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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. |
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| 4. |
- Ge, Meng, 1993-, et al.
(författare)
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Direct Location of Organic Molecules in Framework Materials by Three-Dimensional Electron Diffraction
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:33, s. 15165-15174
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Tidskriftsartikel (refereegranskat)abstract
- In the study of framework materials, probing interactions between frameworks and organic molecules is one of the most important tasks, which offers us a fundamental understanding of host–guest interactions in gas sorption, separation, catalysis, and framework structure formation. Single-crystal X-ray diffraction (SCXRD) is a conventional method to locate organic species and study such interactions. However, SCXRD demands large crystals whose quality is often vulnerable to, e.g., cracking on the crystals by introducing organic molecules, and this is a major challenge to use SCXRD for structural analysis. With the development of three-dimensional electron diffraction (3D ED), single-crystal structural analysis can be performed on very tiny crystals with sizes on the nanometer scale. Here, we analyze two framework materials, SU-8 and SU-68, with organic molecules inside their inorganic crystal structures. By applying 3D ED, with fast data collection and an ultralow electron dose (0.8–2.6 e– Å–2), we demonstrate for the first time that each nonhydrogen atom from the organic molecules can be ab initio located from structure solution, and they are shown as distinct and well-separated peaks in the difference electrostatic potential maps showing high accuracy and reliability. As a result, two different spatial configurations are identified for the same guest molecule in SU-8. We find that the organic molecules interact with the framework through strong hydrogen bonding, which is the key to immobilizing them at well-defined positions. In addition, we demonstrate that host–guest systems can be studied at room temperature. Providing high accuracy and reliability, we believe that 3D ED can be used as a powerful tool to study host–guest interactions, especially for nanocrystals.
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| 5. |
- Ge, Meng, et al.
(författare)
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High-Throughput Electron Diffraction Reveals a Hidden Novel Metal-Organic Framework for Electrocatalysis
- 2021
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 60:20, s. 11391-11397
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Tidskriftsartikel (refereegranskat)abstract
- Metal-organic frameworks (MOFs) are known for their versatile combination of inorganic building units and organic linkers, which offers immense opportunities in a wide range of applications. However, many MOFs are typically synthesized as multiphasic polycrystalline powders, which are challenging for studies by X-ray diffraction. Therefore, developing new structural characterization techniques is highly desired in order to accelerate discoveries of new materials. Here, we report a high-throughput approach for structural analysis of MOF nano- and sub-microcrystals by three-dimensional electron diffraction (3DED). A new zeolitic-imidazolate framework (ZIF), denoted ZIF-EC1, was first discovered in a trace amount during the study of a known ZIF-CO3-1 material by 3DED. The structures of both ZIFs were solved and refined using 3DED data. ZIF-EC1 has a dense 3D framework structure, which is built by linking mono- and bi-nuclear Zn clusters and 2-methylimidazolates (mIm(-)). With a composition of Zn-3(mIm)(5)(OH), ZIF-EC1 exhibits high N and Zn densities. We show that the N-doped carbon material derived from ZIF-EC1 is a promising electrocatalyst for oxygen reduction reaction (ORR). The discovery of this new MOF and its conversion to an efficient electrocatalyst highlights the power of 3DED in developing new materials and their applications.
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| 6. |
- Ge, Meng, 1993-
(författare)
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On the accuracy of crystal structural analysis and the potential of unraveling structural details by 3D electron diffraction
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Knowing the atomic crystal structures of ordered porous solids is essential in understanding their behaviors and properties, developing new applications, and designing new porous materials. Electrons have a much shorter wavelength and much stronger interaction with atoms in a crystal compared with X-ray. Therefore, electron crystallography can effectively determine the structures of nano- and micro-sized crystals. Three-dimensional electron diffraction (3D ED) methods have been developed for the structure determination of various types of complex crystal structures. Continuous rotation electron diffraction (cRED) has unique aspects in both fast data collection and accurate structure determination. This thesis focused on the accuracy of crystal structure analysis and the potential of unraveling structural details by cRED. The cRED method was first applied for the ab initio structure determination of a beam-sensitive biocomposite metal-organic framework (MOF), BSA@ZIF-CO3-1. The atomic structure of BSA@ZIF-CO3-1 obtained by cRED was the same compared to that obtained by single crystal X-ray diffraction (SCXRD). Accurate atomic structures could be obtained by cRED. The sample of BSA@ZIF-CO3-1 was initially regarded as a pure new phase, however, during the cRED data collection and processing procedure, two distinct crystal systems and unit cells were revealed. BSA@ZIF-CO3-1 was identified as the major phase in the sample, and a new MOF, denoted ZIF-EC1, as the minor phase. ZIF-EC1 has a dense 3D framework with high N and Zn densities, which is a promising candidate for electrocatalysis. The discovery of ZIF-EC1 was followed by investigating the effects of improving 3D ED data completeness on the structural analysis. I successfully solved the structures of ZIF-EC1 from each individual dataset with the lowest completeness of 44.5% and refined to a high precession (better than 0.04 Å). Then I merged ten datasets to obtain a high data completeness, the structural model is improved, peaks appear more spherical in the electrostatic potential maps. The next part of this thesis was focused on unraveling structural details. By applying cRED, each non-Hydrogen atom from guest molecules can be separately localized from the difference Fourier map for two open framework germanates, SU-8 and SU-68. The atomic structure of both the framework and the guest molecules obtained by cRED is as reliable and accurate as that obtained by SCXRD. In the last part, the application of cRED into determining structures for new materials are highlighted. The structure of two new MOFs, Cd-MOF and Pb-MOF are successfully determined by cRED.
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| 7. |
- Ge, Meng, et al.
(författare)
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On the completeness of three-dimensional electron diffraction data for structural analysis of metal-organic frameworks
- 2021
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Ingår i: Faraday discussions. - 1359-6640 .- 1364-5498. ; 231
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional electron diffraction (3DED) has been proven as an effective and accurate method for structure determination of nano-sized crystals. In the past decade, the crystal structures of various new complex metal-organic frameworks (MOFs) have been revealed by 3DED, which has been the key to understand their properties. However, due to the design of transmission electron microscopes (TEMs), one drawback of 3DED experiments is the limited tilt range of goniometers, which often leads to incomplete 3DED data, particularly when the crystal symmetry is low. This drawback can be overcome by high throughput data collection using continuous rotation electron diffraction (cRED), where data from a large number of crystals can be collected and merged. Here, we investigate the effects of improving completeness on structural analysis of MOFs. We use ZIF-EC1, a zeolitic imidazolate framework (ZIF), as an example. ZIF-EC1 crystallizes in a monoclinic system with a plate-like morphology. cRED data of ZIF-EC1 with different completeness and resolution were analyzed. The data completeness increased to 92.0% by merging ten datasets. Although the structures could be solved from individual datasets with a completeness as low as 44.5% and refined to a high precision (better than 0.04 angstrom), we demonstrate that a high data completeness could improve the structural model, especially on the electrostatic potential map. We further discuss the strategy adopted during data merging. We also show that ZIF-EC1 doped with cobalt can act as an efficient electrocatalyst for oxygen reduction reactions.
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| 8. |
- Ge, Meng, et al.
(författare)
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Three-Dimensional Electron Diffraction for Structural Analysis of Beam-Sensitive Metal-Organic Frameworks
- 2021
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Ingår i: Crystals. - : MDPI AG. - 2073-4352. ; 11:3
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Forskningsöversikt (refereegranskat)abstract
- Electrons interact strongly with matter, which makes it possible to obtain high-resolution electron diffraction data from nano- and submicron-sized crystals. Using electron beam as a radiation source in a transmission electron microscope (TEM), ab initio structure determination can be conducted from crystals that are 6-7 orders of magnitude smaller than using X-rays. The rapid development of three-dimensional electron diffraction (3DED) techniques has attracted increasing interests in the field of metal-organic frameworks (MOFs), where it is often difficult to obtain large and high-quality crystals for single-crystal X-ray diffraction. Nowadays, a 3DED dataset can be acquired in 15-250 s by applying continuous crystal rotation, and the required electron dose rate can be very low (<0.1 e s(-1) angstrom(-2)). In this review, we describe the evolution of 3DED data collection techniques and how the recent development of continuous rotation electron diffraction techniques improves data quality. We further describe the structure elucidation of MOFs using 3DED techniques, showing examples of using both low- and high-resolution 3DED data. With an improved data quality, 3DED can achieve a high accuracy, and reveal more structural details of MOFs. Because the physical and chemical properties of MOFs are closely associated with their crystal structures, we believe 3DED will only increase its importance in developing MOF materials.
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| 9. |
- Ge, ShuCan, et al.
(författare)
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Characteristic analysis of layered PMSEs measured with different elevation angles at VHF based on an experimental case
- 2021
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Ingår i: Earth and Planetary Physics. - : Earth and Planetary Physics. - 2096-3955. ; 5:1, s. 42-51
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Tidskriftsartikel (refereegranskat)abstract
- Polar Mesosphere Summer Echoes (PMSEs) are very strong radar echoes observed at altitudes near the polar summer mesopause. One of the essential properties of these radar echoes is that they can give useful diagnostic information about the physics of the scattering process. In this paper, the related characteristics of PMSEs measured with the European Incoherent SCATter Very High Frequency (EISCAT VHF) 224 MHz radar on 13-15 July 2010 are studied at different elevation angles from 78 degrees to 90 degrees. It is found that the PMSEs peak power and strongest PMSEs average power occur at the same elevation angles. Also interesting is that the strongest PMSEs occur at off-vertical angles when a PMSEs has a layered (multilayer) structure. And reflection may have more significant effects on PMSEs when there are double or multilayer PMSEs. Possible explanations regarding these observations are discussed.
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| 10. |
- Ge, ShuCan, et al.
(författare)
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On the radar frequency dependence of polar mesosphere summer echoes
- 2020
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Ingår i: Earth and Planetary Physics. - : Earth and Planetary Physics. - 2096-3955. ; 4:6, s. 571-578
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Tidskriftsartikel (refereegranskat)abstract
- Polar mesosphere summer echoes (PMSEs) are very strong radar echoes in the polar mesopause in local summer. Here we present the frequency dependence of the volume reflectivity and the effect of energetic particle precipitation on modulated PMSEs by using PMSEs observations carried out by European Incoherent SCATter (EISCAT) heating equipment simultaneously with very high frequency (VHF) radar and ultra high frequency (UHF) radar on 12 July 2007. According to the experimental observations, the PMSEs occurrence rate at VHF was much higher than that at UHF, and the altitude of the PMSEs maximum observed at VHF was higher than that at UHF. Overlapping regions were observed by VHF radar between high energetic particle precipitation and the PMSEs. In addition, high-frequency heating had a very limited impact on PMSEs when the UHF electron density was enhanced because of energetic particle precipitation. In addition, an updated qualitative method was used to study the relationship between volume reflectivity and frequency. The volume reflectivity was found to be inversely proportional to the fourth power of radar frequency. The theoretical and experimental results provide a definitive data foundation for further analysis and investigation of the physical mechanism of PMSEs.
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