Relevant bibliographies by topics / 3D crystal structure

Academic literature on the topic '3D crystal structure'

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Published: 8 June 2024

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Journal articles on the topic "3D crystal structure":

1

Yang, Quanxin, Xin Zhang, Hongliang Liu, Xuping Wang, Yingying Ren, Shan He, Xiaojin Li, and Pengfei Wu. "Dynamic relaxation process of a 3D super crystal structure in a Cu:KTN crystal." Chinese Optics Letters 18, no. 2 (2020): 021901. http://dx.doi.org/10.3788/col202018.021901.

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Jang, Kiyoung, Hyun Gi Kim, Sandi Hnit San Hlaing, MinSoung Kang, Hui-Woog Choe, and Yong Ju Kim. "A Short Review on Cryoprotectants for 3D Protein Structure Analysis." Crystals 12, no. 2 (January 19, 2022): 138. http://dx.doi.org/10.3390/cryst12020138.

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The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.
3

Lanza, Arianna, Eleonora Margheritis, Enrico Mugnaioli, Valentina Cappello, Gianpiero Garau, and Mauro Gemmi. "Nanobeam precession-assisted 3D electron diffraction reveals a new polymorph of hen egg-white lysozyme." IUCrJ 6, no. 2 (January 15, 2019): 178–88. http://dx.doi.org/10.1107/s2052252518017657.

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Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.
4

Ren, Lin, Yan Li Shi, Xue Hao, and Run Lan Tian. "Experimental System for the Micro-Nanofabrication of Three-Dimensional Structures by Femtosecond Laser Two-Photon Absorption." Advanced Materials Research 760-762 (September 2013): 746–49. http://dx.doi.org/10.4028/www.scientific.net/amr.760-762.746.

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Fundamentals of two-photon photopolymerization have been introduced and a 3D femtosecond laser micro-nanofabrication system has been built. In this paper, 3D CAD data model based on femtosecond laser micro-nanofabrication system have been also discussed. The 3D various sphere-rod photonic crystal structure mimicking real atom structures in electronic crystals have been fabricated.
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Kaminsky, Werner, Trevor Snyder, and Peter Moeck. "3D printing of crystallographic models and open access databases." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1278. http://dx.doi.org/10.1107/s205327331408721x.

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Although introduced 30 years ago, cost and performance improvements have only recently made 3D printing affordable. The industry wide input file format for 3D printers incorporates explicit mesh - `STL' data. Molecules and crystal structures, when including symmetry, crystal morphologies, or crystal defects are encoded in the parametrical `CIF' syntax. Free software for converting directly CIF data to STL files has just been developed, available online [1]. First examples of printed 3D models from STL-files created with these programs include molecules of sucrose, herapathite [2a], caffeine, humulone [2b], an alpha-quartz crystal and its Japanese {112} twin or a brilliant cut diamond. Far more CIF encoded models are available, even open access. The Crystallography Open Database (COD) features over 245,000 entries and has recently developed into the world's premier open-access source for structures of small to medium unit cell-sized inorganic and molecular crystals [3a], complementing the well-established open-access Worldwide Protein Data Bank [3b]. The Cambridge Crystallographic Data Centre in the United Kingdom provides crystal structure data of small (organic) molecules free for bona fide research [3c]. Structural data on inorganic crystals, metals and alloys can be obtained free of charge from the Inorganic Material Database (AtomWork) [3d]. Related to the COD, the crystallographic open-access databases [3e] ("COD offspring") provide CIF data for interdisciplinary college education. With this basic infrastructure in place, any interested college educator may print out her or his favorite crystallographic structure model in 3D and use it in hands on class room demonstrations [3f].
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Yang, Taimin, Steve Waitschat, Andrew Kentaro Inge, Norbert Stock, Xiaodong Zou, and Hongyi Xu. "A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature." Symmetry 13, no. 11 (November 9, 2021): 2131. http://dx.doi.org/10.3390/sym13112131.

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3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).
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Su, Jie, Yue-Biao Zhang, Yifeng Yun, Hiroyasu Furukawa, Felipe Gándara, Adam Duong, Xiaodong Zou, and Omar Yaghi. "The First Covalent Organic Framework solved by Rotation Electron Diffraction." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C191. http://dx.doi.org/10.1107/s2053273314098088.

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Covalent organic frameworks (COFs) represent an exciting new type of porous organic materials, which are constructed with organic building units via strong covalent bonds.[1] The structure determination of COFs is challenging, due to the difficulty in growing sufficiently large crystals suitable for single crystal X-ray diffraction, and low resolution and peak broadening for powder X-ray diffraction. Crystal structures of COFs are typically determined by modelling building with the aid of geometry principles in reticular chemistry and powder X-ray diffraction data. Here, we report the single-crystal structure of a new COF (COF-320) determined by 3D rotation electron diffraction (RED),[2] a technique applied in this context for the first time. The RED method can collect an almost complete three-dimensional electron diffraction dataset, and is a useful technique for structure determination of micron- and nanosized single crystals. To minimize electron beam damage, the RED dataset was collected at 89 K. 3D reciprocal lattice of COF-320 was reconstructed from the ED frames using the RED – data processing software[2]. As the resolution of the RED data only reached 1.6 Å, the simulated annealing parallel tempering algorithm in the FOX software package [3] was used to find a starting molecular arrangement from the 3D RED data. Finally, the crystal structure of COF-320 was solved in the space group of I-42d and refined using the SHELXL software package. The single-crystal structure of COF-320 exhibits a 3D extended framework by linking the tetrahedral organic building blocks and biphenyl linkers through imine-bonds forming a highly porous 9-fold interwoven diamond net.
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Zhang, Chenxi, Xuemin Chen, Bo Liu, Jiachen Zang, Tuo Zhang, and Guanghua Zhao. "Preparation and Unique Three-Dimensional Self-Assembly Property of Starfish Ferritin." Foods 12, no. 21 (October 25, 2023): 3903. http://dx.doi.org/10.3390/foods12213903.

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The structure and assembly properties of ferritin derived from aquatic products remain to be explored. Constructing diverse three-dimensional (3D) protein architectures with the same building blocks has important implications for nutrient delivery, medicine and materials science. Herein, ferritin from Asterias forbesii (AfFer) was prepared, and its crystal structure was resolved at 1.91 Å for the first time. Notably, different from the crystal structure of other reported ferritin, AfFer exhibited a BCT lattice arrangement in its crystals. Bioinspired by the crystal structure of AfFer, we described an effective approach for manufacturing 3D porous, crystalline nanoarchitectures by redesigning the shared protein interface involved in different 3D protein arrays. Based on this strategy, two 3D superlattices of body-centered tetragonal and simple cubicwere constructed with ferritin molecules as the building blocks. This study provided a potentially generalizable strategy for constructing different 3D protein-based crystalline biomaterials with the same building blocks.
9

Chen, S., D. Li, M. Wang, and D. Wei. "Fabrication of a point defect photonic crystal based on diamond structure with a cavity and its microwave properties." Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture 225, no. 11 (September 12, 2011): 2071–77. http://dx.doi.org/10.1177/0954405411398760.

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This paper presents a novel fabrication method for three-dimensional (3D) ceramic point defect photonic crystals. The 3D defect photonic crystal, which possesses an air cavity, has been designed by cutting a rectangular shape (3.5 mm × 3.5 mm × 7 mm) in the centre of a photonic crystal with a diamond lattice structure model (50 mm × 30 mm × 20 mm) with a lattice constant of 7 mm. Stereolithography (SL) technology was applied to fabricate resin moulds with an inverse-diamond structure incorporating the defect, and high solid content aqueous ceramic slurry was prepared and injected into the moulds. After gel-casting, drying, and high-temperature sintering, ceramic 3D photonic crystals with intact structure and minimal shrinkage were obtained. The penetration of an electric field with resonant modes of about 3 mm into the host lattice was observed by measuring the <110> direction of the samples, which resulted from the rectangular air cavity resonator. The results show that this method can be used to fabricate ceramic 3D point defect photonic crystals with a complex 3D structure.
10

Nicolopoulos, Stavros, Mauro Gemmi, Alexander Eggeman, Paul Midgley, and Athanassios Galanis. "TEM Random & Ultra-fast Precession ED Tomography for analysis of nm crystals." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C371. http://dx.doi.org/10.1107/s2053273314096284.

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Since the invention of Precession Electron Diffraction (PED) in Transmission Electron Microscopy (TEM) by Vincent & Midgley [1] in 1994 and mainly after the introduction of dedicated PED devices to different TEM, the structure of various nano-sized crystals have been solved by Electron Crystalography. The most popular technique that was recently developed based on beam precession is the 3D Precession Diffraction Tomography (PEDT) [2]. A series of ED patterns are collected every 10while the sample is tilted around the goniometer axis. By the automatic measurement of ED intensities (ADT 3D software), the unit cell, crystal symmetry and the detailed crystal structure can be determined. A large number of crystal structures, such as complex metals, alloys, organic pigments, MOF, catalysts etc., have been solved by the 3D PEDT technique. A drawback of 3D PEDT (especially for beam sensitive materials) is the long acquisition times (45–120 min), due to the time consuming step of tracking the crystal under the beam during tilting. To deal with this problem, we have developed two novel approaches: the Random Electron Diffraction Tomography (rPEDT) technique and the Ultra-Fast 3D diffraction tomography (UF PEDT) [3]. By rPEDT technique, a sample area (few microns), where several crystals in different (random) orientations are present, is scanned rapidly using an ASTAR precession device (NanoMEGAS SPRL). PED patterns of all scanned crystals are collected by a fast speed CCD camera (up to 120 frames/sec; 8/12 bit). Concerning UF PEDT, the data acquisition time can be 10-20 times faster compared to hitherto 3D PEDT procedure. UF PEDT can be applied when the crystal shift is stable and reproducible during tilting the sample for a specific tilt range. Thus, such crystals can be tracked by shifting the beam following the crystal displacement during tilting (using ASTAR beam scanning). Obtained PED patterns can be recorded with a fast CCD camera, while crystal is tilted. As a conclusion, rPEDT and UF-PEDT can be considered as breakthrough techniques in electron crystallography as they can be performed in any commercial TEM. Both techniques reduce considerable 3D intensity data acquisition time, and allow the analysis of unknown compounds, including beam sensitive organic crystals, as fast techniques prevents crystal beam damage. The authors acknowledge financial support from EU ESTEEM-2 project (European Network for Electron Microscopy www.esteem2.eu).
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Journal articles Dissertations / Theses

Dissertations / Theses on the topic "3D crystal structure":

1

Wennman, Anneli. "The structural basis for the catalytic specificity of manganese lipoxygenases : 3D structure analysis of the lipoxygenase of Magnaporthe oryzae." Doctoral thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-262762.

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Lipoxygenases (LOX) catalyze regio- and stereospecific oxygenation of polyunsaturated fatty acids to hydroperoxides. These hydroperoxides are further metabolized to leukotrienes and lipoxins in mammals, and are involved in asthma and inflammation. LOX of animals and plants contain iron as catalytic metal (FeLOX). Filamentous fungi use both FeLOX, and manganese containing LOX (MnLOX). The role of LOX in fungi is still not known. This thesis focuses on expression of novel MnLOX, analyses of their reaction mechanism and products by HPLC-MS/MS, protein crystallization and analysis of the first MnLOX structure.   MnLOX from G. graminis, M. salvinii, M. oryzae, F. oxysporum and C. gloeosporioides were expressed in Pichia pastoris, purified and characterized by HPLC-MS/MS. All MnLOX catalyzes suprafacial hydrogen abstraction and oxygen insertion. Replacement of one Ile to Phe in the active site of MnLOX of G. graminis could switch the mechanism from suprafacial to mainly antarafacial. MnLOX of F. oxysporum was interesting since it catalyzes oxygenation of linoleic acid to 11R- instead of the more common 11S-hydroperoxides. This feature could be attributed to a single Ser/Phe exchange in the active site.   We found that Gg-MnLOX utilizes hydrogen tunneling in the reaction mechanism, but was slightly more temperature dependent than soybean FeLOX. It is an intriguing question why some fungal LOX use manganese and not iron as catalytic metal and whether the large redox potential of Mn2+/Mn3+ (1.5 V) can be tuned close to that of Fe2+/Fe3+ (0.77 V) for redox cycling and catalysis. We present crystallization conditions for two MnLOX, and the 2.07 Å crystal structure of MnLOX from M. oryzae, solved using sulfur and manganese single anomalous dispersion (SAD). The structure reveals a similar metal coordinating sphere as FeLOX but the metal ligand Asn473 was positioned on a short loop instead of a helix and formed interactions with a conserved Gln. This feature could be essential for the use of manganese as catalytic metal in LOX. We found three Phe residues that likely facilitate the suprafacial hydrogen abstraction and oxygen insertion for MnLOX. These findings provide new insight into the unique reaction mechanism of MnLOX.
2

Markevičius, Andrius. "3D fotoninio kristalo užpildyto nematiniu skystuoju kristalu spektroskopiniai tyrimai." Master's thesis, Lithuanian Academic Libraries Network (LABT), 2010. http://vddb.laba.lt/obj/LT-eLABa-0001:E.02~2010~D_20100708_091750-48466.

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Eksperimentai buvo atliekami su bandinėliais gautais iš Madrido, Maskvos ir St.Peterburgo, tai yra su fotoniniais kristalais. Darbe buvo nagrinėta fotoninio kristalo opalo struktūrą ir optines savybes draustinės stop juostos srityje bei defektų valdymo būdai, keičiant elektrinį lauką. Nagrinėjamas elektrinio lauko poveikis defektams, stop juostai. Nustatyta, kad elektriniame lauke susikuria defektai, kuriuos galima valdyti nuo 0V iki 7V įtampos intervale. Išmatuoti defektinės modos perjungimo laikai kurie sieka 200 s, tai 10 kart greičiau nei stop juostos.
We did structural and spectroscopic studies of bulk and thin film synthetic opal. Demonstrate that the photonic crystal, opal have defects, but these defects may be "good" when use it to control light in stop band.
3

Hossain, A. "Synthesis, crystal structure and properties of complex oxides with the perovskite structure based on neodymium, alkaline earth and 3d-transition metals : dissertation for the degree of candidate of chemical sciences : 02.00.04." Thesis, б. и, 2019. http://hdl.handle.net/10995/82032.

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Hung, Jenny. "3D spherical layer photonic band-gap structures in dichromate gelatin /." View abstract or full-text, 2008. http://library.ust.hk/cgi/db/thesis.pl?PHYS%202008%20HUNG.

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Sylvestre-Gonon, Elodie. "Caractérisation biochimique et structurale de quelques glutathion transférases de la classe Tau d'arabette (Arabidopsis thaliana) et de peuplier (Populus trichocarpa)." Electronic Thesis or Diss., Université de Lorraine, 2020. http://www.theses.fr/2020LORR0253.

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Les glutathion transférases (GSTs) constituent une famille multigénique d’enzymes ubiquitaires impliquées notamment dans la détoxication des xénobiotiques et le métabolisme secondaire. Les GSTs canoniques sont constituées d’un domaine N-terminal de type thiorédoxine et d’un domaine C-terminal formé d’hélices α. Chez les plantes terrestres, les GSTs peuvent être regroupées en 14 classes et selon le résidu conservé au sein de leur motif catalytique en GSTs à cystéine (Cys-GSTs) ou à sérine (Ser-GSTs). Les Ser-GSTs présentent des activités de réduction des peroxydes et/ou de conjugaison de glutathion (GSH) alors que les Cys-GSTs portent des activités de déglutathionylation et déshydroascorbate réductase. Certaines d’entre elles présentent également des propriétés non-catalytiques de type ligandine à des fins de transport ou de stockage de molécules diverses. Les GSTs Tau (GSTUs) correspondent à la classe regroupant le plus d’isoformes chez les plantes et leur sont spécifiques. Les GSTUs sont souvent surexprimées lors de stress biotiques et abiotiques et participent notamment à la détoxication des herbicides. Toutefois, le rôle physiologique des GSTUs reste encore lacunaire in planta. En combinant des approches phylogénétiques, biochimiques et structurales, ces travaux ont conduit à la caractérisation de neuf GSTUs d’Arabidopsis thaliana (AtGSTUs) et de six GSTUs de Populus trichocarpa (PtGSTUs). L’analyse phylogénétique des Ser-GSTs d’organismes photosynthétiques a révélé que l’expansion des GSTUs est apparue de façon concomitante à l’apparition du réseau vasculaire chez les plantes bien que quelques mousses et bryophytes possèdent des GSTUs. Au sein d’un organisme, les GSTUs peuvent être classées en groupes distincts en fonction de leur motif catalytique. Les essais enzymatiques réalisés ont montré que quasiment toutes les GSTUs d’intérêt portent des activités de conjugaison du GSH et de réduction des peroxydes envers différents substrats modèles (CDNB, dérivés d’isothiocyanates, hydroperoxydes). Les structures tridimensionnelles de deux GSTUs ont été résolues et ces dernières présentent le repliement classique des GSTs canoniques avec des différences notables entre elles. Les analyses biochimiques et structurales réalisées sur les protéines AtGSTUs et PtGSTUs d’intérêt ont montré que certaines d’entre elles lient des porphyrines bactériennes et d’autres des composés polyphénoliques. Parmi les complexes enzyme-ligand identifiés, la structure d’un complexe baicaléine-GSTU a été résolue. L’utilisation d’échantillons enrichis en métabolites extraits de plantes représente la prochaine étape sur le chemin de l’analyse fonctionnelle des GSTUs
Glutathione transferases (GSTs) constitute a ubiquitous multigene superfamily of enzymes involved in xenobiotic detoxification and secondary metabolism. Canonical GSTs consist of an N-terminal thioredoxin domain and a α-helical C-terminal domain. In terrestrial plants, GSTs can be grouped in 14 classes but also according to the conserved residue found in their catalytic site either cysteine (Cys-GSTs) or serine (Ser-GSTs) GSTs. Ser-GSTs exhibit reduction of peroxides and/or glutathione (GSH) conjugation activities while Cys-GSTs rather exhibit deglutathionylation and dehydroascorbate reductase activities. Some of them also appear to have non-catalytic ligandin properties for the transport or storage of various molecules. The plant-specific Tau GST (GSTU) class is usually the most expanded one. The GSTUs are often over-expressed during biotic and abiotic stresses contributing notably to herbicide detoxification. However, the physiological role of most GSTUs is still poorly documented in planta. By combining phylogenetic, biochemical and structural approaches, this work led to the characterisation of nine GSTUs from Arabidopsis thaliana (AtGSTUs) and six GSTUs from Populus trichocarpa (PtGSTUs). Phylogenetic analysis of the Ser-GSTs present in photosynthetic organisms revealed that the expansion of GSTUs occurred concomitantly with the appearance of vasculature in plants, although some mosses and bryophytes possess GSTUs. Within an organism, GSTUs can be classified into distinct groups according to their catalytic motif. Enzymatic tests using recombinant proteins showed that almost all studied GSTUs exhibit GSH conjugation and peroxide reduction activities against different model substrates (CDNB, isothiocyanate derivatives, hydroperoxides). The three-dimensional structures of two GSTUs have been resolved and these adopt the classical canonical GST fold with some notable difference between them. The biochemical and structural analyses of these AtGSTUs and PtGSTUs further showed that some of them bind bacterial porphyrins while others bind polyphenolic compounds. Among the enzyme-ligand complexes identified, the structure of a bacalein-GSTU has been solved. The use of metabolites enriched samples extracted from A. thaliana and P. trichocarpa is the next step to decipher the role of GSTUs in planta
6

Cohoon, Gregory A. "Fabrication, Characterization, and Application of Microresonators and Resonant Structures." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/595953.

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Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1-2 μm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10⁸ and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high as 2x10⁶. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2-5 μm and a diameter of 200-400 μm. Applications in pressure sensing and two-photon fluorescence of dye in microbubble resonators is explored. Photonic crystals can have engineered resonant properties by tuning photonic band gaps and introducing defects to create cavities in the photonic structure. In this work, a natural photonic crystal structure is analyzed in the form of diatoms. Diatoms are a type of phytoplankton which are identified by unique ornamentation of each species silica shell, called a frustule. The frustule is composed of a quasi-periodic lattice of pores which closely resembles manmade photonic crystals. The diatom frustules are analyzed using image processing techniques to determine pore-to-pore spacing and identify defects in the quasi-periodic structure which may contribute to optical filtering and photonic band gap effects. The data gathered is used to simulate light propagation through the diatom structure at different incident angles and with different material properties and to verify data gathered experimentally.
7

Do, Mai Trang. "Fabrication of submicrometer 3D structures by one-photon absorption direct laser writing and applications." Thesis, Cachan, Ecole normale supérieure, 2015. http://www.theses.fr/2015DENS0001/document.

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Ce travail porte sur l’étude d’une nouvelle technique de microscopie basée sur le phénomène d’absorption linéaire ultra-faible (LOPA) de matériaux photosensibles pour la fabrication de structures submicrométriques à deux et à trois dimensions (2D, 3D). Premièrement, nous avons étudié théoriquement la distribution de l'intensité lumineuse dans la région focale d’un objectif de microscope de grande ouverture numérique en fonction des différentes conditions de travail, telles que la propagation de la lumière dans un milieu absorbant avec variation d'indice de refraction. Nous avons démontré que lorsque l'on travaille avec un matériau quasi homogène ayant de très faible absorption à la longueur d’onde du faisceau d’excitation, le faisceau laser peut être focalisé en profondeur à l'intérieur du matériau, ce qui permet de manipuler optiquement des objets en 3D. Nous avons ensuite démontré expérimentalement l'utilisation de cette technique pour fabriquer des structures à la demande. Différentes structures 2D et 3D submicrométriques ont été crées en résine SU-8, en utilisant un laser continue de faible puissance à 532 nm. Ces résultats sont similaires à ceux obtenus par la méthode d’absorption à deux photons, mais le coût de fabrication a été énormément réduit. De plus, nous avons démontré qu'il est possible de fabriquer des structures photoniques à base de polymère contenant une seule nanoparticule (NP), en utilisant un procédé à deux étapes. En effet, nous avons d'abord déterminé avec précision la position d'une seule NP d’or, en utilisant une puissance d’excitation très faible, puis nous l'avons insérée dans une structure photonique par une puissance d’excitation plus élevée. Le couplage d'une NP d’or et d'une structure photonique à base de polymère a été ensuite étudié théoriquement et expérimentalement, montrant une amélioration importante de la collection des photons émis par la NP
This work deals with a novel microscopy technique based on the ultra-low one-photon absorption (LOPA) mechanism of photosensitive materials for fabrication of arbitrary two- and three-dimensional (2D, 3D) submicrometer structures. First, we theoretically investigated the intensity distribution at focusing region of a high numerical aperture objective lens as a function of various working conditions, such as propagation of light mismatched refractive index and/or absorbing media. We demonstrated that when working with refractive index mismatch-free and very low absorption conditions, the light could be focused deeply inside the material, allowing a 3D optical manipulation. We then demonstrated experimentally the use of this simple technique for fabrication of desired structures. Different 2D and 3D structures, with a feature as small as 150 nm, have been created in SU-8 photoresist by using a low power and continuous-wave laser emitting at 532 nm. Furthermore, we demonstrated that it is possible to fabricate a polymer-based photonic structure containing a single nanoparticle (NP), by using a double-step method. Indeed, the LOPA microscopy allowed us first to accurately determine the location of a single gold NP and then to embed it as desired into an arbitrary SU-8 photonic structure. The coupling of a gold NP and a polymer-based photonic structure was theoretically and experimentally investigated showing a six-fold photons collection enhancement as compared to that of a NP in unpatterned film
8

Kulkarni, Aditya. "Simulation of three dimensional current spreading in photonic crystal VCSEL structures." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/28254.

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SRIDHAR, SUPRIYA LALAPET. "Design, Simulation and Physical Characterization of 3D Photonic Crystal Woodpile Structures for High Efficacy Incandescent Thermal Emission." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218030876.

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Gaillot, Davy Paul. "Optical Properties of Complex Periodic Media Structurally Modified by Atomic Layer Deposition." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14635.

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In the late eighties, a new class of materials, known as photonic crystals (PCs), emerged enabling the propagation and generation of light to be potentially manipulated with unprecedented control. PCs consist of a periodic modulation of dielectric constant in one, two, or three dimensions, which can result in the formation of directional or omni-directional photonic band gaps (PBGs), spectral regions where light propagation is forbidden, and more remarkably, novel dispersion characteristics. Since PC properties scale with the dimension of the wavelength of interest, significant technological constraints must be fully addressed to manufacture 3D PBG materials for optical or infrared applications such as displays, lightning, and communications. PCs enable the unraveling of unique optical phenomena such as PBGs, spontaneous emission rate manipulation, sub-wavelength focusing, and superprism effects. This research focuses on the feasibility to achieve omni-directional PBGs in synthetic opal-based 3D PCs through precise nanoscale control to the original dielectric architecture. In particular, the optical response to the conformal deposition of dielectric layers using atomic layer deposition (ALD) within the porous template is strongly emphasized. Geometrical models were developed to faithfully model the manipulation of the synthetic opal architecture by ALD and then used in electromagnetic algorithms to predict the resulting optical properties. From these results, this research presents and investigates a scheme used to greatly enhance and adjust the PBG width and position, as well as simultaneously reducing the dielectric contrast threshold at which the PBG forms. This Thesis demonstrates that the unique opal architectures offered by ALD not only supports the formation of larger PBGs with high index materials; but also enables the use of optically transparent materials with reduced refractive index. Additionally, slight alteration of these structures facilitates the incorporation of non-linear (NL) electro-optical (EO) material for dynamic tuning capabilities and potentially offers a pathway for fabricating multi-functional photonic devices. Finally, low-temperature ALD was investigated as a means to manipulate band gaps and dispersion effects in 2D PC silicon slab waveguides and 3D organic biologically-derived templates. The results indicate the unique ability of ALD to achieve composite structures with desirable (large PBGs) or novel (slow light) optical properties.
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Book chapters on the topic "3D crystal structure":

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Vegas, Angel. "FeLi[PO4]: Dissection of a Crystal Structure." In Inorganic 3D Structures, 67–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/430_2010_35.

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Hieu, Do H. M., Do Q. Duyen, Nguyen P. Tai, Nguyen V. Thang, Ngo C. Vinh, and Nguyen Q. Hung. "Crystal Structure and Mechanical Properties of 3D Printing Parts Using Bound Powder Deposition Method." In Lecture Notes in Mechanical Engineering, 54–62. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-3239-6_4.

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Blatov, Vladislav A. "Crystal Structures of Inorganic Oxoacid Salts Perceived as Cation Arrays: A Periodic-Graph Approach." In Inorganic 3D Structures, 31–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/430_2010_34.

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Strickland, Joel, Bogdan Nenchev, Karl Tassenberg, Samuel Perry, Gareth Sheppard, and Hongbiao Dong. "Applying Stereological Characterisation to the Solidification Structure of Single Crystal Alloys to Deduce the 3D Macroscopic Solid/Liquid Interface Shape." In Characterization of Minerals, Metals, and Materials 2021, 15–25. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-65493-1_2.

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Sukhoivanov, Igor A., and Igor V. Guryev. "Band Structure Computation of 2D and 3D Photonic Crystals." In Photonic Crystals, 67–101. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02646-1_5.

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Gordienko, Yuri, Pavel Kuznetsov, Elena Zasimchuk, Rimma Gontareva, Jürgen Schreiber, and Vladimir Karbovsky. "Multiscale 2D Rectangular and 3D Rhombic Gratings Created by Self-Organization of Crystal Structure Defects under Constrained Cyclic Deformation and Fracture." In Materials Science Forum, 421–24. Stafa: Trans Tech Publications Ltd., 2007. http://dx.doi.org/10.4028/0-87849-469-3.421.

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Murr, Lawrence E. "Volume Defects: 3D Imperfections in Crystals." In Handbook of Materials Structures, Properties, Processing and Performance, 313–24. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-01815-7_17.

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Murr, Lawrence E. "Volume Defects: 3D Imperfections in Crystals." In Handbook of Materials Structures, Properties, Processing and Performance, 1–11. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-01905-5_17-1.

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Burger, S., R. Klose, A. Schädle, F. Schmidt, and L. Zschiedrich. "Adaptive FEM Solver for the Computation of Electromagnetic Eigenmodes in 3D Photonic Crystal Structures." In Scientific Computing in Electrical Engineering, 169–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/978-3-540-32862-9_24.

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Zhou, Ming, Chuan Peng Pan, L. P. Liu, R. Yuan, R. F. Ren, and Lan Cai. "Finite Difference Time Domain Method for Computing the Band-Structure of 3D Photonic Crystals." In Solid State Phenomena, 599–602. Stafa: Trans Tech Publications Ltd., 2007. http://dx.doi.org/10.4028/3-908451-30-2.599.

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Conference papers on the topic "3D crystal structure":

1

Wang, Panxiao, Yidong Huang, Wei Zhang, and Jiangde Peng. "Quasi-3D photonic crystal waveguide with matching layer structure." In Asia-Pacific Optical Communications, edited by Shinji Tsuji, Jens Buus, and Yi Luo. SPIE, 2005. http://dx.doi.org/10.1117/12.636389.

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Krivosheina, Marina, Sergey Kobenko, Elena Tuch, and Maria Kozlova. "Modeling of elastic and plastic waves for HCP single crystals in a 3D formulation based on zinc single crystal." In ADVANCED MATERIALS WITH HIERARCHICAL STRUCTURE FOR NEW TECHNOLOGIES AND RELIABLE STRUCTURES 2016: Proceedings of the International Conference on Advanced Materials with Hierarchical Structure for New Technologies and Reliable Structures 2016. Author(s), 2016. http://dx.doi.org/10.1063/1.4966411.

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Notomi, M., T. Tamamura, Y. Ohtera, O. Hanaizumi, and S. Kawakami. "Direct Experimental Visualization of Photonic Band Structure of 3D Photonic Crystal." In Quantum Optoelectronics. Washington, D.C.: OSA, 1999. http://dx.doi.org/10.1364/qo.1999.qma3.

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Chang, Yong, and Zi-sheng Wang. "Research on 3D Visualization of Crystal Molecular Structure Based on Augmented Reality." In 2008 International Conference on Computer Science and Software Engineering. IEEE, 2008. http://dx.doi.org/10.1109/csse.2008.503.

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Saif, Safna, Sree Sanker S S, Karthika Sankar, Milan K Moncy, Harikrishnan P V, Madhusoodanan K N, and Priya Rose T. "Emission studies on carbon dot embedded self-assembled 3D photonic crystal structure." In Women in Optics and Photonics in India 2022, edited by Anita Mahadevan-Jansen, Asima Pradhan, and Sujatha Narayanan Unni. SPIE, 2023. http://dx.doi.org/10.1117/12.2670047.

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Tetik, Halil, and Dong Lin. "3D Freeze Printing: Development of an Experimental Setup and Determination of 3D Printing Parameters." In ASME 2020 15th International Manufacturing Science and Engineering Conference. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/msec2020-8287.

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Abstract:
Abstract 3D freeze printing is a hybrid manufacturing method composed of freeze casting and inkjet-based printing. It is a facile method to fabricate lightweight, porous, and functional structures. Freeze casting is a well-known method for fabricating porous bodies and is capable of manipulating the micro-structure of the resulting product. Freeze casting simply involves solidification of a liquid suspension using low temperature and sublimation of the solvent using low temperature and pressure. After the sublimation of the solvent crystals, we obtain a porous structure where the pores are a replica of solvent crystal. Making use of the temperature gradient, as seen in unidirectional and bidirectional freeze casting, during the solidification with low temperature values, the solvent crystals grow along the temperature gradient. Furthermore, by manipulating the freezing kinetics during solidification, we can have a control on the average pore size distribution. For instance, when lower freezing temperatures result in finer pores with higher amount, higher freezing temperatures result in coarser pores with less amount. Also, the use of some additives inside the suspension leads to changes in the morphology of the solvent crystals as well as the resulting pores. However, the macro-structure of the fabricated body is highly dependent on the mold used during the process. In order to eliminate the dependency on the mold during the freeze casting process, our group recently combined this technique with inkjet-based 3D printing. With inkjet-based 3D printing, we fabricated uniform lines from single droplets, and complex 3D shapes from the lines. This provided us the ability of tailoring the macro structure of the final product without any dependency on a mold as seen in freeze casting. As a result of the 3D freeze printing process, we achieved fabricating lightweight, porous, and functional bodies with engineered micro and macro-structures. However, achieving fine droplets, and uniform lines by merging the droplets requires a good combination of fabrication parameters such as pressure adjustment inside the print head, print head speed, jetting frequency. Also, fabricating complex shapes from uniform lines requires well-adjusted parameters such as line thickness and layer height. In this study, we briefly explained the mechanics of the 3D freeze printing process. Following that we presented the development process of an open-source inkjet-based 3D printer. Finally, we explained the determination of inkjet dispensing and 3D printing parameters required for a high-quality 3D printing. During our experiments for the determination of fabrication parameters, we used a nanocellulose crystals-based ink due to its low cost and ease of preparation.
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Baba, T., M. Ikeda, and N. Kamizawa. "Observation of Photonic Bandgap in GaInAsP/InP 2D Photonic Crystals by Equivalent Transmission Measurement." In Quantum Optoelectronics. Washington, D.C.: Optica Publishing Group, 1997. http://dx.doi.org/10.1364/qo.1997.qtha.3.

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Semiconductor photonic crystals are promising candidates for realizing spontaneous emission control, i.e., enhancement of spontaneous emission rate (SER) and spontaneous emission factor. Schematic structure of various dimensions of photonic crystal and corresponding wave vector space inhibited by photonic bandgaps (PBGs) are summarized in Fig. 1. Due to the almost perfect PBG and single mode localized state, 3D structures are ideal. However, structures for optical wavelength range are still difficult to fabricate. We have studied 2D structures1,2) to confirm preliminary effects of photonic crystals. In this study, we simply predict the spontaneous emission control in 2D structures, and report the experiment to observe PBG in GaInAsP/InP 2D photonic crystals.
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Guo, Qiong, Osama R. Bilal, and Mahmoud I. Hussein. "A Fast Method for Electronic Band Structure Calculations." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-65681.

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Band structure calculation provides a basis for the study of thermal, optical and magnetic properties of crystals. The reduced Bloch mode expansion (RBME) method is a model reduction method in which a selected set of Bloch eigenvectors within the irreducible Brillouin zone at high symmetry points are used to expand the unit cell problem at hand. In this method, a major reduction in computational cost is achieved with minimum loss of accuracy. The method applies to both classical and ab inito band structure calculations of periodic media, and to any type of wave propagation problem: phononic, photonic, electronic, etc. In this work, the applicability of RBME in calculating the three-dimensional (3D) electronic band structure for crystal structures with different symmetries is demonstrated. Using the Kronig-Penney fixed potential, a high-symmetry cubic model and a low-symmetry triclinic model are considered. For both cases, the energy (eigenvalues) and wave functions (eigenvectors) demonstrate very good convergence performance with the number of expansion points.
9

Hislop, Veronica, and Derick Rousseau. "Effect of Dispersed Aqueous Droplet Volume Fraction on the Rheology and Structure of Water-in-oil Emulsions Stabilized with Fat Crystals." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/aydb6547.

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High-calorie foods such as margarine and butter consist of fat crystal-stabilized emulsions comprising a dispersed aqueous phase stabilized by a 3D matrix of fat crystals. The objective of this study was to investigate how the rheology and structure of fat crystal-stabilized water-in-oil emulsions are affected by the aqueous droplet volume fraction in which there is little interaction between the dispersed and continuous phases. Emulsions at water loads containing up to 40 wt% were prepared with a continuous phase consisting of a mixture of soybean oil, hydrogenated soybean oil and polyglycerol polyricinoleate (PGPR), which limits interactions between dispersed droplets and the continuous fat crystal network. Results showed that presence of water up to 10 wt% resulted in a higher rigidity whereas increasing water content from 10 wt% to 40 wt% reduced it. Via polarized light microscopy, the emulsions showed evidence of network stabilization given the presence of a fat crystal network around the dispersed aqueous phase. The outcomes of this study further contribute to the knowledge base underpinning the contribution of dispersed droplets on the consistency of fat crystal-stabilized water-in-oil emulsions.
10

Mitra, Alok K., Gang Ren, Anchi Cheng, Vijay Reddy, and Peter Melnyk. "3D reconstruction from electron micrographs of tilted 2D crystal: structure of a human water channel." In International Symposium on Optical Science and Technology, edited by Michael A. Fiddy and Rick P. Millane. SPIE, 2000. http://dx.doi.org/10.1117/12.409273.

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Reports on the topic "3D crystal structure":

1

Kirchhoff, Helmut, and Ziv Reich. Protection of the photosynthetic apparatus during desiccation in resurrection plants. United States Department of Agriculture, February 2014. http://dx.doi.org/10.32747/2014.7699861.bard.

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In this project, we studied the photosynthetic apparatus during dehydration and rehydration of the homoiochlorophyllous resurrection plant Craterostigmapumilum (retains most of the photosynthetic components during desiccation). Resurrection plants have the remarkable capability to withstand desiccation, being able to revive after prolonged severe water deficit in a few days upon rehydration. Homoiochlorophyllous resurrection plants are very efficient in protecting the photosynthetic machinery against damage by reactive oxygen production under drought. The main purpose of this BARD project was to unravel these largely unknown protection strategies for C. pumilum. In detail, the specific objectives were: (1) To determine the distribution and local organization of photosynthetic protein complexes and formation of inverted hexagonal phases within the thylakoid membranes at different dehydration/rehydration states. (2) To determine the 3D structure and characterize the geometry, topology, and mechanics of the thylakoid network at the different states. (3) Generation of molecular models for thylakoids at the different states and study the implications for diffusion within the thylakoid lumen. (4) Characterization of inter-system electron transport, quantum efficiencies, photosystem antenna sizes and distribution, NPQ, and photoinhibition at different hydration states. (5) Measuring the partition of photosynthetic reducing equivalents between the Calvin cycle, photorespiration, and the water-water cycle. At the beginning of the project, we decided to use C. pumilum instead of C. wilmsii because the former species was available from our collaborator Dr. Farrant. In addition to the original two dehydration states (40 relative water content=RWC and 5% RWC), we characterized a third state (15-20%) because some interesting changes occurs at this RWC. Furthermore, it was not possible to detect D1 protein levels by Western blot analysis because antibodies against other higher plants failed to detect D1 in C. pumilum. We developed growth conditions that allow reproducible generation of different dehydration and rehydration states for C. pumilum. Furthermore, advanced spectroscopy and microscopy for C. pumilum were established to obtain a detailed picture of structural and functional changes of the photosynthetic apparatus in different hydrated states. Main findings of our study are: 1. Anthocyan accumulation during desiccation alleviates the light pressure within the leaves (Fig. 1). 2. During desiccation, stomatal closure leads to drastic reductions in CO2 fixation and photorespiration. We could not identify alternative electron sinks as a solution to reduce ROS production. 3. On the supramolecular level, semicrystalline protein arrays were identified in thylakoid membranes in the desiccated state (see Fig. 3). On the electron transport level, a specific series of shut downs occur (summarized in Fig. 2). The main events include: Early shutdown of the ATPase activity, cessation of electron transport between cyt. bf complex and PSI (can reduce ROS formation at PSI); at higher dehydration levels uncoupling of LHCII from PSII and cessation of electron flow from PSII accompanied by crystal formation. The later could severe as a swift PSII reservoir during rehydration. The specific order of events in the course of dehydration and rehydration discovered in this project is indicative for regulated structural transitions specifically realized in resurrection plants. This detailed knowledge can serve as an interesting starting point for rationale genetic engineering of drought-tolerant crops.

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