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https://www.readbyqxmd.com/read/29156796/downregulation-of-dna-repair-proteins-and-increased-dna-damage-in-hypoxic-colon-cancer-cells-is-a-therapeutically-exploitable-vulnerability
#1
Jennifer M J Jongen, Lizet M van der Waals, Kari Trumpi, Jamila Laoukili, Niek A Peters, Susanne J Schenning-van Schelven, Klaas M Govaert, Inne H M Borel Rinkes, Onno Kranenburg
Surgical removal of colorectal cancer (CRC) liver metastases generates areas of tissue hypoxia. Hypoxia imposes a stem-like phenotype on residual tumor cells and promotes tumor recurrence. Moreover, in primary CRC, gene expression signatures reflecting hypoxia and a stem-like phenotype are highly expressed in the aggressive Consensus Molecular Subtype 4 (CMS4). Therapeutic strategies eliminating hypoxic stem-like cells may limit recurrence following resection of primary tumors or metastases. Here we show that expression of DNA repair genes is strongly suppressed in CMS4 and inversely correlated with hypoxia-inducible factor-1 alpha (HIF1α) and HIF-2α co-expression signatures...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155578/determination-of-hydrophobic-lengths-of-membrane-proteins-with-the-hdgb-implicit-membrane-model
#2
Bercem Dutagaci, Michael Feig
A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane, identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data...
November 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29154164/molecular-insights-into-inclusion-complexes-of-mansonone-e-and-h-enantiomers-with-various-%C3%AE-cyclodextrins
#3
Panupong Mahalapbutr, Bodee Nutho, Peter Wolschann, Warinthorn Chavasiri, Nawee Kungwan, Thanyada Rungrotmongkol
The structural dynamics and stability of inclusion complexes of mansonone E (ME) and H (MH) including their stereoisomers with various βCDs (methylated- and hydroxypropylated-βCDs) were investigated by classical molecular dynamics (MD) simulations and binding free energy calculations. The simulation results revealed that mansonones are able to form inclusion complexes with βCDs. The guest molecules are not completely inserted into the host cavity, their preferably positions are nearby the secondary rim with the oxane ring dipping into the hydrophobic inner cavity...
November 11, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29152568/moir%C3%A3-excitons-from-programmable-quantum-emitter-arrays-to-spin-orbit-coupled-artificial-lattices
#4
Hongyi Yu, Gui-Bin Liu, Jianju Tang, Xiaodong Xu, Wang Yao
Highly uniform and ordered nanodot arrays are crucial for high-performance quantum optoelectronics, including new semiconductor lasers and single-photon emitters, and for synthesizing artificial lattices of interacting quasiparticles toward quantum information processing and simulation of many-body physics. Van der Waals heterostructures of two-dimensional semiconductors are naturally endowed with an ordered nanoscale landscape, that is, the moiré pattern that laterally modulates electronic and topographic structures...
November 2017: Science Advances
https://www.readbyqxmd.com/read/29152370/unusual-thermolysis-of-aza-cyclic-allene-under-microwave-conditions-crystal-structure-of-3rs-3asr-8rs-8ars-methyl-5-6-dimeth-oxy-3a-10-dimethyl-1-phenyl-3-3a-8-8a-tetra-hydro-3-8-epimino-methano-cyclo-penta-a-indene-2-carboxyl-ate-from-synchrotron-x-ray-diffraction
#5
Le Tuan Anh, Alexander A Titov, Maxim S Kobzev, Leonid G Voskressensky, Alexey V Varlamov, Pavel V Dorovatovskii, Victor N Khrustalev
The title compound, C25H27NO4 (I), the product of the unusual thermolysis of aza-cyclic allene methyl 10,11-dimeth-oxy-3,8-dimethyl-6-phenyl-3-aza-benzo[d]cyclo-deca-4,6,7-triene-5-carboxyl-ate, represents a bicyclic heterosystem and crystallizes in the monoclinic space group P21/c with three crystallographically independent mol-ecules in the unit cell. These independent mol-ecules adopt very similar geometries and differ only in the conformations of the two meth-oxy substituents on the benzene ring. In two of the three independent mol-ecules, both meth-oxy groups are almost coplanar with the benzene ring [the C-C-O-Me torsion angles are 10...
November 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/29150599/publisher-correction-interlayer-excitons-in-a-bulk-van-der-waals-semiconductor
#6
Ashish Arora, Matthias Drüppel, Robert Schmidt, Thorsten Deilmann, Robert Schneider, Maciej R Molas, Philipp Marauhn, Steffen Michaelis de Vasconcellos, Marek Potemski, Michael Rohlfing, Rudolf Bratschitsch
A correction to this article has been published and is linked from the HTML version of this article.
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29149637/antiviral-potential-of-natural-compounds-against-influenza-virus-hemagglutinin
#7
S Kannan, P Kolandaivel
Influenza virus of different subtypes H1N1, H2N2, H3N2 and H5N1 cause many human pandemic deaths and threatening the people worldwide. The Hemagglutinin (HA) protein mediates viral attachment to host receptors act as an attractive target. The sixteen natural compounds have been chosen to target the HA protein. Molecular docking studies have been performed to find binding affinity of the compounds. Out of the sixteen, three compounds CI, CII and CIII found to posses a higher binding affinity. The molecular dynamics (MD) simulation has been performed to study the structural, dynamical properties for the nine different complexes CI, CII, CIII bound with H1, H2, H3 proteins and the results were compared...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29146916/deposition-of-topological-silicene-germanene-and-stanene-on-graphene-covered-sic-substrates
#8
Filipe Matusalem, Daniel S Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K Teles
Growth of X-enes, such as silicene, germanene and stanene, requires passivated substrates to ensure the survival of their exotic properties. Using first-principles methods, we study as-grown graphene on polar SiC surfaces as suitable substrates. Trilayer combinations with coincidence lattices with large hexagonal unit cells allow for strain-free group-IV monolayers. In contrast to the Si-terminated SiC surface, van der Waals-bonded honeycomb X-ene/graphene bilayers on top of the C-terminated SiC substrate are stable...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146907/giant-magnetic-splitting-inducing-near-unity-valley-polarization-in-van-der-waals-heterostructures
#9
Philipp Nagler, Mariana V Ballottin, Anatolie A Mitioglu, Fabian Mooshammer, Nicola Paradiso, Christoph Strunk, Rupert Huber, Alexey Chernikov, Peter C M Christianen, Christian Schüller, Tobias Korn
Monolayers of semiconducting transition metal dichalcogenides exhibit intriguing fundamental physics of strongly coupled spin and valley degrees of freedom for charge carriers. While the possibility of exploiting these properties for information processing stimulated concerted research activities towards the concept of valleytronics, maintaining control over spin-valley polarization proved challenging in individual monolayers. A promising alternative route explores type II band alignment in artificial van der Waals heterostructures...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145002/different-transport-behaviors-of-bacillus-subtilis-cells-and-spores-in-saturated-porous-media-implications-for-contamination-risks-associated-with-bacterial-sporulation-in-aquifer
#10
Qi Li, Jiakuan Yang, Wei Fan, Dandan Zhou, Xiaoyu Wang, Leilei Zhang, Mingxin Huo, John C Crittenden
In this study, we compared the transport characteristics of Bacillus subtilis cells and their spores in saturated porous media. Both the bacteria cells and spores were readily transported under lower ionic strengths (IS) (1mM), featuring high mass recovery rates (>75%). The bacteria cells recovery rate declined to 58.05% when the IS increased to 100mM; but the spores recovery rate remained at 74.54%. Spores appear to be more mobile than bacterial cells over wide range of IS. Surface properties and breakthrough curves analysis of the two bio-particles (cells and spores) indicated that attachment, straining and blocking mechanisms contribute differently to deposition processes...
November 11, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29144144/structural-emergence-in-particle-dispersions
#11
Andrew Mulderig, Gregory Beaucage, Karsten Vogtt, Hanqiu Jiang, Yan Jin, Lisa Clapp, Donald Henderson
Particle dispersions, such as pigment-based inks, comprise weakly bound, milled nanoparticles. The properties of these pigments depend on both their chemical composition, as well as a rather complex structural hierarchy, which emerges from these dispersions. The emergence of structure under semi-dilute conditions is related to the structure of the dilute particles, the particle spacing (mesh size), processing history, and the interaction potential. Kinetic simulations could predict such emergence using these input parameters...
November 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29143004/adsorption-parameters-and-phase-behaviour-of-non-ionic-surfactants-at-liquid-interfaces
#12
Radomir Iliev Slavchov, Ivan Boyanov Ivanov
A reasonable adsorption model is one that allows all adsorption parameters (adsorption constant, hard-disc area α, attraction parameter β) of a surfactant at a liquid interface to be predicted accurately as a function of the molecular structure and medium conditions. However, the established adsorption models of van der Waals and Frumkin lead to inconsistencies, such as negative β at water|oil, α significantly larger than the crystallographic area of the molecule, and phase behaviour that contradicts the experimental observations...
November 16, 2017: Soft Matter
https://www.readbyqxmd.com/read/29143003/a-mixed-dimensional-light-emitting-diode-based-on-a-p-mos2-nanosheet-and-an-n-cdse-nanowire
#13
Pan Li, Kai Yuan, Der-Yuh Lin, Xiaolong Xu, Yilun Wang, Yi Wan, Haoran Yu, Kun Zhang, Yu Ye, Lun Dai
The construction of the mixed-dimensional van der Waals (vdW) heterostructures with two-dimensional (2D) and one-dimensional (1D) materials can advantageously integrate their respective dimensional properties to produce new device functionalities and/or enhance device performance. In this case, a single semiconductor nanowire (NW) can function as an optical cavity and a gain medium, while the atomically thin 2D material does not strongly absorb the NW's light emission or disturb the optical propagation mode...
November 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/29142616/scaling-relations-for-acidity-and-reactivity-of-zeolites
#14
Chong Liu, Ionut Tranca, Rutger A van Santen, Emiel J M Hensen, Evgeny A Pidko
Zeolites are widely applied as solid acid catalysts in various technological processes. In this work we have computationally investigated how catalytic reactivity scales with acidity for a range of zeolites with different topologies and chemical compositions. We found that straightforward correlations are limited to zeolites with the same topology. The adsorption energies of bases such as carbon monoxide (CO), acetonitrile (CH3CN), ammonia (NH3), trimethylamine (N(CH3)3), and pyridine (C5H5N) give the same trend of acid strength for FAU zeolites with varying composition...
October 26, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/29138954/identification-of-compounds-from-palicourea-rigida-leaves-with-topical-anti-inflammatory-potential-using-experimental-models
#15
Rafael P Pinheiro, Muiara A Moraes, Bruna C S Santos, Rodrigo L Fabri, Glauciemar Del-Vechio-Vieira, Célia H Yamamoto, Ana Lúcia S M Araújo, Aílson L A Araújo, Orlando V Sousa
Palicourea rigida Kunth is traditionally used for the treatment of skin diseases, kidney pains and ovarian inflammation. Based on these traditional uses, this study evaluated the topical anti-inflammatory activity of the ethanol extract from P. rigida leaves (EEPR) and identified bioactive compounds. Ear edema was induced in Swiss mice by the topical application of Croton oil, arachidonic acid, phenol and capsaicin. Histopathological analysis and myeloperoxidase and N-acetyl-β-D-glucosaminidase activities were determined...
November 14, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/29138773/cooperating-dipole-dipole-and-van-der-waals-interactions-driven-2d-self-assembly-of-fluorenone-derivatives-ester-chain-length-effect
#16
Meiqiu Dong, Kai Miao, Yi Hu, Juntian Wu, Jinxing Li, Peng Pang, Xinrui Miao, Wenli Deng
Two-dimensional supramolecular assemblies of a series of 2,7-bis(10-n-alkoxycarbonyl-decyloxy)-9-fluorenone derivatives (BAF-Cn, n = 1, 3-6) consisting of polar fluorenone moieties and ester alkoxy chains were investigated by scanning tunneling microscopy on highly oriented pyrolytic graphite surfaces. The chain-length effect was observed in the self-assembly of BAF-Cn. Self-assembly of BAF-C1 was composed of a linear I pattern, where the side chains adopted a fully interdigitated arrangement. As the length of side chains increased, the coexistence of a linear I pattern and a cyclic pattern for the self-assembly of BAF-C3 was observed...
November 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29134796/enhanced-electrical-and-optoelectronic-characteristics-of-few-layer-type-ii-snse-mos2-van-der-waals-heterojunctions
#17
Shengxue Yang, Minghui Wu, Bin Wang, Li-Dong Zhao, Li Huang, Chengbao Jiang, Su-Huai Wei
Van der Waals heterojunctions formed by stacking various two-dimensional (2D) materials have a series of attractive physical properties, thus offering an ideal platform for versatile electronic and optoelectronic applications. Here, we report few-layer SnSe/MoS2 van der Waals heterojunctions and study their electrical and optoelectronic characteristics. The new heterojunctions present excellent electrical transport characteristics with a distinct rectification effect and a high current on/off ratio (~ 1 × 105)...
November 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29133933/photoacoustic-and-modulated-reflectance-studies-of-indirect-and-direct-band-gap-in-van-der-waals-crystals
#18
Szymon J Zelewski, Robert Kudrawiec
Photoacoustic (PA) and modulated reflectance (MR) spectroscopy have been applied to study the indirect and direct band gap for van der Waals (vdW) crystals: dichalcogenides (MoS2, MoSe2, MoTe2, HfS2, HfSe2, WS2, WSe2, ReS2, ReSe2, SnS2 and SnSe2) and monochalcogenides (GaS, GaSe, InSe, GeS, and GeSe). It is shown that the indirect band gap can be determined by PA technique while the direct band gap can be probed by MR spectroscopy which is not sensitive to indirect optical transitions. By measuring PA and MR spectra for a given compound and comparing them with each other it is easy to conclude about the band gap character in the investigated compound and the energy difference between indirect and direct band gap...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133779/probing-optical-anisotropy-of-nanometer-thin-van-der-waals-microcrystals-by-near-field-imaging
#19
Debo Hu, Xiaoxia Yang, Chi Li, Ruina Liu, Ziheng Yao, Hai Hu, Stephanie N Gilbert Corder, Jianing Chen, Zhipei Sun, Mengkun Liu, Qing Dai
Most van der Waals crystals present highly anisotropic optical responses due to their strong in-plane covalent bonding and weak out-of-plane interactions. However, the determination of the polarization-dependent dielectric constants of van der Waals crystals remains a nontrivial task, since the size and dimension of the samples are often below or close to the diffraction limit of the probe light. In this work, we apply an optical nano-imaging technique to determine the anisotropic dielectric constants in representative van der Waals crystals...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29131229/phonon-coupling-and-transport-in-individual-polyethylene-chains-a-comparison-study-with-the-bulk-crystal
#20
Xinjiang Wang, Massoud Kaviany, Baoling Huang
Using the first-principles-based anharmonic lattice dynamics, we calculate the thermal conductivities (κ) of both bulk and single-chain polyethylene (PE) and characterize the mode-wise phonon transport and scattering channels. A significantly higher room-temperature axial thermal conductivity in single-chain PE (1400 W m(-1) K(-1)) is observed compared to bulk PE crystals (237 W m(-1) K(-1)). The reduction of scattering phase space caused by the diminished inter-chain van der Waals interactions explains the much larger κ in single-chain PE...
November 13, 2017: Nanoscale
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