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Nanoporous

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https://www.readbyqxmd.com/read/29334379/highly-parallel-direct-rna-sequencing-on-an-array-of-nanopores
#1
Daniel R Garalde, Elizabeth A Snell, Daniel Jachimowicz, Botond Sipos, Joseph H Lloyd, Mark Bruce, Nadia Pantic, Tigist Admassu, Phillip James, Anthony Warland, Michael Jordan, Jonah Ciccone, Sabrina Serra, Jemma Keenan, Samuel Martin, Luke McNeill, E Jayne Wallace, Lakmal Jayasinghe, Chris Wright, Javier Blasco, Stephen Young, Denise Brocklebank, Sissel Juul, James Clarke, Andrew J Heron, Daniel J Turner
Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29331138/role-of-non-equilibrium-conformations-on-driven-polymer-translocation
#2
H H Katkar, M Muthukumar
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations...
January 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29325009/efficient-generation-of-complete-sequences-of-mdr-encoding-plasmids-by-rapid-assembly-of-minion-barcoding-sequencing-data
#3
Ruichao Li, Miaomiao Xie, Ning Dong, Dachuan Lin, Xuemei Yang, Marcus Ho Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time-consuming...
January 9, 2018: GigaScience
https://www.readbyqxmd.com/read/29324669/nanoporous-polymers-based-on-liquid-crystals
#4
REVIEW
Jody Lugger, Dirk Jan Mulder, Rint Sijbesma, Albert Schenning
In the present review, we discuss recent advances in the field of nanoporous networks based on polymerisable liquid crystals. The field has matured in the last decade, yielding polymers having 1D, 2D, and 3D channels with pore sizes on the nanometer scale. Next to the current progress, some of the future challenges are presented, with the integration of nanoporous membranes in functional devices considered as the biggest challenge.
January 11, 2018: Materials
https://www.readbyqxmd.com/read/29323375/confinement-of-polysulfides-within-bi-functional-metal-organic-frameworks-for-high-performance-lithium-sulfur-batteries
#5
Xu-Jia Hong, Tian-Xiong Tan, Yu-Kai Guo, Xue-Ying Tang, Jian-Yi Wang, Wei Qin, Yue-Peng Cai
A lithium-sulfur (Li-S) battery is regarded as the most promising candidate for next generation energy storage systems, because of its high theoretical specific capacity (1675 mA h g-1) and specific energy (2500 W h kg-1), as well as the abundance, low cost and environmental benignity of sulfur. However, the soluble polysulfides Li2Sx (4 ≤ x ≤ 8) produced during the discharge process can cause the so-called "shuttle effect" and lead to low coulombic efficiency and rapid capacity fading of the batteries, which seriously restrict their practical application...
January 11, 2018: Nanoscale
https://www.readbyqxmd.com/read/29323159/temperature-induced-surface-reconstruction-and-interface-structure-evolution-on-ligament-of-nanoporous-copper
#6
Wenbo Liu, Peng Cheng, Jiazhen Yan, Ning Li, Sanqiang Shi, Shichao Zhang
Micromorphology and atomic arrangement on ligament surface of nanoporous metals play a vital role in maintaining the structural stability, adjusting the reaction interface and endowing the functionality. Here we offer an instructive scientific understanding for temperature-induced surface reconstruction and interface structure evolution on ligament of nanoporous copper (NPC) based on systematically experimental observations and theoretical calculations. The results show that with dealloying temperature increasing, ligament surface micromorphology of NPC evolves from smooth to irregularity and to uniformly compressed semisphere, and finally to dispersed single-crystal nanoparticles accompanying with significant changes of interface structure from coherence to semi-coherence and to noncoherence...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322780/signal-and-noise-in-fet-nanopore-devices
#7
William M Parkin, Marija Drndic
The combination of a nanopore with a local field-effect transistor (FET-nanopore), like a nanoribbon, nanotube, or nanowire, in order to sense single molecules translocating through the pore is promising for DNA sequencing at megahertz bandwidths. Previously, it was experimentally determined that the detection mechanism was due to local potential fluctuations that arise when an analyte enters a nanopore and constricts ion flow through it, rather than the theoretically proposed mechanism of direct charge coupling between the DNA and nanowire...
January 11, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29320159/bioinspired-nanostructured-surfaces-for-on-demand-bubble-transportation
#8
Xin Tang, Hairui Xiong, Tiantian Kong, Ye Tian, Wen-Di Li, Liqiu Wang
The maneuver of small bubbles in a programmed way will advance numerous processes, including gas evolution reaction and aeration. Unlike in-air droplets, rapidly rising bubbles in liquid medium can hardly be steered through interaction with solid substrates, causing difficulties in maneuvering bubbles. We pattern and lubricate nanoporous substrates with regions of contrasting wettability that is similar to the back of Namib desert beetles and subsequently immerse the lubricated surface underwater to spontaneously form spatially patterned Nepenthes-inspired slippery surfaces after the dewetting of lubricants...
January 10, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29319103/computational-characterisation-of-dried-and-hydrated-graphene-oxide-membranes
#9
C D Williams, P Carbone, F R Siperstein
A multi-step molecular dynamics procedure was developed to construct fully flexible atomistic models of graphene oxide (GO) membranes. The method of preparation replicates the experimental synthesis of the material; i.e. the flow-directed self-assembly of individual flakes onto a substrate or filter. A total of 180 GO membrane models were prepared with water contents varying between 0 and 20%, providing an insight into changes in the membrane's interlayer distance with swelling. Membranes with 15% water content have an average interlayer distance (0...
January 10, 2018: Nanoscale
https://www.readbyqxmd.com/read/29315923/switching-the-proton-conduction-in-nanoporous-crystalline-materials-by-light
#10
Kai Müller, Julian Helfferich, Fangli Zhao, Rupal Verma, Anemar Bruno Kanj, Velimir Meded, David Bléger, Wolfgang Wenzel, Lars Heinke
Proton conducting nanoporous materials attract substantial attention with respect to applications in fuel cells, supercapacitors, chemical sensors, and information processing devices inspired by biological systems. Here, a crystalline, nanoporous material which offers dynamic remote-control over the proton conduction is presented. This is realized by using surface-mounted metal-organic frameworks (SURMOFs) with azobenzene side groups that can undergo light-induced reversible isomerization between the stable trans and cis states...
January 8, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29315868/influence-of-flexibility-on-the-separation-of-chiral-isomers-in-the-stw-type-zeolite
#11
Rocio Bueno-Perez, Salvador R G Balestra, Miguel A Camblor, Jung Gi Min, Suk Bong Hong, Patrick J Merkling, Sofia Calero
Molecular simulation, through the computation of adsorption isotherms, is a useful predictive tool for the selective capacity of nanoporous materials. Generally, adsorbents are modelled as rigid frameworks, as opposed to allowing for vibrations of the lattice, and this approximation is assumed have negligible impact on adsorption. In this work, we test this approach in an especially challenging system by computing the adsorption of the chiral molecules 2-pentanol, 2-methylbutanol and 3-methyl-2-butanol in the all-silica and germanosilicate chiral zeolites STW, and study their lattice vibrations upon adsorption...
January 5, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29315344/culture-independent-analysis-of-liver-abscess-using-nanopore-sequencing
#12
Liang Gong, Yao-Ting Huang, Chee-Hong Wong, Wen-Cheng Chao, Zong-Yen Wu, Chia-Lin Wei, Po-Yu Liu
The identification of microbial species has depended predominantly upon culture-based techniques. However, the difficulty with which types of organisms are cultured implies that the grown species may be overrepresented by both cultivation and plate counts. In recent years, culture-independent analysis using high-throughput sequencing has been advocated for use as a point-of-care diagnostic tool. Although it offers a rapid and unbiased survey to characterize the pathogens in clinical specimens, its accuracy is reduced by the high level of contamination of human DNA...
2018: PloS One
https://www.readbyqxmd.com/read/29306278/optimal-design-of-graphene-nanopores-for-seawater-desalination
#13
Zhongwu Li, Yinghua Qiu, Kun Li, Jingjie Sha, Tie Li, Yunfei Chen
Extensive molecular dynamics simulations are employed to optimize nanopore size and surface charge density in order to obtain high ionic selectivity and high water throughput for seawater desalination systems. It is demonstrated that with the help of surface charge exclusion, nanopores with diameter as large as 3.5 nm still have high ionic selectivity. The mechanism of the salt rejection in a surface-charged nanopore is mainly attributed to the ion concentration difference between the cations and anions induced by the surface charges...
January 7, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29306080/hybrid-micro-nanostructural-surface-offering-improved-stress-distribution-and-enhanced-osseointegration-properties-of-the-biomedical-titanium-implant
#14
Ping-Jen Hou, Keng-Liang Ou, Chin-Chieh Wang, Chiung-Fang Huang, Muhammad Ruslin, Erwan Sugiatno, Tzu-Sen Yang, Hsin-Hua Chou
OBJECTIVES: The aim of the present study was to investigate the surface characteristic, biomechanical behavior, hemocompatibility, bone tissue response and osseointegration of the optimal micro-arc oxidation surface-treated titanium (MST-Ti) dental implant. MATERIALS AND METHODS: The surface characteristic, biomechanical behavior and hemocompatibility of the MST-Ti dental implant were performed using scanning electron microscope, finite element method, blood dripping and immersion tests...
November 27, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/29304551/engineering-the-interface-between-lipid-membranes-and-nanoporous-gold-a-study-by-quartz-crystal-microbalance-with-dissipation-monitoring
#15
Patricia Losada-Pérez, Ozge Polat, Atul N Parikh, Erkin Seker, Frank Uwe Renner
Nanoporous gold (np-Au) is a nanostructured metal with many desirable attributes. Despite the growing number of applications of nanoporous materials, there are still open questions regarding their fabrication and subsequent surface functionalization. For example, the hydrophobic nature of gold surfaces makes the formation of planar supported lipid layers challenging. Here, the authors engineer the interface between np-Au and 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid layers using well-differentiated approaches based on vesicle adsorption and solvent exchange methods...
January 5, 2018: Biointerphases
https://www.readbyqxmd.com/read/29303587/voltage-induced-modulation-of-ionic-concentrations-and-ion-current-rectification-in-mesopores-with-highly-charged-pore-walls
#16
Chih-Yuan Lin, Li-Hsien Yeh, Zuzanna S Siwy
It is believed that ion current rectification (ICR), a property which assures preferential ionic transport in one direction, can only be observed in nanopores when the pore size is comparable to the thickness of the electric double layer (EDL). Rectifying nanopores became the basis of biological sensors and components of ionic circuits. Here we report that appreciable ICR can also occur in highly charged conical, polymer mesopores whose tip diameters are as large as 400 nm thus over 100-fold larger than the EDL thickness...
January 5, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29303556/metal-organic-framework-thin-film-coated-optical-fiber-sensors-a-novel-waveguide-based-chemical-sensing-platform
#17
Ki-Joong Kim, Ping Lu, Jeffrey T Culp, Paul R Ohodnicki
Integration of optical fiber with sensitive thin films offers great potential for the realization of novel chemical sensing platforms. In this study, we present a simple design strategy and high performance of nanoporous metal organic frame-work (MOF) based optical gas sensors, which enables to detect a wide range of concentrations of small molecules based upon extremely small differences in refractive indices as a function of analyte adsorption within the MOF framework. Thin and compact MOF films can be uniformly formed and tightly bound on the surface of etched optical fiber through a simple solution method which is critical for manufacturability of MOF-based sensor devices...
January 5, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29303175/nanoporous-anodic-aluminum-oxide-internalized-with-gold-nanoparticles-for-on-chip-pcr-and-direct-detection-by-surface-enhanced-raman-scattering
#18
B M Tran, N N Nam, S J Son, N Y Lee
Nanoporous anodic aluminum oxide internalized with gold nanoparticles was utilized as an integrated platform miniaturized for consecutively performing on-chip PCR and downstream detection of the amplified product of a 183 bp eaeA gene fragment from Escherichia coli O157:H7 using surface-enhanced Raman scattering (SERS).
January 5, 2018: Analyst
https://www.readbyqxmd.com/read/29301227/ethanol-mediated-2d-growth-of-cu%C3%A2-o-nanoarchitectures-on-nanoporous-cu-templates-in-anhydrous-ethanol
#19
Zhenhua Dan, Jiafei Lu, Feng Li, Fengxiang Qin, Hui Chang
Two types of cupric oxide (Cu₂O) nanoarchitectures (nanobelts and nanopetal networks) have been achieved via immersion nanoporous copper (NPC) templates in anhydrous ethanol. NPC templates with different defect densities have been prepared by dealloying amorphous Ti60Cu40 ribbons in a mixture solution of hydrofluoric acid and polyvinylpyrrolidone (PVP) with different ratios of HF/PVP. Both a water molecule reactant acting as OH- reservoir and the ethanol molecule serving as stabilizing or capping reagent for inhibiting the random growth of Cu₂Oplayed a role of the formation of 2-dimensional Cu₂O nanoarchitectures...
December 31, 2017: Nanomaterials
https://www.readbyqxmd.com/read/29300312/in-silico-design-synthesis-and-evaluation-of-a-nanostructured-hydrogel-as-a-dimethoate-removal-agent
#20
Fabian Avila-Salas, Adolfo Marican, Jorge Villaseñor, Mauricio Arenas-Salinas, Yerko Argandoña, Julio Caballero, Esteban F Durán-Lara
This study describes the in-silico design, synthesis, and evaluation of a cross-linked PVA hydrogel (CLPH) for the absorption of organophosphorus pesticide dimethoate from aqueous solutions. The crosslinking effectiveness of 14 dicarboxilic acids was evaluated through in-silico studies using semiempirical quantum mechanical calculations. According to the theoretical studies, the nanopore of PVA cross-linked with malic acid (CLPH-MA) showed the best interaction energy with dimethoate. Later, using all-atom molecular dynamics simulations, three hydrogels with different proportions of PVA:MA (10:2, 10:4, and 10:6) were used to evaluate their interactions with dimethoate...
January 4, 2018: Nanomaterials
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