536 research outputs found
QuantumATK: An integrated platform of electronic and atomic-scale modelling tools
QuantumATK is an integrated set of atomic-scale modelling tools developed
since 2003 by professional software engineers in collaboration with academic
researchers. While different aspects and individual modules of the platform
have been previously presented, the purpose of this paper is to give a general
overview of the platform. The QuantumATK simulation engines enable
electronic-structure calculations using density functional theory or
tight-binding model Hamiltonians, and also offers bonded or reactive empirical
force fields in many different parametrizations. Density functional theory is
implemented using either a plane-wave basis or expansion of electronic states
in a linear combination of atomic orbitals. The platform includes a long list
of advanced modules, including Green's-function methods for electron transport
simulations and surface calculations, first-principles electron-phonon and
electron-photon couplings, simulation of atomic-scale heat transport, ion
dynamics, spintronics, optical properties of materials, static polarization,
and more. Seamless integration of the different simulation engines into a
common platform allows for easy combination of different simulation methods
into complex workflows. Besides giving a general overview and presenting a
number of implementation details not previously published, we also present four
different application examples. These are calculations of the phonon-limited
mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model
simulation of lithium ion drift through a battery cathode in an external
electric field, and electronic-structure calculations of the
composition-dependent band gap of SiGe alloys.Comment: Submitted to Journal of Physics: Condensed Matte
Bacterial diversity in snow on North Pole ice floes
The microbial abundance and diversity in snow on ice floes at three sites near the North Pole was assessed using quantitative PCR and 454 pyrosequencing. Abundance of 16S rRNA genes in the samples ranged between 43 and 248 gene copies per millilitre of melted snow. A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity. Two sites were dominated by Cyanobacteria (72 and 61 %, respectively), including chloroplasts. The third site differed by consisting of 95 % Proteobacteria. Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water. The Shannon indices ranged from 2.226 to 3.758, and the Chao1 indices showed species richness between 293 and 353 for the three samples. The relatively low abundances and diversity found in the samples indicate a lower rate of microbial input to this snow habitat compared to snow in the proximity of terrestrial and anthropogenic sources of microorganisms. The differences in species composition and diversity between the sites show that apparently similar snow habitats contain a large variation in biodiversity, although the differences were smaller than the differences to the underlying environment. The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00792-014-0660-y) contains supplementary material, which is available to authorized users
Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug-omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug-drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities. [Abstract copyright: © 2023. The Author(s).
Study of Inclusive J/psi Production in Two-Photon Collisions at LEP II with the DELPHI Detector
Inclusive J/psi production in photon-photon collisions has been observed at
LEP II beam energies. A clear signal from the reaction gamma gamma -> J/psi+X
is seen. The number of observed N(J/psi -> mu+mu-) events is 36 +/- 7 for an
integrated luminosity of 617 pb^{-1}, yielding a cross-section of
sigma(J/psi+X) = 45 +/- 9 (stat) +/- 17 (syst) pb. Based on a study of the
event shapes of different types of gamma gamma processes in the PYTHIA program,
we conclude that (74 +/- 22)% of the observed J/psi events are due to
`resolved' photons, the dominant contribution of which is most probably due to
the gluon content of the photon.Comment: 13 pages, 8 figures, Accepted by Phys. Lett.
Search for charginos in e+e- interactions at sqrt(s) = 189 GeV
An update of the searches for charginos and gravitinos is presented, based on
a data sample corresponding to the 158 pb^{-1} recorded by the DELPHI detector
in 1998, at a centre-of-mass energy of 189 GeV. No evidence for a signal was
found. The lower mass limits are 4-5 GeV/c^2 higher than those obtained at a
centre-of-mass energy of 183 GeV. The (\mu,M_2) MSSM domain excluded by
combining the chargino searches with neutralino searches at the Z resonance
implies a limit on the mass of the lightest neutralino which, for a heavy
sneutrino, is constrained to be above 31.0 GeV/c^2 for tan(beta) \geq 1.Comment: 22 pages, 8 figure
Hadronization properties of b quarks compared to light quarks in e+e- -> q qbar from 183 to 200 GeV
The DELPHI detector at LEP has collected 54 pb^{-1} of data at a
centre-of-mass energy around 183 GeV during 1997, 158 pb^{-1} around 189 GeV
during 1998, and 187 pb^{-1} between 192 and 200 GeV during 1999. These data
were used to measure the average charged particle multiplicity in e+e- -> b
bbar events, _{bb}, and the difference delta_{bl} between _{bb} and the
multiplicity, _{ll}, in generic light quark (u,d,s) events: delta_{bl}(183
GeV) = 4.55 +/- 1.31 (stat) +/- 0.73 (syst) delta_{bl}(189 GeV) = 4.43 +/- 0.85
(stat) +/- 0.61 (syst) delta_{bl}(200 GeV) = 3.39 +/- 0.89 (stat) +/- 1.01
(syst). This result is consistent with QCD predictions, while it is
inconsistent with calculations assuming that the multiplicity accompanying the
decay of a heavy quark is independent of the mass of the quark itself.Comment: 13 pages, 2 figure
Search for supersymmetric particles in scenarios with a gravitino LSP and stau NLSP
Sleptons, neutralinos and charginos were searched for in the context of
scenarios where the lightest supersymmetric particle is the gravitino. It was
assumed that the stau is the next-to-lightest supersymmetric particle. Data
collected with the DELPHI detector at a centre-of-mass energy near 189 GeV were
analysed combining the methods developed in previous searches at lower
energies. No evidence for the production of these supersymmetric particles was
found. Hence, limits were derived at 95% confidence level.Comment: 31 pages, 14 figure
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