| 1. |
- 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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| 2. |
- Gao, Bin, et al.
(författare)
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A density functional theory study of shake-up satellites in photoemission of carbon fullerenes and nanotubes
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:23, s. 234704-1-234704-7
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Tidskriftsartikel (refereegranskat)abstract
- Carbon 1s shake-up spectra of fullerenes C-60, C-70, and C-82 and single-walled carbon nanotubes (SWCNTs) of (5,5), (6,5), and (7,6) have been investigated by using equivalent core hole Kohn-Sham density functional theory approach, in which only one-electron transition between molecular orbitals within core-hole potential is considered. The calculated spectra are generally in good agreement with results of equivalent core-hole time-dependent density functional theory calculations and available experiments, and reliable assignments for the complicated shake-up spectra of such large systems are provided. Calculations have also been performed for endohedral metallofullerene Gd@C-82 to demonstrate the possible use of shake-up processes to identify the charge transfer between the metal ion and the carbon cage. It is found that the exciton binding energy of all systems under investigation is around 0.5 eV.
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| 3. |
- Gao, Bin, et al.
(författare)
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An efficient first-principle approach for electronic structures calculations of nanomaterials
- 2008
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:3, s. 434-444
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Tidskriftsartikel (refereegranskat)abstract
- An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.
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| 4. |
- Gao, Bin, et al.
(författare)
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Chirality and diameter dependent x-ray absorption of single walled carbon nanotubes
- 2009
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 131:3, s. 034704-1-034704-7
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Tidskriftsartikel (refereegranskat)abstract
- The lack of good understanding on the electronic structure of individual carbon nanotubes severely limited the applications of carbon nanotubes. By employing density functional theory in combination with the equivalent core hole approximation, we are able to provide near edge x-ray absorption fine structure (NEXAFS) spectra of all possible single walled carbon nanotubes (SWCNTs) with diameters below 1.45 nm. It is shown that the pi(*) absorption edges in NEXAFS spectra of SWCNTs are converged already at the length of 3 nm, while a good description of the full spectra can only be obtained after 7 nm. A recent high resolution experimental spectrum of a bundle of SWCNTs with diameters 1.37 +/- 0.08 nm has been successfully assigned by the calculations. Noticeable chirality and diameter dependence have been identified for the simulated NEXAFS spectra. The collection of calculated spectra serves as a useful reference for experimental identification of individual carbon nanotubes.
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| 5. |
- Gao, Bin, et al.
(författare)
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Energy gaps, electronic structures, and x-ray spectroscopies of finite semiconductor single-walled carbon nanotubes
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:8, s. 084707-1-084707-8
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Tidskriftsartikel (refereegranskat)abstract
- We report hybrid density functional theory calculations for electronic structures of hydrogen-terminated finite single-walled carbon nanotubes (6,5) and (8,3) up to 100 nm in length. Gap states that are mainly arisen from the hydrogen-terminated edges have been found in (8,3) tubes, but their contributions to the density of states become invisible when the tube is longer than 10 nm. The electronic structures of (6,5) and (8,3) tubes are found to be converged around 20 nm. The calculated band-gap energies of 100 nm long nanotubes are in good agreement with experimental results. The valence band structures of (6,5), (8,3), as well as (5,5) tubes are also investigated by means of ultraviolet photoelectron spectra (UPS), x-ray emission spectroscopy (XES), and the resonant inelastic x-ray scattering (RIXS) spectra theoretically. The UPS, XES and RIXS spectra become converged already at 10 nm. The length-dependent oscillation behavior is found in the RIXS spectra of (5,5) tubes, indicating that the RIXS spectra may be used to determine the size and length of metallic nanotubes. Furthermore, the chiral dependence observed in the simulated RIXS spectra suggests that RIXS spectra could be a useful technique for the determination of chirality of carbon nanotubes.
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| 6. |
- Gao, Bin, et al.
(författare)
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Spectral identification of fullerene C82 isomers
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 127:16, s. 164314-1-164314-8
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Tidskriftsartikel (refereegranskat)abstract
- Ultraviolet photoelectron spectra (UPS) of C-82 isomers have been calculated using hybrid density functional theory in combination with the Gelius model [Proceedings of the International Conference on Electron spectroscopy, edited by D. A. Shirley (North-Holland, Amsterdam, 1972), p. 311; J. Electron Spectrosc. Relat. Phenom. 5, 985 (1974)]. The calculated UPS spectra are found to be isomer dependent and in good agreement with the experimental counterparts. Near-edge x-ray absorption fine structure (NEXAFS), x-ray photoelectron spectroscopy (XPS), x-ray emission spectroscopy, and the resonant inelastic x-ray scattering (RIXS) spectra of three important isomers [3(C-2), 6(C-s), and 9(C-2v)] have also been simulated. Strong isomer dependence has also been found for NEXAFS, XPS, and RIXS spectra.
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| 7. |
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| 8. |
- Jiang, Jun, et al.
(författare)
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Structure dependent quantum confinement effect in hydrogen-terminated nanodiamond clusters
- 2010
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 108:9, s. 094303-
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Tidskriftsartikel (refereegranskat)abstract
- Size-dependent quantum confinement effect on electronic structure of hydrogen-terminated carbon nanodiamond (ND) cluster has been investigated at the hybrid density functional theory level. Large scale all-electron calculations have been carried out for ND clusters of 0.76 nm (29 carbons) to 7.3 nm (20 959 carbons) in diameter. It is demonstrated that the quantum confinement effect in these clusters shows strong structural dependence. An important structural factor, describing the ratio between the number of atoms within the inner core and outer shell of the cluster, is identified which dictates the size-dependent behavior of the electronic states. For ND clusters with diameter smaller than 1.5 nm, the core-shell ratio changes fast with the increase in cluster size, and the evolution of electronic properties does not follow conventional quantum confinement models. For ND clusters exceeding the threshold of 1.5 nm in diameter, the change in the core-shell ratio saturates and quantum confinement effect becomes visible. Electronic states within the inner core and surface show different size dependence, but a general formula is proposed and describes their structure dependent quantum confinement effects. This formula provides useful insights into quantum confinement behavior in ND clusters, and thereby leads to important physical property information. The calculated electron effective masses for core and surface states of ND clusters are in very good agreement with the experiments.
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| 9. |
- Jiang, Ziyu, et al.
(författare)
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HLA class I genes modulate disease risk and age at onset together with DR-DQ in Chinese patients with insulin-requiring type 1 diabetes
- 2021
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 64:9, s. 2026-2036
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Tidskriftsartikel (refereegranskat)abstract
- Aims/hypothesis: The study aimed to investigate the effects of HLA class I genes on susceptibility to type 1 diabetes with different onset ages, in addition to the well-established effects of HLA class II genes. Methods: A total of 361 patients with type 1 diabetes (192 patients with onset <18 years and 169 patients with onset ≥18 years) and 500 healthy control participants from China were enrolled and genotyped for the HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes using next-generation sequencing. Results: The susceptible DR3 (β = −0.09, p = 0.0009) and DR4-DQ8 (β = −0.13, p = 0.0059) haplotypes were negatively associated with onset age, while the protective DR11 (β = 0.21, p = 0.0314) and DR12 (β = 0.27, p < 0.0001) haplotypes were positively associated with onset age. After adjustment for linkage disequilibrium with DR-DQ haplotypes, A*11:01:01 was positively associated with onset age (β = 0.06, p = 0.0370), while the susceptible C*15:02:01 was negatively associated with onset age (β = −0.21, p = 0.0050). The unit for β was double square-root (fourth root) transformed years of change in onset age associated with per copy of the HLA haplotype/allele. In addition, B*46:01:01 was protective (OR 0.41, 0.46; pc [corrected for multiple comparisons] = 0.0044, 0.0040), whereas A*24:02:01 (OR 2.71, 2.25; pc = 0.0003, 0.0002) and B*54:01:01 (OR 3.96, 3.79; pc = 0.0018, 0.0004) were predisposing in both the <18 group and the ≥18 group compared with healthy control participants. In the context of DR4-DQ4, A*11:01:01 (61.29% vs 28.26%, pc = 0.0144) was increased while the predisposing A*24:02:01 (19.35% vs 47.83%, pc = 0.0403) was decreased in patients with onset ≥18 years when compared with patients with onset <18 years. Conclusions/interpretation: In addition to DR-DQ haplotypes, novel HLA class I alleles were detected to play a role in susceptibility to type 1 diabetes with different onset ages, which could improve the understanding of disease heterogeneity and has implications for the design of future studies. Graphical abstract: [Figure not available: see fulltext.].
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| 10. |
- Liu, Lei, et al.
(författare)
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The structural determination of endohedral metallofullerene Gd@C-82 by XANES
- 2008
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; :4, s. 474-476
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Tidskriftsartikel (refereegranskat)abstract
- Although the Gd ion in Gd@C-82 has been shown to lie above the C-C bond on the C-2 axis as an anomalous structure from the MEM/Rietveld analysis, the present XANES study reveals that it lies above the hexagon on the C-2 axis as a normal structure, and Gd oscillates around its equilibrium position with an amplitude increasing with temperature increase.
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