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

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

Site recurrence of open and unitary quantum walks on the line

We study the problem of site recurrence of discrete time nearest neighbor open quantum random walks (OQWs) on the integer line, proving basic properties and some of its relations with the corresponding problem for unitary (coined) quantum walks (UQWs). For both kinds of walks our discussion concerns two notions of recurrence, one given by a monitoring procedure, another in terms of P\'olya numbers, and we study their similarities and differences. In particular, by considering UQWs and OQWs induced by the same pair of matrices, we discuss the fact that recurrence of these walks are related by an additive interference term in a simple way. Based on a previous result of positive recurrence we describe an open quantum version of Kac's lemma for the expected return time to a site

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

Electromagnetic dipole moments of charged baryons with bent crystals at the LHC

We propose a unique program of measurements of electric and magnetic dipole moments of charm, beauty and strange charged baryons at the LHC, based on the phenomenon of spin precession of channeled particles in bent crystals. Studies of crystal channeling and spin precession of positively- and negatively-charged particles are presented, along with feasibility studies and expected sensitivities for the proposed experiment using a layout based on the LHCb detector.Comment: 19 pages, 13 figure

Italian Science Case for ALMA Band 2+3

The Premiale Project "Science and Technology in Italy for the upgraded ALMA Observatory - iALMA" has the goal of strengthening the scientific, technological and industrial Italian contribution to the Atacama Large Millimeter/submillimeter Array (ALMA), the largest ground based international infrastructure for the study of the Universe in the microwave. One of the main objectives of the Science Working Group (SWG) inside iALMA, the Work Package 1, is to develop the Italian contribution to the Science Case for the ALMA Band 2 or Band 2+3 receiver. ALMA Band 2 receiver spans from ~67 GHz (bounded by an opaque line complex of ozone lines) up to 90 GHz which overlaps with the lower frequency end of ALMA Band 3. Receiver technology has advanced since the original definition of the ALMA frequency bands. It is now feasible to produce a single receiver which could cover the whole frequency range from 67 GHz to 116 GHz, encompassing Band 2 and Band 3 in a single receiver cartridge, a so called Band 2+3 system. In addition, upgrades of the ALMA system are now foreseen that should double the bandwidth to 16 GHz. The science drivers discussed below therefore also discuss the advantages of these two enhancements over the originally foreseen Band 2 system.Comment: 43 pages, 21 figure

3D Visualization of Cultural Heritage Artefacts with Virtual Reality devices

Although 3D models are useful to preserve the information about historical artefacts, the potential of these digital contents are not fully accomplished until they are not used to interactively communicate their significance to non-specialists. Starting from this consideration, a new way to provide museum visitors with more information was investigated. The research is aimed at valorising and making more accessible the Egyptian funeral objects exhibited in the Sforza Castle in Milan. The results of the research will be used for the renewal of the current exhibition, at the Archaeological Museum in Milan, by making it more attractive. A 3D virtual interactive scenario regarding the "path of the dead", an important ritual in ancient Egypt, was realized to augment the experience and the comprehension of the public through interactivity. Four important artefacts were considered for this scope: two ushabty, a wooden sarcophagus and a heart scarab. The scenario was realized by integrating low-cost Virtual Reality technologies, as the Oculus Rift DK2 and the Leap Motion controller, and implementing a specific software by using Unity. The 3D models were implemented by adding responsive points of interest in relation to important symbols or features of the artefact. This allows highlighting single parts of the artefact in order to better identify the hieroglyphs and provide their translation. The paper describes the process for optimizing the 3D models, the implementation of the interactive scenario and the results of some test that have been carried out in the lab

Organic molecules in the protoplanetary disk of DG Tau revealed by ALMA

Planets form in protoplanetary disks and inherit their chemical compositions. It is thus crucial to map the distribution and investigate the formation of simple organics, such as formaldehyde and methanol, in protoplanetary disks. We analyze ALMA observations of the nearby disk-jet system around the T Tauri star DG Tau in the o-H$_2$CO $3_{1,2}-2_{1,1}$ and CH$_3$OH $3_{-2,2}-4_{-1,4}$ E, $5_{0,5}-4_{0,4}$ A transitions at an unprecedented resolution of $\sim0.15"$, i.e., $\sim18$ au at a distance of 121 pc. The H$_2$CO emission originates from a rotating ring extending from $\sim40$ au with a peak at $\sim62$ au, i.e., at the edge of the 1.3mm dust continuum. CH$_3$OH emission is not detected down to an r.m.s. of 3 mJy/beam in the 0.162 km/s channel. Assuming an ortho-to-para ratio of 1.8-2.8 the ring- and disk-height-averaged H$_2$CO column density is $\sim0.3-4\times10^{14}$ cm$^{-2}$, while that of CH$_3$OH is $<0.04-0.7\times10^{14}$ cm$^{-2}$. In the inner $40$ au no o-H$_2$CO emission is detected with an upper limit on its beam-averaged column density of $\sim0.5-6\times10^{13}$ cm$^{-2}$. The H$_2$CO ring in the disk of DG Tau is located beyond the CO iceline (R$_{\rm CO}\sim30$ au). This suggests that the H$_2$CO abundance is enhanced in the outer disk due to formation on grain surfaces by the hydrogenation of CO ice. The emission peak at the edge of the mm dust continuum may be due to enhanced desorption of H$_2$CO in the gas phase caused by increased UV penetration and/or temperature inversion. The CH$_3$OH/H$_2$CO abundance ratio is $<1$, in agreement with disk chemistry models. The inner edge of the H$_2$CO ring coincides with the radius where the polarization of the dust continuum changes orientation, hinting at a tight link between the H$_2$CO chemistry and the dust properties in the outer disk and at the possible presence of substructures in the dust distribution.Comment: 8 pages, 6 figures, accepted for publication on A&A Letter