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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 4. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 5. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 6. |
- Munoz, William Armando, et al.
(författare)
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Insulator to semimetallic transition in conducting polymers
- 2016
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 94:20
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Tidskriftsartikel (refereegranskat)abstract
- We report a multiscale modeling of electronic structure of a conducting polymer poly(3,4-ethylenedioxythiopehene) (PEDOT) based on a realistic model of its morphology. We show that when the charge carrier concentration increases, the character of the density of states (DOS) gradually evolves from the insulating to the semimetallic, exhibiting a collapse of the gap between the bipolaron and valence bands with the drastic increase of the DOS between the bands. The origin of the observed behavior is attributed to the effect of randomly located counterions giving rise to the states in the gap. These results are discussed in light of recent experiments. The method developed in this work is general and can be applied to study the electronic structure of other conducting polymers.
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| 7. |
- Munoz, William Armando, et al.
(författare)
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Understanding the Impact of Film Disorder and Local Surface Potential in Ultraviolet Photoelectron Spectroscopy of PEDOT
- 2018
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Ingår i: Macromolecular rapid communications. - : WILEY-V C H VERLAG GMBH. - 1022-1336 .- 1521-3927. ; 39:4
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Tidskriftsartikel (refereegranskat)abstract
- The spectra of conducting polymers obtained using ultraviolet photoelectron spectroscopy (UPS) exhibit a typical broadening of the tail sigma(UPS) approximate to 1 eV, which by an order of magnitude exceeds a commonly accepted value of the broadening of the tail of the density of states sigma(DOS) approximate to 0.1 eV obtained using transport measurements. In this work, an origin of this anomalous broadening of the tail of the UPS spectra in a doped conducting polymer, PEDOT (poly(3,4-ethylenedioxythiophene)), is discussed. Based on the semiempirical approach and using a realistic morphological model, the density of valence states in PEDOT doped with molecular counterions is computed. It is shown that due to a disordered character of the material with randomly distributed counterions, the localized charge carriers in PEDOT crystallites experience spatially varying electrostatic potential. This leads to spatially varying local vacuum levels and binding energies. Taking this variation into account the UPS spectrum is obtained with the broadening of the tail comparable to the experimentally observed one. The results imply that the observed broadening of the tail of the UPS spectra in PEDOT provides information about a disordered spatially varying potential in the material rather than the broadening of the DOS itself.
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| 8. |
- Ångqvist, Mattias, 1989, et al.
(författare)
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ICET - A Python Library for Constructing and Sampling Alloy Cluster Expansions
- 2019
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Ingår i: Advanced Theory and Simulations. - : Wiley. - 2513-0390. ; 2:7
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Tidskriftsartikel (refereegranskat)abstract
- Alloy cluster expansions (CEs) provide an accurate and computationally efficient mapping of the potential energy surface of multi-component systems that enables comprehensive sampling of the many-dimensional configuration space. Here, integrated cluster expansion toolkit (ICET), a flexible, extensible, and computationally efficient software package, is introduced for the construction and sampling of CEs. ICET is largely written in Python for easy integration in comprehensive workflows, including first-principles calculations for the generation of reference data and machine learning libraries for training and validation. The package enables training using a variety of linear regression algorithms with and without regularization, Bayesian regression, feature selection, and cross-validation. It also provides complementary functionality for structure enumeration and mapping as well as data management and analysis. Potential applications are illustrated by two examples, including the computation of the phase diagram of a prototypical metallic alloy and the analysis of chemical ordering in an inorganic semiconductor.
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