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Van der Waals

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https://www.readbyqxmd.com/read/28338825/modular-organization-of-residue-level-contacts-shape-the-selection-pressure-on-individual-amino-acid-sites-of-ribosomal-proteins
#1
Saurav Mallik, Sudip Kundu
Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly and stability is of central importance. Here we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, inter-nucleotide contacts are disregarded)...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338139/adsorption-of-small-inorganic-molecules-on-a-defective-mos2-monolayer
#2
César González, Blanca Biel, Yannick J Dappe
We present a theoretical study of molecular adsorption on defects on a MoS2 monolayer. Based on Density Functional Theory, our calculations confirm that small inorganic molecules, such as CO2, CO, H2O, NO, NO2, H2 and N2, remain bonded to the pristine monolayer through weak van der Waals interactions, suggesting that the molecules may easily diffuse over the clean monolayer. On the other hand, the introduction of defects can lead to three different situations, depending on the defect and the molecule considered: physisorption, chemical (strong) bonding to the metallic defects, namely the Mo substitutional atoms on the S vacancies, and dissociation, that can take place spontaneously at 0 K in some specific cases or by the effect of thermal agitation in molecules such as CO2 or NO2 on the S vacancy...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28336904/optoelectronic-properties-of-van-der-waals-hybrid-structures-fullerenes-on-graphene-nanoribbons
#3
Julián David Correa, Pedro Alejandro Orellana, Mónica Pacheco
The search for new optical materials capable of absorbing light in the frequency range from visible to near infrared is of great importance for applications in optoelectronic devices. In this paper, we report a theoretical study of the electronic and optical properties of hybrid structures composed of fullerenes adsorbed on graphene and on graphene nanoribbons. The calculations are performed in the framework of the density functional theory including the van der Waals dispersive interactions. We found that the adsorption of the C 60 fullerenes on a graphene layer does not modify its low energy states, but it has strong consequences for its optical spectrum, introducing new absorption peaks in the visible energy region...
March 20, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28335370/vibration-of-piezoelectric-zno-swcnt-nanowires
#4
Yao Xiao, Chengyuan Wang, Yuantian Feng
A hybrid nanowire (HNW) was constructed by coating a single-wall carbon nanotube (SWCNT) with piezoelectric zinc oxide (ZnO). The two components of the HNW interact with each other via the van der Waals (vdW) force. This paper aims to study the effect of the piezoelectricity in the ZnO layer and the inter-phase vdW interaction on the fundamental vibration of the HNWs. In doing this, a new model was developed where the two components of the HNWs were modeled as Euler beams coupled via the interphase vdW interaction...
December 15, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335321/two-dimensional-semiconductor-optoelectronics-based-on-van-der-waals-heterostructures
#5
REVIEW
Jae Yoon Lee, Jun-Hwan Shin, Gwan-Hyoung Lee, Chul-Ho Lee
Two-dimensional (2D) semiconductors such as transition metal dichalcogenides (TMDCs) and black phosphorous have drawn tremendous attention as an emerging optical material due to their unique and remarkable optical properties. In addition, the ability to create the atomically-controlled van der Waals (vdW) heterostructures enables realizing novel optoelectronic devices that are distinct from conventional bulk counterparts. In this short review, we first present the atomic and electronic structures of 2D semiconducting TMDCs and their exceptional optical properties, and further discuss the fabrication and distinctive features of vdW heterostructures assembled from different kinds of 2D materials with various physical properties...
October 27, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334649/binding-of-tem-1-beta-lactamase-to-beta-lactam-antibiotics-by-frontal-affinity-chromatography
#6
Xiu Chen, Yuhua Li, Yan Zhang, Jianting Yang, Liujiao Bian
TEM-1 beta-lactamases can accurately catalyze the hydrolysis of the beta-lactam rings in beta-lactam antibiotics, which make beta-lactam antibiotics lose its activity, and the prerequisite for the hydrolysis procedure in the binding interaction of TEM-1 beta-lactamases with beta-lactam antibiotics is the beta-lactam rings in beta-lactam antibiotics. Therefore, the binding of TEM-1 beta-lactamase to three beta-lactam antibiotics including penicillin G, cefalexin as well as cefoxitin was explored here by frontal affinity chromatography in combination with fluorescence spectra, adsorption and thermodynamic data in the temperature range of 278-288K under simulated physiological conditions...
March 18, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28333687/band-engineering-of-mos2-stanene-heterostructure-strain-and-electrostatic-gating
#7
Wenqi Xiong, Congxin Xia, Juan Du, Tianxing Wang, Yuting Peng, Zhongming Wei, Jingbo Li
As a fast developing field, van der Waals (vdW) heterostructure can overcome the weakness of single two-dimensional (2D) layered material and extend its electronic and optoelectronic applications. Through first-principles methods, the studied MoS2/stanene heterostructure preserves high-speed carrier characteristics and opens the direct band gap. Meanwhile, the band alignment shows that the electrons transfer from stanene to MoS2, which forms an internal electric field. As an effective strategy, the out-of-plane strain remarkably change the band gaps of heterostructure and enhances its carrier concentration...
March 23, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28333441/direct-chemical-vapor-deposition-growth-and-band-gap-characterization-of-mos2-h-bn-van-der-waals-heterostructures-on-au-foils
#8
Zhepeng Zhang, Xujing Ji, Jianping Shi, Xiebo Zhou, Shuai Zhang, Yue Hou, Yue Qi, Qiyi Fang, Qingqing Ji, Yu Zhang, Min Hong, Pengfei Yang, Xinfeng Liu, Qing Zhang, Lei Liao, Chuanhong Jin, Zhongfan Liu, Yanfeng Zhang
Stacked transition-metal dichalcogenides on hexagonal boron nitride (h-BN) are platforms for high-performance electronic devices. However, such vertical stacks are usually constructed by the layer-by-layer polymer-assisted transfer of mechanically exfoliated layers. This inevitably causes interfacial contamination and device performance degradation. Herein, we develop a two-step, low-pressure chemical vapor deposition synthetic strategy incorporating the direct growth of monolayer h-BN on Au foil with the subsequent growth of MoS2...
March 23, 2017: ACS Nano
https://www.readbyqxmd.com/read/28330869/molecular-mechanisms-of-isocitrate-dehydrogenase-1-idh1-mutations-identified-in-tumors-the-role-of-size-and-hydrophobicity-at-residue-132-on-catalytic-efficiency
#9
Diego Avellaneda Matteo, Adam J Grunseth, Eric R Gonzalez, Stacy L Anselmo, Madison A Kennedy, Precious Moman, David A Scott, An Hoang, Christal D Sohl
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate (ICT) to α-ketoglutarate (αKG) in the cytosol and peroxisomes. Mutations in IDH1 have been implicated in > 80% of lower grade gliomas and secondary glioblastomas and primarily affect residue 132, which helps coordinate substrate binding. However, other mutations found in the active site have also been identified in tumors. IDH1 mutations typically result in a loss of catalytic activity, but many also can catalyze a new reaction, the NADPH-dependent reduction of αKG to D-2-hydroxyglutarate (D2HG)...
March 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28330413/molecular-dynamic-simulation-and-dft-study-on-the-drug-dna-interaction-crocetin-as-an-anticancer-and-dna-nanostructure-model
#10
Ebrahim Azarhazin, Mohammad Izadyar, Mohammad Reza Housaindokht
In this research, the interaction of Crocetin as an anticancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of twelve base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA...
March 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28330345/coexistence-of-low-and-high-overlap-phases-in-a-supercooled-liquid-an-integral-equation-investigation
#11
Jean-Marc Bomont, Giorgio Pastore, Jean-Pierre Hansen
The pair structure, free energy, and configurational overlap order parameter Q of an annealed system of two weakly coupled replicas of a supercooled "soft sphere" fluid are determined by solving the hypernetted-chain (HNC) and self-consistent Rogers-Young (RY) integral equations over a wide range of thermodynamic conditions ρ (number-density), T (temperature), and inter-replicas couplings ε12. Analysis of the resulting effective (or Landau) potential W(ρ,T; Q) and of its derivative with respect to Q confirms the existence of a "precursor transition" between weak and strong overlap phases below a critical temperature Tc well above the temperature To of the "ideal glass" transition observed in the limit ε12→0...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28328198/all-printable-zno-quantum-dots-graphene-van-der-waals-heterostructures-for-ultrasensitive-detection-of-ultraviolet-light
#12
Maogang Gong, Qingfeng Liu, Brent Cook, Bhupal Kattel, Ti Wang, Wai-Lun Chan, Dan Ewing, Matthew Casper, Alex Stramel, Judy Z Wu
In ZnO quantum dot/graphene heterojunction photodetectors, fabricated by printing quantum dots (QDs) directly on the graphene field-effect transistor (GFET) channel, the combination of the strong quantum confinement in ZnO QDs and the high charge mobility in graphene allows extraordinary quantum efficiency (or photoconductive gain) in visible-blind ultraviolet (UV) detection. Key to the high performance is a clean van der Waals interface to facilitate an efficient charge transfer from ZnO QDs to graphene upon UV illumination...
March 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28326656/skin-cancer-diagnosed-by-using-artificial-intelligence-on-clinical-images
#13
Isaäc van der Waal
In a recent Research Letter in Nature an automated classification of a few selected skin lesions has been published, using a deep convolutional neural network (CNN) (Esteva et al, 2017). Convolutional neural network is an important innovation in the field of computer vision. A popular use is for image processing, e.g. applied in face recognition. In the reported study CNN has been applied to a dataset of almost 130,000 clinical images, including some 3,000 dermoscopic images. This article is protected by copyright...
March 22, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28322563/molecular-aggregation-in-binary-mixtures-of-pyrrolidine-n-methylpyrrolidine-piperidine-and-n-methylpiperidine-with-water-thermodynamic-sans-and-theoretical-studies
#14
Wojciech Marczak, Mikhail A Varfolomeev, Ilnaz T Rakipov, Piotr Lodowski, Katarzyna Kowalska-Szojda, Marta Łężniak, Laszlo Almasy, Adél Len
Piperidine and N-methylpiperidine hydrates aggregate in liquid aqueous solutions due to hydrogen bonds between hydration water molecules. No such effects occur in the mixtures of the amines with methanol, that supports the idea of active role of water solvent in the aggregation. However, the question of contributions in thermodynamic functions due to specific interactions, van der Waals forces, and the size and shape of the molecules remains open. In the present study, limiting partial molar enthalpies of solution of pyrrolidine, N-methylpyrrolidine, piperidine and N-methylpiperidine in water and methanol and vice versa were measured and compared with those assessed from theoretically calculated molecular interaction energies using a simple "chemical reaction" model...
March 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28322229/periodic-potentials-in-hybrid-van-der-waals-heterostructures-formed-by-supramolecular-lattices-on-graphene
#15
Marco Gobbi, Sara Bonacchi, Jian X Lian, Yi Liu, Xiao-Ye Wang, Marc-Antoine Stoeckel, Marco A Squillaci, Gabriele D'Avino, Akimitsu Narita, Klaus Müllen, Xinliang Feng, Yoann Olivier, David Beljonne, Paolo Samorì, Emanuele Orgiu
The rise of 2D materials made it possible to form heterostructures held together by weak interplanar van der Waals interactions. Within such van der Waals heterostructures, the occurrence of 2D periodic potentials significantly modifies the electronic structure of single sheets within the stack, therefore modulating the material properties. However, these periodic potentials are determined by the mechanical alignment of adjacent 2D materials, which is cumbersome and time-consuming. Here we show that programmable 1D periodic potentials extending over areas exceeding 10(4) nm(2) and stable at ambient conditions arise when graphene is covered by a self-assembled supramolecular lattice...
March 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28322041/printable-transfer-free-and-wafer-size-mos2-graphene-van-der-waals-heterostructures-for-high-performance-photodetection
#16
Qingfeng Liu, Brent Cook, Maogang Gong, Youpin Gong, Ewing Dan, Matthew Casper, Alex Stramel, Judy Z Wu
Two-dimensional (2D) MoS2/graphene van der Waals heterostructures integrate the superior light-solid interaction in MoS2 and charge mobility in graphene for high-performance optoelectronic devices. Key to the device performance lies in a clean MoS2/graphene interface to facilitate efficient transfer of photo-generated charges. Here we report a printable and transfer-free process for fabrication of wafer-size MoS2/graphene van der Waals heterostructures obtained using a metal-free-grown graphene, followed by low-temperature growth of MoS2 from the printed thin film of ammonium thiomolybdate on graphene...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28321487/benzene-degradation-in-a-denitrifying-biofilm-reactor-activity-and-microbial-community-composition
#17
Marcelle J van der Waals, Siavash Atashgahi, Ulisses Nunes da Rocha, Bas M van der Zaan, Hauke Smidt, Jan Gerritse
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions...
March 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28319842/two-dimensional-growth-of-crystalline-nanofiber-fabricated-from-gemini-type-amphiphilic-diamide-derivative-inducing-the-thixotropic-property
#18
Manami Iizuka, Yuto Nakagawa, Kyohei Ohmura, Eiichi Satou, Atsuhiro Fujimori
The formation of a nanofiber morphology at the mesoscopic scale and the molecular-level packing of a gemini-type amphiphilic diamide derivative with two hydrocarbons were investigated from two perspectives. First, it was confirmed that a diamide derivative with two hydrocarbons forms crystalline nanofibers even in a monomolecular layer. The height, thickness, and lattice spacing of the two-dimensional orthorhombic system of this crystalline nanofiber in the monolayer of a diamide derivative with two hydrocarbons are 5, 30, and 0...
March 4, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28318270/prediction-of-stable-ground-state-lithium-polyhydrides-under-high-pressures
#19
Yangmei Chen, Hua Y Geng, Xiaozhen Yan, Yi Sun, Qiang Wu, Xiangrong Chen
Hydrogen-rich compounds are important for understanding the dissociation of dense molecular hydrogen, as well as searching for room temperature Bardeen-Cooper-Schrieffer (BCS) superconductors. A recent high pressure experiment reported the successful synthesis of novel insulating lithium polyhydrides above 130 GPa. However, the results are in sharp contrast to a previous theoretical prediction by the PBE functional that around this pressure range all lithium polyhydrides (LiHn (n = 2-8)) should be metallic...
March 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28318001/contrasting-diffusion-behaviors-of-o-and-f-atoms-on-graphene-and-within-bilayer-graphene
#20
Seho Yi, Jin-Ho Choi, Hyun-Jung Kim, Chul Hong Park, Jun-Hyung Cho
Chemical modification of graphene with adatoms is of importance for nanoelectronics applications. Based on first-principles density-functional theory calculations including van der Waals interactions, we present a comparative study of the diffusion characteristics of oxygen (O) and fluorine (F) atoms both on graphene and between the layers of bilayer graphene. We find that the calculated diffusion barrier for the O atom increases slightly from 0.81 eV on graphene to 0.85 eV within bilayer graphene, while that for the F atom largely decreases from 0...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
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