Search results for " clusters"
showing 10 items of 1091 documents
FragClust and TestClust, two informatics tools for chemical structure hierarchical clustering analysis applied to lipidomics. The example of Alzheime…
2016
Lipidomic analysis is able to measure simultaneously thousands of compounds belonging to a few lipid classes. In each lipid class, compounds differ only by the acyl radical, ranging between C10:0 (capric acid) and C24:0 (lignoceric acid). Although some metabolites have a peculiar pathological role, more often compounds belonging to a single lipid class exert the same biological effect. Here, we present a lipidomics workflow that extracts the tandem mass spectrometry data from individual files and uses them to group compounds into structurally homogeneous clusters by chemical structure hierarchical clustering analysis (CHCA). The case-to-control peak area ratios of the metabolites are then a…
Evaluation of HIV transmission clusters among natives and foreigners living in Italy
2020
We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2&ndash
Out-of-plane orientation of luminescent excitons in two-dimensional indium selenide.
2019
Van der Waals materials offer a wide range of atomic layers with unique properties that can be easily combined to engineer novel electronic and photonic devices. A missing ingredient of the van der Waals platform is a two-dimensional crystal with naturally occurring out-of-plane luminescent dipole orientation. Here we measure the far-field photoluminescence intensity distribution of bulk InSe and two-dimensional InSe, WSe2 and MoSe2. We demonstrate, with the support of ab-initio calculations, that layered InSe flakes sustain luminescent excitons with an intrinsic out-of-plane orientation, in contrast with the in-plane orientation of dipoles we find in two-dimensional WSe2 and MoSe2 at room-…
High-throughput sequencing (HTS) for the analysis of viral populations
2020
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely appli…
Prospects and challenges for computer simulations of monolayer-protected metal clusters
2021
Precise knowledge of chemical composition and atomic structure of functional nanosized systems, such as metal clusters stabilized by an organic molecular layer, allows for detailed computational work to investigate structure-property relations. Here, we discuss selected recent examples of computational work that has advanced understanding of how these clusters work in catalysis, how they interact with biological systems, and how they can make self-assembled, macroscopic materials. A growing challenge is to develop effective new simulation methods that take into account the cluster-environment interactions. These new hybrid methods are likely to contain components from electronic structure t…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Interaction of C 60 fullerenes with asymmetric and curved lipid membranes: a molecular dynamics study
2015
Interaction of fullerenes with asymmetric and curved DOPC/DOPS bicelles is studied by means of coarse-grained molecular dynamics simulations. The effects caused by asymmetric lipid composition of the membrane leaflets and the curvature of the membrane are analyzed. It is shown that the aggregates of fullerenes prefer to penetrate into the membrane in the regions of the moderately positive mean curvature. Upon penetration into the hydrophobic core of the membrane fullerenes avoid the regions of the extreme positive or the negative curvature. Fullerenes increase the ordering of lipid tails, which are in direct contact with them, but do not influence other lipids significantly. Our data sugges…
$^{78}$Ni revealed as a doubly magic stronghold against nuclear deformation
2019
Nuclear magic numbers, which emerge from the strong nuclear force based on quantum chromodynamics, correspond to fully occupied energy shells of protons, or neutrons inside atomic nuclei. Doubly magic nuclei, with magic numbers for both protons and neutrons, are spherical and extremely rare across the nuclear landscape. While the sequence of magic numbers is well established for stable nuclei, evidence reveals modifications for nuclei with a large proton-to-neutron asymmetry. Here, we provide the first spectroscopic study of the doubly magic nucleus $^{78}$Ni, fourteen neutrons beyond the last stable nickel isotope. We provide direct evidence for its doubly magic nature, which is also predi…
The richest superclusters : I Morphology
2007
We study the morphology of the richest superclusters from the catalogues of superclusters of galaxies in the 2dF Galaxy Redshift Survey and compare the morphology of real superclusters with model superclusters in the Millennium Simulation. We use Minkowski functionals and shapefinders to quantify the morphology of superclusters: their sizes, shapes, and clumpiness. We generate empirical models of simple geometry to understand which morphologies correspond to the supercluster shapefinders. We show that rich superclusters have elongated, filamentary shapes with high-density clumps in their core regions. The clumpiness of superclusters is determined using the fourth Minkowski functional $V_3$.…
Ab initio calculations of pure and Co+2-doped MgF2 crystals
2020
This research was partly supported by the Kazakhstan Science Project № AP05134367«Synthesis of nanocrystals in track templates of SiO2/Si for sensory, nano- and optoelectronic applications», as well as by Latvian Research Council project lzp-2018/1-0214. Calculations were performed on Super Cluster (LASC) in the Institute of Solid State Physics (ISSP) of the University of Latvia. Authors are indebted to S. Piskunov for stimulating discussions.