High Performance Algorithms for Counting Collisions and Pairwise Interactions

The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject, mainly focused on techniques that allow calculations to be performed within pruned sets of objects. This paper focuses on how interaction calculation (such as collisions) within these sets can be done more efficiently than existing approaches. Two algorithms are proposed: a sequential algorithm that has linear complexity at the cost of high memory usage; and a parallel algorithm, mathematically proved to be correct, that manages to use GPU resources more efficiently than existing approaches. The proposed and existing algorithms were implemented, and experiments show a speedup of 21.7 for the sequential algorithm (on small problem size), and 1.12 for the parallel proposal (large problem size). By improving interaction calculation, this work contributes to research areas that promote interconnection in the modern world, such as computer graphics and robotics.Comment: Accepted in ICCS 2019 and published in Springer's LNCS series. Supplementary content at https://mjsaldanha.com/articles/1-hpc-ssp

High-spin structures of 136Cs

Odd-odd 136Cs nuclei have been produced in the 18O + 208Pb and 12C + 238U fusion-fission reactions and their gamma rays studied with the Euroball array. The high-spin level scheme has been built up to ~ 4.7 MeV excitation energy and spin I ~ 16 hbar from the triple gamma-ray coincidence data. The configurations of the three structures observed above ~ 2 MeV excitation energy are first discussed by analogy with the proton excitations identified in the semi-magic 137Cs nucleus, which involve the three high-j orbits lying above the Z=50 gap, pi g_{7/2}, pi d_{5/2} and pi h_{11/2}. This is confirmed by the results of shell-model calculations performed in this work.Comment: 6 pages, 4 figures, 3 table

Evolution of shell structure in neutron-rich calcium isotopes

We employ interactions from chiral effective field theory and compute the binding energies and low-lying excitations of calcium isotopes with the coupled-cluster method. Effects of three-nucleon forces are included phenomenologically as in-medium two-nucleon interactions, and the coupling to the particle continuum is taken into account using a Berggren basis. The computed ground-state energies and the low-lying 2+ states for the isotopes 42,48,50,52Ca are in good agreement with data, and we predict the excitation energy of the first 2+ state in 54Ca at 1.9 MeV, displaying only a weak sub-shell closure. In the odd-mass nuclei 53,55,61Ca we find that the positive parity states deviate strongly from the naive shell model.Comment: 5 pages, 4 figures; small correction of effective 3NF and slight change of the corresponding parameters; updated figures and tables; main results and conclusions unchange

Dewetting of thin polymer films near the glass transition

Dewetting of ultra-thin polymer films near the glass transition exhibits unexpected front morphologies [G. Reiter, Phys. Rev. Lett., 87, 186101 (2001)]. We present here the first theoretical attempt to understand these features, focusing on the shear-thinning behaviour of these films. We analyse the profile of the dewetting film, and characterize the time evolution of the dry region radius, $R_{d}(t)$, and of the rim height, $h_{m}(t)$. After a transient time depending on the initial thickness, $h_{m}(t)$ grows like $\sqrt{t}$ while $R_{d}(t)$ increases like $\exp{(\sqrt{t})}$. Different regimes of growth are expected, depending on the initial film thickness and experimental time range.Comment: 4 pages, 5 figures Revised version, published in Physical Review Letters: F. Saulnier, E. Raphael and P.-G. de Gennes, Phys. Rev. Lett. 88, 196101 (2002

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME†

Summary: Analysing large amounts of data generated by next-generation sequencing (NGS) technologies is difficult for researchers or clinicians without computational skills. They are often compelled to delegate this task to computer biologists working with command line utilities. The availability of easy-to-use tools will become essential with the generalization of NGS in research and diagnosis. It will enable investigators to handle much more of the analysis. Here, we describe Knime4Bio, a set of custom nodes for the KNIME (The Konstanz Information Miner) interactive graphical workbench, for the interpretation of large biological datasets. We demonstrate that this tool can be utilized to quickly retrieve previously published scientific findings

High-spin states with seniority v=4,4,6 in 119-126Sn

The 119-126Sn nuclei have been produced as fission fragments in two reactions induced by heavy ions: 12C+238U at 90 MeV bombarding energy, 18O+208Pb at 85 MeV. Their level schemes have been built from gamma rays detected using the Euroball array. High-spin states located above the long-lived isomeric states of the even- and odd-A 120-126Sn nuclei have been identified. Moreover isomeric states lying around 4.5 MeV have been established in 120,122,124,126Sn from the delayed coincidences between the fission fragment detector SAPhIR and the Euroball array. The states located above 3-MeV excitation energy are ascribed to several broken pairs of neutrons occupying the nu h11/2 orbit. The maximum value of angular momentum available in such a high-j shell, i.e. for mid-occupation and the breaking of the three neutron pairs, has been identified. This process is observed for the first time in spherical nuclei.Comment: 20 pages, 22 figures, 12 tables, accepted for publication in Physical Review

Cyclin L1 (CCNL1) gene alterations in human head and neck squamous cell carcinoma

We evaluated the expression and amplification of cyclin L1 (CCNL1) gene, a potential oncogene localised in the commonly amplified 3q25–28 region, in human head and neck squamous cell carcinomas (HNSCCs). Overexpression was observed in 55 out of 96 cases (57%) and amplification in nine out of 35 tumours (26%) with no relationships to the clinico-pathological parameters. The Cyclin L1 antibody we developed labels nuclear speckles in tumour cells compatible with a role for CCNL1 in RNA splicing

Copy number variant detection in inbred strains from short read sequence data

Summary: We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets

Hypertension and atrial fibrillation: diagnostic approach, prevention and treatment. Position paper of the Working Group 'Hypertension Arrhythmias and Thrombosis' of the European Society of Hypertension.

Hypertension is the most common cardiovascular disorder and atrial fibrillation is the most common clinically significant arrhythmia. Both these conditions frequently coexist and their prevalence increases rapidly with aging. There are different risk factors and clinical conditions predisposing to the development of atrial fibrillation, but due its high prevalence, hypertension is still the main risk factor for the development of atrial fibrillation. Several pathophysiologic mechanisms (such as structural changes, neurohormonal activation, fibrosis, atherosclerosis, etc.) have been advocated to explain the onset of atrial fibrillation. The presence of atrial fibrillation per se increases the risk of stroke but its coexistence with high blood pressure leads to an abrupt increase of cardiovascular complications. Different risk models are available for the risk stratification and the prevention of thromboembolism in patients with atrial fibrillation. In all of them hypertension is present and is an important risk factor. Antihypertensive treatment may contribute to reduce this risk, and it seems some classes are superior to others in the prevention of new-onset atrial fibrillation and prevention of stroke. Antithrombotic treatment with warfarin is effective in the prevention of thromboembolic events, although quite recently, new classes of anticoagulants that do not require international normalized ratio monitoring have been introduced with promising results