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

Neutron Spectrometry with Scintillating Bolometers of LiF and Sapphire

Two scintillating bolometers of LiF (33 g) and Al2O3 (50 g) at 20 mK, inside a lead shielding at the Canfranc Underground Laboratory, were irradiated with neutrons from a source of 252Cf. The analysis of nuclear recoils registered by sapphire and (n, a) captures by 6Li shows the feasibility of these cryogenic devices to measure the spectral flux of a neutron field. Data unfolding was done assuming that the spectral flux is a piecewise constant function defined on six energy groups. It can be solved by using non-negative least squares without additional assumptions on the neutron flux. The model provides consistent results with the spectra of the observed events in bolometers, giving a fast neutron flux of F(E > 0.1 MeV) = 0.20 n s-1cm-2 with a 15% uncertainty after 3 hours of live time. After our analysis, it can be concluded that nuclear recoils in sapphire are more useful than (n, a) captures in LiF for spectrometry of fast neutrons

Energy partition in Sapphire and BGO scintillating bolometers

International audienceScintillating bolometers are particle detectors with a high particle discrimination power with many applications in nuclear and particle physics. This discrimination power is based on the different scintillation yield for different particles, and is strongly dependent on the target used. At the very low temperatures required for the operation of the bolometers, very few data about the scintillation yields are available. In this paper we present estimates of absolute light yields and energy partition among heat, light and trapping channels in Sapphire (AlO) and BGO (BiGeO) scintillating bolometers operated at 20 mK. The estimate relies on the observed negative correlation between the light and heat signals produced by γ-ray absorption in scintillating bolometers and on the study of the x-ray stimulated luminescence properties of BGO at temperatures down to 77 K

Response of parylene-coated NaI(Tl) scintillators at low temperature

Despite that it is widely used as a scintillator at room temperature, the hygroscopicity of NaI complicates its handling and limits its application for many purposes, for example as a cryogenic detector. To overcome this problem we study coating materials that can act as humidity barriers, in particular parylene, a polymer that can be deposited in very radiopure, thin and conformal layers. In this work, several NaI(Tl) samples coated with 2-5 µm parylene-C were tested at low temperature. Luminescence spectra under X-ray excitation are presented at several temperatures as well as the light output vs temperature at 1.5-300 K. Several thermoluminescence peaks were observed at around 60, 95 and 150 K during warm up to room temperature The mechanical resistance of the coating under thermal cycles was also investigated, and we observed a degradation of the optical appearance and the light output after cooling down to about 100 mK, which compromises the reusability of the samples

Capillary Bridge Formation and Breakage: A Test to Characterize Antiadhesive Surfaces

In order to characterize very weak adhesive surfaces, we have developed a quantitative test inspired by the Johnson, Kendall, and Roberts adhesion test for soft adhesives, which relies on the formation and then the rupture of a capillary bridge between the surface to be tested and a liquid bath. Both the shape and the kinetics of breakage of the capillary bridge for various coatings put into contact with liquids of various viscosities and surface tensions have been studied. Several pull off regimes can be distinguished. For low pull off velocities, a quasi-static regime is observed, well described by capillary equations and sensitive to the hysteresis of the contact angle of the fluid on the coating. Above a critical pull off velocity that depends on the fluid viscosity, a dynamic regime is observed, characterized by the formation of a flat pancake of fluid on the coating that recedes more slowly than the capillary bridge itself. After the breakage of the capillary bridge, a small drop can remain attached to the surface. The volume of this drop depends on the dynamical regime and is strongly affected by very small differences between the coatings. The aptitude of this test in characterizing very weakly adhesive surfaces is exemplified by a comparison between three different perfluorinated coatings

The nutrigenetic influence of the interaction between dietary vitamin E and TXN and COMT gene polymorphisms on waist circumference: a case control study

Journal Article; Research Support, Non-U.S. Gov't;BACKGROUND Abdominal obesity (AO) is a common modifiable risk factor for certain non-communicable diseases associated with enhanced oxidative stress (OS). The objective of this work was to investigate whether the interaction between antioxidant vitamin intake and OS-related polymorphisms modulates gene-associated anthropometry in a Spanish population. METHODS A total of 246 subjects with AO, and 492 age and gender matched non-AO subjects were included in the study. Anthropometric, biochemical, and OS parameters, and antioxidant dietary intake data were assessed using validated procedures. DNA from white blood cells was isolated and the genotype of seven polymorphisms from genes involved in OS (pro-oxidant and antioxidant) were analyzed using the SNPlex system. The effects of the c.-793T > C polymorphism on promoter activity and thus thioredoxin (TXN) activity were examined using reporter assays. RESULTS The AO group had higher 8-Oxo-2'-deoxyguanosine levels and took in less vitamin A and vitamin E compared to the non-AO group. Logistic regression analysis revealed that the rs2301241 polymorphism in TXN and rs740603 in catechol-O-methyltransferase (COMT) were associated with waist circumference (WC) and AO. Moreover, these polymorphisms were more strongly associated with variations in WC in subjects with low vitamin E intakes. A promoter assay revealed that the T to C conversion at c.-793 (rs2301241) induced a more than two fold increase in reporter gene expression. CONCLUSIONS WC is associated both with dietary vitamin E intake and genetic variants of TXN and COMT suggesting that existence of a complex nutrigenetic pathway that involves regulation of AO.This work was co-funded with European Funds for Regional Development (FEDER), the Spanish Science and Technology Ministry [SAF2005-02883]; the health research fund from the Carlos III Health Institute [PI070497], CIBER Fisiopatología Obesidad y Nutrición (CIBERobn) [CB06/03], and CIBER de Diabetes y Enfermedades Metabólicas Relacionadas (CIBERDEM). CIBEROB and CIBERDEM are initiatives by the Carlos III Health Institute in Madrid and the Spanish Health Ministry. Funding also came from GRUPOS 03/101, PROMETEO/2009/029 and 2005/027, AMP07/075, and ACOMP/2009/201 from the Valencian Government and European Network of Excellence InGenious HyperCare (EPSS-037093) from the European Commission.Ye

Proceedings of the third French-Ukrainian workshop on the instrumentation developments for HEP

The reports collected in these proceedings have been presented in the third French-Ukrainian workshop on the instrumentation developments for high-energy physics held at LAL, Orsay on October 15-16. The workshop was conducted in the scope of the IDEATE International Associated Laboratory (LIA). Joint developments between French and Ukrainian laboratories and universities as well as new proposals have been discussed. The main topics of the papers presented in the Proceedings are developments for accelerator and beam monitoring, detector developments, joint developments for large-scale high-energy and astroparticle physics projects, medical applications.Comment: 3rd French-Ukrainian workshop on the instrumentation developments for High Energy Physics, October 15-16, 2015, LAL, Orsay, France, 94 page

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A classification model for distinguishing copy number variants from cancer-related alterations

<p>Abstract</p> <p>Background</p> <p>Both somatic copy number alterations (CNAs) and germline copy number variants (CNVs) that are prevalent in healthy individuals can appear as recurrent changes in comparative genomic hybridization (CGH) analyses of tumors. In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively.</p> <p>Results</p> <p>We develop a prediction model that distinguishes CNVs from CNAs based on the information contained in the DGV and several other variables, including segment's length, height, closeness to a telomere or centromere and occurrence in other patients. The models are fitted on data from glioblastoma and their corresponding normal samples that were collected as part of The Cancer Genome Atlas project and hybridized to Agilent 244 K arrays.</p> <p>Conclusions</p> <p>Using the DGV alone CNVs in the test set can be correctly identified with about 85% accuracy if the outliers are removed before segmentation and with 72% accuracy if the outliers are included, and additional variables improve the prediction by about 2-3% and 12%, respectively. Final models applied to data from ovarian tumors have about 90% accuracy with all the variables and 86% accuracy with the DGV alone.</p