Gotowe bibliografie tematyczne / Hydrophobic clusters

Gotowa bibliografia na temat „Hydrophobic clusters”

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Data publikacji: 25 maja 2024

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Artykuły w czasopismach na temat "Hydrophobic clusters"

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Arunachalam, J., i N. Gautham. "Hydrophobic clusters in protein structures". Proteins: Structure, Function, and Bioinformatics 71, nr 4 (10.01.2008): 2012–25. http://dx.doi.org/10.1002/prot.21881.

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Xie, Xuan, i Chunfu Zhang. "Controllable Assembly of Hydrophobic Superparamagnetic Iron Oxide Nanoparticle with mPEG-PLA Copolymer and Its Effect on MR Transverse Relaxation Rate". Journal of Nanomaterials 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/152524.

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Assembly of individual superparamagnetic iron oxide nanoparticles (SPION) into cluster is an effective way to prepare MRI contrast agent with high relaxivity. In this study, we fabricated SPION clusters with different sizes and configurations by assembly of amphiphilic mPEG-PLA copolymer with hydrophobic SPION in aqueous solution. The evolution of cluster size and configuration with the amount of copolymer and the effect of cluster size on the transverse relaxivity was studied.T2relaxation rates of clusters with different sizes at iron concentration of 0.1 mM were compared with the theoretical predictions. We found that the relative amount of copolymer/SPION was crucial for the formation of SPION cluster. The transverse relaxivity of the condense SPION clusters (CSC) was size-dependent. The experimentally measuredT2relaxation rates of the clusters were lower than the theoretical predictions. In motional average regime (MAR) region,T2relaxation rates were more consistent with the theoretical values when transmission electron microscope (TEM) evaluated size was used. Therefore, for fabrication of SPION clusters with assembly of mPEG-PLA and hydrophobic SPION, delicate balance between the amount of copolymer and SPION should be pursued, and for comparison of experimentalT2relaxation rate with theoretical predictions, TEM evaluated size was more suitable.
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Feketeová, Linda, Paul Bertier, Thibaud Salbaing, Toshiyuki Azuma, Florent Calvo, Bernadette Farizon, Michel Farizon i Tilmann D. Märk. "Impact of a hydrophobic ion on the early stage of atmospheric aerosol formation". Proceedings of the National Academy of Sciences 116, nr 45 (21.10.2019): 22540–44. http://dx.doi.org/10.1073/pnas.1911136116.

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Atmospheric aerosols are one of the major factors affecting planetary climate, and the addition of anthropogenic molecules into the atmosphere is known to strongly affect cloud formation. The broad variety of compounds present in such dilute media and their specific underlying thermalization processes at the nanoscale make a complete quantitative description of atmospheric aerosol formation certainly challenging. In particular, it requires fundamental knowledge about the role of impurities in water cluster growth, a crucial step in the early stage of aerosol and cloud formation. Here, we show how a hydrophobic pyridinium ion within a water cluster drastically changes the thermalization properties, which will in turn change the corresponding propensity for water cluster growth. The combination of velocity map imaging with a recently developed mass spectrometry technique allows the direct measurement of the velocity distribution of the water molecules evaporated from excited clusters. In contrast to previous results on pure water clusters, the low-velocity part of the distributions for pyridinium-doped water clusters is composed of 2 distinct Maxwell–Boltzmann distributions, indicating out-of-equilibrium evaporation. More generally, the evaporation of water molecules from excited clusters is found to be much slower when the cluster is doped with a pyridinium ion. Therefore, the presence of a contaminant molecule in the nascent cluster changes the energy storage and disposal in the early stages of gas-to-particle conversion, thereby leading to an increased rate of formation of water clusters and consequently facilitating homogeneous nucleation at the early stages of atmospheric aerosol formation.
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Lesnikowski, Zbigniew J. "Boron Units as Pharmacophores - New Applications and Opportunities of Boron Cluster Chemistry". Collection of Czechoslovak Chemical Communications 72, nr 12 (2007): 1646–58. http://dx.doi.org/10.1135/cccc20071646.

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Carboranes (dicarba-closo-dodecaboranes) are a class of carbon-containing polyhedral boron-cluster compounds showing remarkable hydrophobic character, chemical and thermal stability, and resistance to catabolism in biological environment. These features allow application of boron clusters as new hydrophobic core structure in biologically active molecules that interact hydrophobically with proteins, thus facilitating new drug design. A review with 45 references.
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Sakibaev, Farkhat, Marina Holyavka, Victoria Koroleva i Valeriy Artyukhov. "Distribution of Charged and Hydrophobic Amino Acids on the Surfaces of Two Types of Beta-Fructosidase from Thermotoga Maritima". Chemistry Proceedings 2, nr 1 (9.11.2020): 4. http://dx.doi.org/10.3390/eccs2020-07550.

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Thermotoga maritima beta-fructosidases are enzymes that release beta-D-fructose from sucrose, raffinose, and fructan polymers such as inulin. The surfaces of beta-fructosidases 1UYP and 1W2T from Thermotoga maritima were studied in this work. It was showed that amino acids are not distributed equally on the surfaces of the enzymes. Several clusters of charged and hydrophobic residues were detected at pH 7.0. Such clusters were detected by calculation of the distances between them. It was determined that on surfaces of beta-fructosidases PDB ID: 1UYP and PDB ID: 1W2T, 96% and 95% of charged amino acids and also 50% and 42% of hydrophobic amino acids form clusters, respectively. Six clusters of charged amino acids on the surface of beta-fructosidase 1UYP and five clusters on the surface of beta-fructosidase 1W2T were detected. The composition of such clusters is presented. Both types of beta-fructosidase have three clusters of hydrophobic amino acids on their surface. These facts should be considered when choosing immobilization conditions. It was shown that a charged matrix is more promising for the immobilization of beta-fructosidases 1UYP and 1W2T from Thermotoga maritima due to the possibility of binding without any significant loss of activity due to their overlapping active center. Hydrophobic carriers are less promising due to the probable active site overlap. Such binding may have a loss of enzyme activity as a result.
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Tavares, Marina Rodrigues, Kaplan Kirakci, Nikolay Kotov, Michal Pechar, Kamil Lang, Robert Pola i Tomáš Etrych. "Octahedral Molybdenum Cluster-Based Nanomaterials for Potential Photodynamic Therapy". Nanomaterials 12, nr 19 (26.09.2022): 3350. http://dx.doi.org/10.3390/nano12193350.

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Photo/radiosensitizers, such as octahedral molybdenum clusters (Mo6), have been intensively studied for photodynamic applications to treat various diseases. However, their delivery to the desired target can be hampered by its limited solubility, low stability in physiological conditions, and inappropriate biodistribution, thus limiting the therapeutic effect and increasing the side effects of the therapy. To overcome such obstacles and to prepare photofunctional nanomaterials, we employed biocompatible and water-soluble copolymers based on N-(2-hydroxypropyl)methacrylamide (pHPMA) as carriers of Mo6 clusters. Several strategies based on electrostatic, hydrophobic, or covalent interactions were employed for the formation of polymer-cluster constructs. Importantly, the luminescent properties of the Mo6 clusters were preserved upon association with the polymers: all polymer-cluster constructs exhibited an effective quenching of their excited states, suggesting a production of singlet oxygen (O2(1Δg)) species which is a major factor for a successful photodynamic treatment. Even though the colloidal stability of all polymer-cluster constructs was satisfactory in deionized water, the complexes prepared by electrostatic and hydrophobic interactions underwent severe aggregation in phosphate buffer saline (PBS) accompanied by the disruption of the cohesive forces between the cluster and polymer molecules. On the contrary, the conjugates prepared by covalent interactions notably displayed colloidal stability in PBS in addition to high luminescence quantum yields, suggesting that pHPMA is a suitable nanocarrier for molybdenum cluster-based photosensitizers intended for photodynamic applications.
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Nishigami, Hiroshi, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Kazuhiko Yamasaki i Masaru Tateno. "Is it possible for short peptide composed of positively- and negatively-charged “hydrophilic” amino acid residue-clusters to form metastable “hydrophobic” packing?" Physical Chemistry Chemical Physics 21, nr 19 (2019): 9683–93. http://dx.doi.org/10.1039/c9cp00103d.

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Gallo, Mariana, Simone Luti, Fabio Baroni, Ivan Baccelli, Eduardo Maffud Cilli, Costanza Cicchi, Manuela Leri, Alberto Spisni, Thelma A. Pertinhez i Luigia Pazzagli. "Plant Defense Elicitation by the Hydrophobin Cerato-Ulmin and Correlation with Its Structural Features". International Journal of Molecular Sciences 24, nr 3 (23.01.2023): 2251. http://dx.doi.org/10.3390/ijms24032251.

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Cerato-ulmin (CU) is a 75-amino-acid-long protein that belongs to the hydrophobin family. It self-assembles at hydrophobic–hydrophilic interfaces, forming films that reverse the wettability properties of the bound surface: a capability that may confer selective advantages to the fungus in colonizing and infecting elm trees. Here, we show for the first time that CU can elicit a defense reaction (induction of phytoalexin synthesis and ROS production) in non-host plants (Arabidopsis) and exerts its eliciting capacity more efficiently when in its soluble monomeric form. We identified two hydrophobic clusters on the protein’s loops endowed with dynamical and physical properties compatible with the possibility of reversibly interconverting between a disordered conformation and a β-strand-rich conformation when interacting with hydrophilic or hydrophobic surfaces. We propose that the plasticity of those loops may be part of the molecular mechanism that governs the protein defense elicitation capability.
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Czaplewski, C. "Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles". Biophysical Chemistry 105, nr 2-3 (wrzesień 2003): 339–59. http://dx.doi.org/10.1016/s0301-4622(03)00085-1.

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Matsumoto, H., E. Rozi Ismail, Y. Seki i K. Soda. "3P031 Role of Hydrophobic Clusters in Protein Folding". Seibutsu Butsuri 45, supplement (2005): S211. http://dx.doi.org/10.2142/biophys.45.s211_3.

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Rozprawy doktorskie na temat "Hydrophobic clusters"

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Lazar, Laurentiu. "Controlled aggregation of polymer latices and encapsulation of hydrophobic substances in polymer clusters". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq35969.pdf.

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Le, Tuan Khanh. "Hydrophobic Cluster analysis : prédiction de structures secondaires à partir d'une séquence unique : implémentation de la procédure "Secondary Structure Prediction" (SSP)". Paris 6, 2003. http://www.theses.fr/2003PA066541.

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Bruley, Apolline. "Exploitation de signatures des repliements protéiques pour décrire le continuum ordre/désordre au sein des protéomes". Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS474.

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Une fraction significative des protéomes reste non annotée, laissant inaccessible une partie du répertoire fonctionnel de la vie, incluant des innovations moléculaires ayant une valeur thérapeutique ou environnementale. Le manque d'annotation fonctionnelle est en partie dû aux limites des approches actuelles pour la détection de relations cachées, ou à des caractéristiques spécifiques telles que le désordre. L'objectif de ma thèse a été de développer des approches méthodologiques reposant sur les signatures structurales des domaines repliés, afin de caractériser plus avant les séquences protéiques dont la fonction est inconnue, même en l'absence d'informations évolutives. Tout d'abord, j'ai développé un score permettant d'estimer le potentiel de repliement d'une séquence d'acides aminés, basé sur sa densité en amas hydrophobes, correspondant principalement aux structures secondaires régulières. J'ai décrit le continuum entre l'ordre et le désordre, couvrant différents états allant des conformations étendues aux globules fondus et ai caractérisé des cas d'ordre conditionnel. Ensuite, j'ai combiné ce score avec les prédictions de structure 3D d'AlphaFold2 (AF2) disponibles pour 21 protéomes de référence. Une grande fraction des acides aminés des modèles AF2 associés à un très faible index de confiance est incluse dans des segments non repliables, soutenant la qualité d'AF2 comme prédicteur du désordre. Cependant, dans chaque protéome, de longs segments repliables avec des prédictions AF2 de faible confiance présentent également des caractéristiques de domaines solubles et repliés. Cela suggère un ordre caché (conditionnel ou inconditionnel), qui n'est pas détecté par AF2 en raison du manque d'informations évolutives, ou des motifs de repliement non répertoriés. Enfin, à l'aide de ces outils, j'ai effectué une exploration préliminaire de protéines ou de régions non annotées, identifiées via le développement et l'application d'une nouvelle procédure d'annotation. Bien que ces séquences soient enrichies en désordre, une part importante d'entre elles présente des caractéristiques de type globulaire soluble. Ces séquences constituent de bons candidats pour de futures validations et caractérisations expérimentales. De plus, l'analyse de gènes de novo validés expérimentalement m'a permis de contribuer au débat encore ouvert sur les caractéristiques structurales des protéines codées par ces gènes, qui présentent un enrichissement en désordre et une grande diversité d'états structuraux
A significant fraction of the proteomes remains unannotated, leaving inaccessible a part of the functional repertoire of life, including molecular innovations with therapeutic or environmental value. Lack of functional annotation is partly due to the limitations of the current approaches in detecting hidden relationships, or to specific features such as disorder. The aim of my PhD thesis was to develop methodological approaches based on the structural signatures of folded domains, in order to further characterize the protein sequences with unknown function even in absence of evolutionary information. First, I developed a scoring system in order to estimate the foldability potential of an amino acid sequence, based on its density in hydrophobic clusters, which mainly correspond to regular secondary structures. I disentangled the continuum between order and disorder, covering various states from extended conformations (random coils) to molten globules and characterize cases of conditional order. Next, I combined this scoring system with the AlphaFold2 (AF2) 3D structure predictions available for 21 reference proteomes. A large fraction of the amino acids with very low AF2 model confidence are included in non-foldable segments, supporting the quality of AF2 as a predictor of disorder. However, within each proteome, long segments with very low AF2 model confidence also exhibit characteristics of soluble, folded domains. This suggests hidden order (conditional or unconditional), which is undetected by AF2 due to lack of evolutionary information, or unrecorded folding patterns. Finally, using these tools, I made a preliminary exploration of unannotated proteins or regions, identified through the development and application of a new annotation workflow. Even though these sequences are enriched in disorder, an important part of them showcases soluble globular-like characteristics. These would make good candidates for further experimental validation and characterization. Moreover, the analysis of experimentally validated de novo genes allowed me to contribute to the still-open debate on the structural features of proteins encoded by these genes, enriched in disorder and displaying a great diversity of structura
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Albeau, Karine. "Analyse à grande échelle des textures des séquences protéiques via l'approche Hydrophobic Cluster Analysis (HCA)". Phd thesis, Université de Versailles-Saint Quentin en Yvelines, 2005. http://tel.archives-ouvertes.fr/tel-00011139.

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Découper, a priori et de façon précise, les séquences en domaines est d'une grande importance dans le champ de la biologie, notamment pour optimiser les études de génomique structurale et de génomique fonctionnelle. Différentes approches basées sur la composition en acides aminés, la complexité de la séquence ou la construction de modèles 3D ab initio, ont été développées par le passé. Nous proposons, dans le cadre de ce travail, une approche nouvelle et originale pour le découpage automatique et sensible des séquences protéiques en domaines structurés distincts par exploitation de leur texture. Cette approche bénéficie de l'information de voisinage 2D apportée par la méthodologie « Hydrophobic Cluster Analysis » (HCA). La distribution des différentes catégories d'amas hydrophobes, tels que définis par l'intermédiaire de HCA, ainsi que l'analyse de leurs caractéristiques en termes de structures secondaires, permettent d'appréhender de façon différenciée les textures des régions globulaires, non globulaires et/ou désordonnées, répétitives, passages membranaires isolés ou multiples.... L'approche développée, DomHCA, permet in fine de segmenter une séquence protéique en une série de régions et sous-régions caractérisées par des textures précises, segmentation qui, appliquée à l'échelle des génomes, autorise une comparaison rapide et originale de l'ensemble des séquences. Une des applications concerne les séquences du génome de Plasmodium falciparum qui, par leurs fortes proportions en acides aminés N et K, rendent les méthodes classiques de détection de similarité peu efficaces.
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Dulin, Fabienne. "Exploration des caractéristiques tridimensionnelles des amas protéiques hydrophobes issus du formalisme "Hydrophobic Cluster Analysis" (HCA) : modélisation de formes oligomériques solubles du peptide Aβ impliqué dans la maladie d'Alzheimer, et identification d'un 'point chaud" commun à différentes protéines amyloïdes". Paris 6, 2006. http://www.theses.fr/2006PA066465.

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Nous avons d’abord exploré les caractéristiques 3D des amas d’acides aminés hydrophobes issus de la méthode "Hydrophobic Cluster Analysis" (HCA), au travers d’une représentation originale en tesselation de Voronoï. Chaque amas peut être ainsi caractérisé dans ses conformations  ou  et ses affinités préférentielles pour d’autres amas peuvent être décrites. Le repliement protéique peut alors être décrit comme l’assemblage de ces amas HCA 3D. Nous avons ensuite construit, en utilisant des outils d’alignement tels que HCA, des modèles 3D des formes oligomériques solubles du peptide A. Ce peptide, impliqués dans la maladie d’Alzheimer, serait neurotoxique sous cette forme soluble. Ce travail nous a permis de proposer une hypothèse expliquant le comportement différencié de p3, sans la région N-terminale d’A. Enfin, nous avons pu mettre en évidence la présence d’un ou plusieurs "points chauds" communs aux protéines amyloïdes, pouvant être à l’origine de leur propriété à former des fibres.
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Hennetin, Jérôme. "Texture hydrophobe HCA des séquences protéiques : regards sur les introns". Paris 7, 2003. http://www.theses.fr/2003PA077055.

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Levivier, Emilie. "Exploration des similitudes de séquences protéiques à haut niveau de divergence évolutive : perspectives de l'approche Hydrophobic Cluster Analysis (HCA)". Paris 7, 2003. http://www.theses.fr/2003PA077069.

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Eudes, Richard. "Développements méthodologiques relatifs à l'attribution et à la prédiction des structures secondaires des protéines globulaires : classification structurale de mutations du transporteur CFTR, observées chez des patients atteints de mucoviscidose". Paris 6, 2006. http://www.theses.fr/2006PA066170.

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Schümmer, Tobias [Verfasser], Thomas [Akademischer Betreuer] Kiefhaber i Michael [Akademischer Betreuer] Groll. "The role of a hydrophobic cluster for stability and assembly kinetics of the trimeric foldon domain from T4 fibritin / Tobias Schümmer. Gutachter: Michael Groll ; Thomas Kiefhaber. Betreuer: Thomas Kiefhaber". München : Universitätsbibliothek der TU München, 2011. http://d-nb.info/1056936428/34.

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Kantari, Chahrazade. "Rôle pro-inflammatoire de la protéinase 3 membranaire du neutrophile : identification de la phospholipide scramblase 1 comme nouveau partenaire moléculaire et du site d’interaction avec la membrane". Paris 6, 2008. http://www.theses.fr/2008PA066171.

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La protéinase 3 (PR3) est une protéase granulaire antibiotique du neutrophile qui peut également être exprimée à la membrane plasmique où elle est la cible d’auto-anticorps appelés ANCA dans une vascularite systémique. Mon projet de thèse est focalisé sur la caractérisation structurale et fonctionnelle de la PR3 membranaire. Dans un premier temps, j’ai démontré que la PR3 est mobilisée à la membrane plasmique au cours de l’apoptose via son association avec la phospholipide scramblase 1. Cette expression lui confère un rôle pro-inflammatoire puisqu’elle interfère avec la phagocytose des cellules apoptotiques et donc avec la résolution de l’inflammation. Dans un second temps, j’ai identifié dans la séquence de la PR3 le domaine d’interaction avec la membrane plasmique. En conclusion, ce travail démontre que la PR3 ne peut plus être considérée seulement comme une protéine antibiotique mais aussi comme une protéine régulant l’inflammation.
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Części książek na temat "Hydrophobic clusters"

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Azevedo, Paulo J., Cândida G. Silva, J. Rui Rodrigues, Nuno Loureiro-Ferreira i Rui M. M. Brito. "Detection of Hydrophobic Clusters in Molecular Dynamics Protein Unfolding Simulations Using Association Rules". W Biological and Medical Data Analysis, 329–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11573067_33.

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Vanderheeren, G., i I. Hanssens. "The Perception of Hydrophobic Clusters in the Native and Partially Unfolded States of a Protein". W Proteome and Protein Analysis, 211–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-59631-5_15.

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Naseem, Z., K. Sagoe-Crentsil i W. Duan. "Graphene-Induced Nano- and Microscale Modification of Polymer Structures in Cement Composite Systems". W Lecture Notes in Civil Engineering, 527–33. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-3330-3_56.

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AbstractRedispersible polymers such as ethylene–vinyl acetate copolymer (EVA) have attracted attention in construction due to their enhanced flexural strength, adhesion, flexibility and resistance against water penetration. However, EVA particles cluster in a highly alkaline cementitious matrix and exhibit poor interaction with the cement matrix. The underlying mechanism of poor dispersibility of EVA is attributed to hydrophobic groups of polymers, a variation in the adsorption rate and molecular diffusion to the interface where they cluster together. This phenomenon can negatively affect the fresh properties of cement and produce a weak microstructure, adversely affecting the resulting composites’ performance. This study highlights how graphene oxide (GO) nanomaterial alters the nano- and microscale structural characteristics of EVA to minimize the negative effects. Transmission electron microscopy (TEM) revealed that the GO sheets modify EVA’s clustered nanostructure and disperse it through electrostatic and steric interactions. Furthermore, scanning electron microscopy (SEM) confirmed altered microscale structural characteristics (viz. surface features) by GO. The altered and enhanced material scale engineering performance, such as the compressive strength of the resulting cement composite, was notable.
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Konat, R. K., S. Golic Grdadolnik, W. Schmitt i H. Kessler. "Conformational studies on cyclic tetrapeptides: Hydrophobic cluster formation". W Peptides 1994, 521–22. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-1468-4_235.

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Atkins, Peter, George Ratcliffe, Mark Wormald i Julio de Paula. "Entropy in biology". W Physical Chemistry for the Life Sciences. Oxford University Press, 2023. http://dx.doi.org/10.1093/hesc/9780198830108.003.0009.

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This chapter concentrates on entropy in biology. All processes in biology are accompanied by an increase in entropy of the universe, i.e., those that include the biochemical processes of metabolism and the processes that result in the formation of structure. To assess whether a reaction can occur spontaneously, the chapter shows how we can evaluate the total change in entropy that occurs when pure, unmixed reactants change into pure, unmixed products. It also discusses a very important aspect of the role of entropy and its ability to drive the emergence of form — the hydrophobic effect in which hydrophobic groups, which are groups of atoms that have little or no ability to attract water molecules, tend to cluster together and away from the aqueous environment in which they are immersed. The chapter concludes with a case study which utilises hydrophobicities to predict protein structure.
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Bunker, Bruce C., i William H. Casey. "Solvated Ions in Water". W The Aqueous Chemistry of Oxides. Oxford University Press, 2016. http://dx.doi.org/10.1093/oso/9780199384259.003.0009.

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In most undergraduate chemistry classes, students are taught to consider reactions in which cations and anions dissolved in water are depicted as isolated ions. For example, the magnesium ion is depicted as Mg2+, or at best Mg2+(aq). For anions, these descriptions may be adequate (if not accurate). However, for cations, these abbreviations almost always fail to describe the critical chemical attributes of the dissolved species. A much more meaningful description of Mg2+ dissolved in water is [Mg(H2O)6]2+, because Mg2+ in water does not behave like a bare Mg2+ ion, nor do the waters coordinated to the Mg2+ behave anything like water molecules in the bulk fluid. In many respects, the [Mg(H2O)6]2+ ion acts like a dissolved molecular species. In this chapter, we discuss the simple solvation of anions and cations as a prelude to exploring more complex reactions of soluble oxide precursors called hydrolysis products. The two key classes of water–oxide reactions introduced here are acid–base and ligand exchange. First, consider how simple anions modify the structure and properties of water. As discussed in Chapter 3, water is a dynamic and highly fluxional “oxide” containing transient rings and clusters based on tetrahedral oxygen anions held together by linear hydrogen bonds. Simple halide ions can insert into this structure by occupying sites that would normally be occupied by other water molecules because they have radii (ranging from 0.13 to 0.22 nm in the series from F− to I−) that are comparable to that of the O2− ion (0.14 nm). Such substitution is clearly seen in the structures of ionic clathrate hydrates, where the anion can replace one and sometimes even two water molecules. Larger anions can also replace water molecules within clathrate hydrate cages. For example, carboxylate hydrate structures incorporate the carboxylate group within the water framework whereas the hydrophobic hydrocarbon “tails” occupy a cavity within the water framework, as in methane hydrate (see Chapter 3). Water molecules form hydrogen bonds to dissolved halide ions just as they can to other water molecules, as designated by OH−Y−.
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Semertzidis, Michel T., Etienne Thoreau, Anne Tasso, Bernard Henrissat, Isabelle Callebaut i Jean Paul Mornon. "Visualization of Protein Sequences Using the Two-Dimensional Hydrophobic Cluster Analysis Method". W Visualizing Biological Information, 129–44. WORLD SCIENTIFIC, 1995. http://dx.doi.org/10.1142/9789812832054_0012.

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Koskela, Heikki O., Tuomas A. Selander i Anne M. Lätti. "Cluster Analysis in 975 Patients with Current Cough Identifies a Phenotype with Several Cough Triggers, Many Background Disorders, and Low Quality of Life". W Statistical Inference for Ergodic Algorithmic Model (EAM), Applied to Hydrophobic Hydration Processes. Vide Leaf, Hyderabad, 2021. http://dx.doi.org/10.37247/pacard.1.21.6.

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Streszczenia konferencji na temat "Hydrophobic clusters"

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Chen, Peng, Chunmei Liu, Legand Burge, Mahmood Mohammad, Bill Southerland i Clay Gloster. "Prediction of Inter-residue Contact Clusters from Hydrophobic Cores". W 2008 Seventh International Conference on Machine Learning and Applications. IEEE, 2008. http://dx.doi.org/10.1109/icmla.2008.74.

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Chakraborty, Indrani, Bhagyashree A. Chalke, Smita Gohil i Pushan Ayyub. "Self-assembly of metal nanorod arrays into hierarchical clusters and evolution of their hydrophobic behaviour". W PROCEEDING OF INTERNATIONAL CONFERENCE ON RECENT TRENDS IN APPLIED PHYSICS AND MATERIAL SCIENCE: RAM 2013. AIP, 2013. http://dx.doi.org/10.1063/1.4810166.

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Chen, Peng-Yu, Wei-Hui Chen i Che-Wun Hong. "Nanofludic Analysis on Methanol Crossover of Direct Methanol Fuel Cells". W ASME 2008 First International Conference on Micro/Nanoscale Heat Transfer. ASMEDC, 2008. http://dx.doi.org/10.1115/mnht2008-52095.

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Direct methanol fuel cells (DMFCs) are considered as a competitive power source candidate for portable electronic devices. Nafion® has been widely used for the electrolyte of DMFCs because of its good proton conductivity and high chemical and mechanical stability. However, the major problem that must be solved before commercialization is the high methanol crossover through the membrane. There are a number of studies on experiments about the methanol crossover rate through the membrane but only few theoretical investigations have been presented [1–3]. In this paper, an atomistic model [4] is presented to analyze the molecular structure of the electrolyte and dynamic properties of nanofluids at different methanol concentration. In the same time, the nano-scopic phenomenon of methanol crossover through the membrane is observed. The simulation system consists of the Nafion fragments, hydronium ions, water clusters and methanol molecules. Fig. 1 shows the simplified Nafion fragment in our simulation. Both intra- and inter-molecular interactions were involved in this study. Intermolecular interactions include the van der Waals and the electrostatic potentials. Intramolecular interactions consist of bond, angle and dihedral potentials. The force constants used above were determined from the DREIDING force field. The SPC/E model was employed for water molecules. The three-site OPLS potential model was utilized for the intermolecular potential in methanol. Each proton which migrates inside the electrolyte is assumed to combine with one water molecule to form the hydronium (H3O+). The force parameters for the hydronium were taken from Burykin et al [5]. The atomistic simulation was carried out on the software DLPOLY. First, a 500 ps NPT ensemble was performed to make the system reach a proper configuration. This step was followed by another 500 ps NVT simulation. All molecular simulations were performed at a temperature of 323K with three-dimensional periodic boundary conditions. The intermolecular interactions were truncated at 10 Å and the equations of motion were solved using the Verlet scheme with a time step of 1 fs. Fig. 2 shows the calculated density of the simulation system for different methanol concentrations at 323K. It can be seen that the density decreases with the methanol uptakes. The volume of the system increases as the methanol concentration increases, which means that the membrane swelling with methanol uptakes. The radial distribution functions (RDFs) of the ether-like oxygen (O2) toward water and methanol molecules for different methanol concentrations at 323K are shown in Fig. 3. From this figure, we find that methanol molecules can reside in the vicinity of the hydrophobic part of the side chain while water can not. Fig. 4 shows the RDFs between the oxygen atom of the sulfonic acid groups (O3) and solvents for different methanol concentrations at 323K. As shown in Fig. 4, both water and methanol have a tendency to cluster near the sulfonic acid groups, but water molecules prefer to associate with the sulfonic acid groups in comparison with methanol molecules. The mean square displacements (MSDs) of water and methanol molecules for different methanol concentrations at 323K are displayed in Fig. 5. It is shown that MSD curves have a linear tendency, which means both water and methanol molecules are diffusing in the system during the simulation. As the methanol concentration increases, the slope of MSD curve increases for methanol and decreases for water. This indicates higher methanol content constrains the mobility of water molecules but enhances the mobility of methanol molecules that cross the electrolyte. In summary, molecular simulations of the Nafion membrane swollen in different methanol concentrations (0, 11.23, 21.40, 46.92 wt%) at 323K have been carried out. Both methanol migration mechanism and hydronium diffusion phenomenon have been visualized by monitoring the trajectories of the specific species in the system. MSDs are used to evaluate the mobility and shows that the higher the methanol concentration, the greater the tendency of methanol crossover.
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Suciu, Claudiu Valentin. "Thermal Effects on Nano-Energy Absorption Systems (Nano-EAS)". W 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. ASMEDC, 2008. http://dx.doi.org/10.1115/micronano2008-70039.

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Development of intelligent and ecological energy absorption systems (EAS) is important to various fields such as automotive (vehicle suspensions, bumpers, engine mounts), construction (protections against seismic and wind-induced vibrations), and defense (parachuted objects, armors). Usual EAS use composites, shape-memory alloys and foams. Recently, liquid adsorption/desorption in/from nanoporous solids was employed to develop high-performance nano-EAS. Energy loss is based on the well-known capillary phenomenon: external work must be done to spread a non-wetting liquid on a solid surface. Nano-EAS provide considerably higher dissipated energies, about 1–10J/g at deformability of 30–70%, compared with the energy absorption of Ti-Ni alloys, about 0.01–0.05J/g at deformability of 5–8%. For water against hydrophobic nanoporous silica gel (artificial sand), the nano-EAS become ecological; they can be also made intelligent by thermo-electrical control. Relative to thermal effects, Qiao et al. have investigated, for nanoporous silica gel with insufficient coverage of the alkyl-based hydrophobic coating, the problem of hysteresis recovery by increasing the temperature in the range 20∼80°C. Energy loss capacity reduced severely after the first loading-unloading cycle, so, the hysteresis was found as irreversible. Shape of the first hysteresis, the accessible specific pore volume and the desorption pressure were almost unaffected by the temperature change. At temperature augmentation the second hysteresis was partially recovered and when the temperature exceeded 50°C the system became almost fully reusable. Water inflow was found as governed by Laplace-Washburn equation but the outflow process was perceived as thermally aided. On the other hand, Eroshenko et al. have contradictorily obtained for nanoporous silica gel with full coverage of the alkyl-based hydrophobic coating, a stable hysteresis at repeated working cycles. Adsorption pressure decreased and desorption pressure increased at temperature augmentation, this producing a reduction of the hysteresis area and damping. However, the accessible specific pore volume was found as thermally unaffected. Oppositely, both the in- and out-flows were found as governed by Laplace-Washburn equation. In this work, for nanoporous silica gels with partial and full coverage of the alkyl and fluorocarbon based hydrophobic coatings, the thermal effects on the hysteresis and damping performances are studied. Test rig used is a compression-decompression chamber introduced inside of an incubator that allows temperature adjustment in the range of −10∼50°C. Results reveal that, depending on the hydrophobic coating coverage, findings reported by Qiao et al. and Eroshenko et al. are in fact not contradictory but complementary. However, as expected, the accessible specific pore volume was found to decrease at temperature reduction. In order to explain all these apparently opposite experimental findings, a model based on the water cluster size distribution versus temperature, the pore size distribution of silica gel and the ability of water molecules to form hydrogen bonds with the uncovered hydroxyl groups on the solid surface is proposed.
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Handa, M., K. Titani, K. Takio i Z. M. Ruggeri. "CHARACTERIZATION OF THE VON WILLEBRAND FACTOR-BINDING DOMAIN OF PLATELET MEMBRANE GLYCOPROTEIN Ib". W XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642925.

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We have previously obtained immunochemical evidence that the von Willebrand factor (vWF)-binding domain of the platelet membrane glycoprotein (GP) Ib is located near the amino terminus of the a subunit (Journal of Biological Chemistry 261: 12579-12585, 1986). We have now determined the complete amino acid sequence of the 45 kDa tryptic fragment of glycocalicin that contains this domain. Purified glycocalicin was subjected to limited digestion with trypsin and the proteolytic fragments were separated by size-exclusion high-pressure liquid chromatography. Two fragments of 45 kDa and 84 kDa, respectively, were obtained under nonreducing conditions. After reduction and S-carboxymethylation, the 84 kDa fragment was unchanged, while the 45 kDa fragment yielded two new fragments, one of 35 kDa and the other of 7 kDa. This finding proves the existence of a trypsin cleavage site within a disulfide loop. Two primary sets of overlapping fragments were obtained by cleavage of the carboxymethylated protein at methionyl and lysyl bonds following treatment with cyanogen bromide and Achromobacter protease I, respectively. Additional fragments were obtained by treatment of glycocalicin with Staphylococcus aureus V8 protease and Serratia marcescens protease. Analysis of all these fragments provided data that allowed determination of the sequence of the amino terminal 299 residues of the GP Ib a-chain. This includes the 45 kDa tryptic fragment containing the vWF-binding domain. This 299-residue sequence, corresponding approximately to two thirds of the α-chain polypeptide, is largely hydrophobic and contains only two N-linked and one O-linked carbohydrate chains. A hydrophilic region exists between residues 215-299, with a cluster of ten negatively charged residues at 269-287. This area is likely to attract positively charged molecules. The hydrophilic, highly glycosylated (at Ser/Thr residues) region corresponding to the previously described "macroglycopeptide" begins at residue 292. The determined sequence of glycocalicin contains a region with seven repeats, indicative of gene duplication, and is highly homologous to human leucine-rich α2-glycoprotein.
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