent scattering on stochastic deflection of high-energy negative particle beams in bent crystals

An investigation on stochastic deflection of high-energy negatively charged particles in a bent crystal was carried out. On the basis of analytical calculation and numerical simulation it was shown that it exists a maximum angle at which most of the beam is deflected. The existence of a maximum, which is taken in the correspondence of the optimal radius of curvature, is a novelty with respect to the case of positively charged particles, for which the deflection angle can be freely increased by increasing the crystal length. This difference has to be ascribed to the stronger contribution of incoherent scattering affecting the dynamics of negative particles that move closer to atomic nuclei and electrons. We therefore identified the ideal parameters for the exploitation of axial confinement for negatively charged particle beam manipulation in future high-energy accelerators, e.g., ILC or muon colliders

Reasoning About a Service-oriented Programming Paradigm

This paper is about a new way for programming distributed applications: the service-oriented one. It is a concept paper based upon our experience in developing a theory and a language for programming services. Both the theoretical formalization and the language interpreter showed us the evidence that a new programming paradigm exists. In this paper we illustrate the basic features it is characterized by

A model for the interaction of high-energy particles in straight and bent crystals implemented in Geant4

A model for the simulation of orientational effects in straight and bent periodic atomic structures is presented. The continuum potential approximation has been adopted.The model allows the manipulation of particle trajectories by means of straight and bent crystals and the scaling of the cross sections of hadronic and electromagnetic processes for channeled particles. Based on such a model, an extension of the Geant4 toolkit has been developed. The code has been validated against data from channeling experiments carried out at CERN

Planar channeling and quasichanneling oscillations in a bent crystal

Particles passing through a crystal under planar channeling experience transverse oscillations in their motion. As channeled particles approach the atomic planes of a crystal, they are likely to be dechanneled. This effect was used in ion-beam analysis with MeV energy. We studied this effect in a bent crystal for positive and negative particles within a wide range of energies in sight of application of such crystals at accelerators. We found the conditions for the appearance or not of channeling oscillations. Indeed a new kind of oscillations, strictly related to the motion of over-barrier particles, i.e. quasichanneling particles, has been predicted. Such oscillations, named planar quasichanneling oscillations, possess a different nature than channeling oscillations. Through computer simulation, we studied this effect and provided a theoretical interpretation for them. We show that channeling oscillations can be observed only for positive particles while quasichanneling oscillations can exist for particles with either sign. The conditions for experimental observation of channeling and quasichanneling oscillations at existing accelerators with available crystal has been found and optimized.Comment: 25 pages, 11 figure

Exotic magnetism on the quasi-FCC lattices of the d3d^3 double perovskites La2_2NaB′'O6_6 (B′' == Ru, Os)

We find evidence for long-range and short-range ($\zeta$ $=$ 70 \AA~at 4 K) incommensurate magnetic order on the quasi-face-centered-cubic (FCC) lattices of the monoclinic double perovskites La$_2$NaRuO$_6$ and La$_2$NaOsO$_6$ respectively. Incommensurate magnetic order on the FCC lattice has not been predicted by mean field theory, but may arise via a delicate balance of inequivalent nearest neighbour and next nearest neighbour exchange interactions. In the Ru system with long-range order, inelastic neutron scattering also reveals a spin gap $\Delta$ $\sim$ 2.75 meV. Magnetic anisotropy is generally minimized in the more familiar octahedrally-coordinated $3d^3$ systems, so the large gap observed for La$_2$NaRuO$_6$ may result from the significantly enhanced value of spin-orbit coupling in this $4d^3$ material.Comment: 5 pages, 4 figure