| 1. |
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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 3. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 4. |
- Brännström, Kristoffer, et al.
(author)
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Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips
- 2018
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In: Data in Brief. - : Elsevier. - 2352-3409. ; 19, s. 1166-1170
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Journal article (peer-reviewed)abstract
- We demonstrate the use of Scanning Electron microscopy (SEM) in combination with Surface Plasmon Resonance (SPR) to probe and verify the formation of amyloid and its morphology on an SPR chip. SPR is a technique that measures changes in the immobilized weight on the chip surface and is frequently used to probe the formation and biophysical properties of amyloid structures. In this context it is of interest to also monitor the morphology of the formed structures. The SPR chip surface is made of a layer of gold, which represent a suitable material for direct analysis of the surface using SEM. The standard SPR chip used here (CM5-chip, GE Healthcare, Uppsala, Sweden) can easily be disassembled and directly analyzed by SEM. In order to verify the formation of amyloid fibrils in our experimental conditions we analyzed also in-solution produced structures by using Transmission Electron Microscopy (TEM). For further details and experimental findings, please refer to the article published in Journal of Molecular Biology, (Brännström K. et al., 2018) [1].
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| 5. |
- Brännström, Kristoffer, et al.
(author)
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The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation
- 2018
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In: Journal of Molecular Biology. - : Elsevier. - 0022-2836 .- 1089-8638. ; 430:13, s. 1940-1949
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Journal article (peer-reviewed)abstract
- Fibril formation of the amyloid-β peptide (Aβ) follows a nucleation-dependent polymerization process and is associated with Alzheimer's disease. Several different lengths of Aβ are observed in vivo, but Aβ1-40 and Aβ1-42 are the dominant forms. The fibril architectures of Aβ1-40 and Aβ1-42 differ and Aβ1-42 assemblies are generally considered more pathogenic. We show here that monomeric Aβ1-42 can be cross-templated and incorporated into the ends of Aβ1-40 fibrils, while incorporation of Aβ1-40 monomers into Aβ1-42 fibrils is very poor. We also show that via cross-templating incorporated Aβ monomers acquire the properties of the parental fibrils. The suppressed ability of Aβ1-40 to incorporate into the ends of Aβ1-42 fibrils and the capacity of Aβ1-42 monomers to adopt the properties of Aβ1-40 fibrils may thus represent two mechanisms reducing the total load of fibrils having the intrinsic, and possibly pathogenic, features of Aβ1-42 fibrils in vivo. We also show that the transfer of fibrillar properties is restricted to fibril-end templating and does not apply to cross-nucleation via the recently described path of surface-catalyzed secondary nucleation, which instead generates similar structures to those acquired via de novo primary nucleation in the absence of catalyzing seeds. Taken together these results uncover an intrinsic barrier that prevents Aβ1-40 from adopting the fibrillar properties of Aβ1-42 and exposes that the transfer of properties between amyloid-β fibrils are determined by their path of formation.
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| 6. |
- Islam, Tohidul, et al.
(author)
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Morphological analysis of Apolipoprotein E binding to A beta Amyloid using a combination of Surface Plasmon Resonance, Immunogold Labeling and Scanning Electron Microscopy
- 2019
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In: BMC Biotechnology. - : BMC. - 1472-6750. ; 19:1
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Journal article (peer-reviewed)abstract
- Background: Immunogold labeling in combination with transmission electron microscopy analysis is a technique frequently used to correlate high-resolution morphology studies with detailed information regarding localization of specific antigens. Although powerful, the methodology has limitations and it is frequently difficult to acquire a stringent system where unspecific low-affinity interactions are removed prior to analysis.Results: We here describe a combinatorial strategy where surface plasmon resonance and immunogold labeling are used followed by a direct analysis of the sensor-chip surface by scanning electron microscopy. Using this approach, we have probed the interaction between amyloid-beta fibrils, associated to Alzheimer's disease, and apolipoprotein E, a well-known ligand frequently found co-deposited to the fibrillar form of A beta in vivo. The results display a lateral binding of ApoE along the amyloid fibrils and illustrates how the gold-beads represent a good reporter of the binding.Conclusions: This approach exposes a technique with generic features which enables both a quantitative and a morphological evaluation of a ligand-receptor based system. The methodology mediates an advantage compared to traditional immunogold labeling since all washing steps can be monitored and where a high stringency can be maintained throughout the experiment.
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| 7. |
- Kwong, Wai Ling, et al.
(author)
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Cationic Vacancy Defects in Iron Phosphide : A Promising Route toward Efficient and Stable Hydrogen Evolution by Electrochemical Water Splitting
- 2017
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In: ChemSusChem. - : Wiley-Blackwell. - 1864-5631 .- 1864-564X. ; 10:22, s. 4544-4551
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Journal article (peer-reviewed)abstract
- Engineering the electronic properties of transition metal phosphides has shown great effectiveness in improving their intrinsic catalytic activity for the hydrogen evolution reaction (HER) in water splitting applications. Herein, we report for the first time, the creation of Fe vacancies as an approach to modulate the electronic structure of iron phosphide (FeP). The Fe vacancies were produced by chemical leaching of Mg that was introduced into FeP as "sacrificial dopant". The obtained Fe-vacancy-rich FeP nanoparticulate films, which were deposited on Ti foil, show excellent HER activity compared to pristine FeP and Mg-doped FeP, achieving a current density of 10 mAcm(-2) at overpotentials of 108 mV in 1 m KOH and 65 mV in 0.5 m H2SO4, with a near-100% Faradaic efficiency. Our theoretical and experimental analyses reveal that the improved HER activity originates from the presence of Fe vacancies, which lead to a synergistic modulation of the structural and electronic properties that result in a near-optimal hydrogen adsorption free energy and enhanced proton trapping. The success in catalytic improvement through the introduction of cationic vacancy defects has not only demonstrated the potential of Fe-vacancy-rich FeP as highly efficient, earth abundant HER catalyst, but also opens up an exciting pathway for activating other promising catalysts for electrochemical water splitting.
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| 8. |
- Kwong, Wai Ling, et al.
(author)
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Cobalt- doped hematite thin films for electrocatalytic water oxidation in highly acidic media
- 2019
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In: Chemical Communications. - : The Royal Society of Chemistry. - 1359-7345 .- 1364-548X. ; 55:34, s. 5017-5020
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Journal article (peer-reviewed)abstract
- Earth-abundant cobalt-doped hematite thin-film electrocatalysts were explored for acidic water oxidation. The strategically doped hematite produced a stable geometric current density of 10 mA cm(-2) for up to 50 h at pH 0.3, as a result of Co-enhanced intrinsic catalytic activity and charge transport properties across the film matrix.
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| 9. |
- Kwong, Wai Ling, et al.
(author)
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High-performance iron (III) oxide electrocatalyst for water oxidation in strongly acidic media
- 2018
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In: Journal of Catalysis. - : Academic Press. - 0021-9517 .- 1090-2694. ; 365, s. 29-35
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Journal article (peer-reviewed)abstract
- Stable and efficient oxygen evolution reaction (OER) catalysts for the oxidation of water to dioxygen in highly acidic media are currently limited to expensive noble metal (Ir and Ru) oxides since presently known OER catalysts made of inexpensive earth-abundant materials generally suffer anodic corrosion at low pH. In this study, we report that a mixed-polymorph film comprising maghemite and hematite, prepared using spray pyrolysis deposition followed by low-temperature annealing, showed a sustained OER rate (>24 h) corresponding to a current density of 10 mA cm−2 at an initial overpotential of 650 mV, with a Tafel slope of only 56 mV dec−1 and near-100% Faradaic efficiency in 0.5 M H2SO4 (pH 0.3). This performance is remarkable, since iron (III) oxide films comprising only maghemite were found to exhibit a comparable intrinsic activity, but considerably lower stability for OER, while films of pure hematite were OER-inactive. These results are explained by the differences in the polymorph crystal structures, which cause different electrical conductivity and surface interactions with water molecules and protons. Our findings not only reveal the potential of iron (III) oxide as acid-stable OER catalyst, but also highlight the important yet hitherto largely unexplored effect of crystal polymorphism on electrocatalytic OER performance.
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| 10. |
- Kwong, Wai Ling, et al.
(author)
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Scalable Two-Step Synthesis of Nickel Iron Phosphide Electrodes for Stable and Efficient Electrocatalytic Hydrogen Evolution
- 2017
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 121:1, s. 284-292
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Journal article (peer-reviewed)abstract
- The development of efficient, durable, and inexpensive hydrogen evolution electrodes remains a key challenge for realizing a sustainable H-2 fuel production via electrocatalytic water splitting. Herein, nickel-iron phosphide porous films with precisely controlled metal content were synthesized on Ti foil using a simple and scalable two-step strategy of spray-pyrolysis deposition followed by low-temperature phosphidation. The nickel-iron phosphide of an optimized Ni:Fe ratio of 1:4 demonstrated excellent overall catalytic activity for hydrogen evolution reaction (HER) in 0.5 M H2SO4, achieving current densities of -10 and -30 mA cm(-2) at overpoteritials of 101 and 123 mV, respectively, with a Tafel slope of 43 mV dec(-1). Detailed analysis obtained by X-ray diffraction, electron microscopy, electrochemistry, and X-ray photoelectron spectroscopy revealed that the superior overall HER activity of nickel iron phosphide as compared to nickel phosphide and iron phosphide was a combined effect of differences in the morphology (real surface area) and the intrinsic catalytic properties (electronic structure). Together with a long-term stability and a near-100% Faradaic efficiency, the nickel-iron phosphide electrodes produced in this study provide blueprints for large-scale H-2 production.
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| 11. |
- Kwong, Wai Ling, et al.
(author)
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Transparent Nanoparticulate FeOOH Improves the Performance of a WO3 Photoanode in a Tandem Water-Splitting Device
- 2016
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 120:20, s. 10941-10950
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Journal article (peer-reviewed)abstract
- Oxygen evolution catalysts (OEC) are often employed on the surface of photoactive, semiconducting photoanodes to boost their kinetics and stability during photoelectrochemical water oxidation. However, the necessity of using optically transparent OEC to avoid parasitic light absorption by the OEC under front-side illumination is often neglected. Here, we show that furnishing the surface of a WO3 photoanode with suitable loading of FeOOH as a transparent OEC improved the photocurrent density by 300% at 1 V versus RHE and the initial photocurrent-to-O-2 Faradaic efficiency from similar to 70 to similar to 100%. The data from the photo-voltammetry, electrochemical impedance, and gas evolution measurements these improvements were a combined result of reduced hole-transfer resistance for water oxidation, minimized surface recombination of charge carriers, and improved stability against photocorrosion of WO3. We demonstrate the utility of transparent FeOOH-coated W(O)3 in a solar-powered, tandem water-splitting device by combining it with a double-junction Si solar cell and a Ni-Mo hydrogen evolution catalyst. This device performed at a solar-to-hydrogen conversion efficiency of 1.8% in near-neutral K2SO4 electrolyte.
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| 12. |
- Ménard, Delphine, et al.
(author)
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Dynamic incorporation of specific lignin residues controls the biomechanics of the plant vasculature and its resilience to environmental changes
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Other publication (other academic/artistic)abstract
- The accumulation of the cell wall polymer lignin in vascular cells enables long-distance water conduction and structural support in plants. Independently of the plant species, each different vascular cell type accumulates specific lignin amount and composition affecting both aromatic and aliphatic substitutions of its residues. However, the biological role of this conserved and specific lignin chemistry for each cell type remains unclear. Herein, we performed single cell analyses on plant vascular cell morphotypes to investigate the role of specific lignin composition for cellular function. We showed that distinct amounts and compositions of lignin accumulated in the different morphotypes of the sap conducting vascular cells. We discovered that lignin accumulates dynamically, increasing in quantity and changing composition, to fine-tune the cell wall mechanical properties of each conducting cell morphotype. Modification this lignin specificity impaired specifically the cell wall mechanical properties of each morphotype and consequently their capacity to optimally conduct water in normal but also to recover from drought conditions. Altogether, our findings provide the biological role of specific lignin chemistry in sap conducting cells, to dynamically adjust the hydraulic properties of each conducting cell during developmental and environmental constraints.
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| 13. |
- Ménard, Delphine, et al.
(author)
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Plant biomechanics and resilience to environmental changes are controlled by specific lignin chemistries in each vascular cell type and morphotype
- 2022
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In: The Plant Cell. - : Oxford University Press. - 1040-4651 .- 1532-298X. ; 34:12, s. 4877-4896
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Journal article (peer-reviewed)abstract
- The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.
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| 14. |
- Samikannu, Ajaikumar, et al.
(author)
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Highly dispersed NbOPO4/SBA-15 as a versatile acid catalyst upon production of renewable jet-fuel from bio-based furanics via hydroxyalkylation-alkylation (HAA) and hydrodeoxygenation (HDO) reactions
- 2020
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In: Applied Catalysis B. - : Elsevier. - 0926-3373 .- 1873-3883. ; 272
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Journal article (peer-reviewed)abstract
- Herein, we report the synthesis of a highly active and mesoporous Brønsted acidic NbOPO4/SBA-15 catalyst. The prepared catalysts were thoroughly characterized by means of analytical techniques such as XRD, FT-IR, XPS, NH3-TPD, SEM-EDS, TEM, TGA, 31P-MAS-NMR and N2-physisorption. The H3PO4 free deposition method was found to be effective for preserving the structure of Silica based carrier. In terms of catalytic performance, these materials demonstrated high activity upon C-C coupling of 2-methyl furan with carbonyl compounds and outperforming bulk NbOPO4, Nb2O5/SBA-15 and traditional solid acid catalysts (Al-MCM-41, Si/Al and H-ZSM-5). The NbOPO4/SBA-15 catalysts were stable and maintained high activity upon reuse and continuous operation (∼65 h). Furthermore, the Pd loaded counterparts (Pd/NbOPO4/SBA-15 and Pd/Nb2O5/SBA-15) also functioned as bifunctional catalysts and exhibited excellent activity upon subsequent hydrodeoxygenation of C-C coupling products. Most importantly, in terms of jet-fuel range hydrocarbons selectivity, these catalysts outperformed monofunctional Pd/carbon and aluminosilicate based bifunctional catalysts.
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| 15. |
- Tollefsen, Elin, et al.
(author)
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Ikaite nucleation at 35°C challenges the use of glendonite as a paleotemperature indicator
- 2020
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
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Journal article (peer-reviewed)abstract
- Glendonites have been found worldwide in marine sediments from the Neoproterozoic Era to the Quaternary Period. The precursor of glendonite, ikaite (CaCO3 · 6H2O), is metastable and has only been observed in nature at temperatures <7 °C. Therefore, glendonites in the sedimentary record are commonly used as paleotemperature indicators. However, several laboratory experiments have shown that the mineral can nucleate at temperatures>7 °C. Here we investigate the nucleation range for ikaite as a function of temperature and pH. We found that ikaite precipitated at temperatures of at least 35 °C at pH 9.3 −10.3 from a mixture of natural seawater and sodium carbonate rich solution. At pH 9.3, we observed pseudomorphic replacement of ikaite by porous calcite during the duration of the experiment (c. 5 hours). These results imply that ikaite can form at relatively high temperatures but will then be rapidly replaced by a calcite pseudomorph. This finding challenges the use of glendonites as paleotemperature indicators.
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| 16. |
- Tollefsen, Elin, et al.
(author)
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Ikaite nucleation at 35 degrees C challenges the use of glendonite as a paleotemperature indicator
- 2020
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10
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Journal article (peer-reviewed)abstract
- Glendonites have been found worldwide in marine sediments from the Neoproterozoic Era to the Quaternary Period. The precursor of glendonite, ikaite (CaCO3 . 6H(2)O), is metastable and has only been observed in nature at temperatures <7 degrees C. Therefore, glendonites in the sedimentary record are commonly used as paleotemperature indicators. However, several laboratory experiments have shown that the mineral can nucleate at temperatures>7 degrees C. Here we investigate the nucleation range for ikaite as a function of temperature and pH. We found that ikaite precipitated at temperatures of at least 35 degrees C at pH 9.3 -10.3 from a mixture of natural seawater and sodium carbonate rich solution. At pH 9.3, we observed pseudomorphic replacement of ikaite by porous calcite during the duration of the experiment (c. 5hours). These results imply that ikaite can form at relatively high temperatures but will then be rapidly replaced by a calcite pseudomorph. This finding challenges the use of glendonites as paleotemperature indicators.
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| 17. |
- Yeşilbaş, Merve, et al.
(author)
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Ice and cryosalt formation in saline microporous clay gels
- 2018
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In: ACS Earth and Space Chemistry. - : American Chemical Society (ACS). - 2472-3452. ; 2:4, s. 314-319
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Journal article (peer-reviewed)abstract
- Hydrated clay minerals that are common to Earth’s atmosphere and terrestrial and aquatic environments can form gels that host saline solutions. Using cryogenic electron microscopy and vibration spectroscopy, we show that saline gels of montmorillonite frozen at < −90 °C host elongated hexagonal ice (Ih) microcrystals embedded in a network of honeycomb micropores. Freezing segregates salts into walls of aggregated clay nanoparticles sharing face-to-face contacts. Above ∼ −50 °C, clay gels that are sufficiently dense (≫10 g/L) and flexible (Na-exchanged montmorillonite) also host the cryosalt mineral hydrohalite (NaCl·2H2O), either co-existing or entirely replacing Ih in the gels. Hydrohalite does not form in gels of low-density (<10 g/L) or rigid (Ca-exchange montmorillonite) clay particles. These results suggest that hydrohalite forms in expandable clay gels that are sufficiently dense and flexible to retain saline solutions within their walls, possibly through interparticle capillary and hydration forces. These forces effectively oppose water diffusion to growing ice microcrystals within micropores, thus prolonging the lifetime of hydrohalite within these hydrated clay gels. Our findings tie the fate of ice and cryosalt nucleation and growth to the water-retention capability of expandable clay gels.
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