Atomic Scale Sliding and Rolling of Carbon Nanotubes

A carbon nanotube is an ideal object for understanding the atomic scale aspects of interface interaction and friction. Using molecular statics and dynamics methods different types of motion of nanotubes on a graphite surface are investigated. We found that each nanotube has unique equilibrium orientations with sharp potential energy minima. This leads to atomic scale locking of the nanotube. The effective contact area and the total interaction energy scale with the square root of the radius. Sliding and rolling of nanotubes have different characters. The potential energy barriers for sliding nanotubes are higher than that for perfect rolling. When the nanotube is pushed, we observe a combination of atomic scale spinning and sliding motion. The result is rolling with the friction force comparable to sliding.Comment: 4 pages (two column) 6 figures - one ep

The Additional Line Component within the Iron K\alpha Profile in MCG-6-30-15: Evidence for Blob Ejection?

The EPIC data of MCG -6-30-15 observed by XMM-Newton were analyzed for the complexities of the iron K-alpha line. Here we report that the additional line component (ALC) at 6.9 keV undoubtedly appears within the broad iron Kalpha; line profile at the high state, whereas it disappears at the low state. These state-dependent behaviors exclude several possible origins and suggest an origin of the ALC in matter being ejected from the vicinity of the black hole. At the low state, the newborn blob ejected from the accretion disk is so Thomson-thick that hard X-rays are blocked from ionizing the old blobs, leading to the disappearance of the ALC. When the blob becomes Thomson-thin as a result of expansion, the hard X-ray will penetrate it and ionize the old ones, emitting the ALC at the high state. The blob ejection is the key to switching the ALC on or off.Comment: 6 pages, 4 Figure

Engineering Clostridium Strain to Accept Unmethylated DNA

It is difficult to genetically manipulate the medically and biotechnologically important genus Clostridium due to the existence of the restriction and modification (RM) systems. We identified and engineered the RM system of a model clostridial species, C. acetobutylicum, with the aim to allow the host to accept the unmethylated DNA efficiently. A gene CAC1502 putatively encoding the type II restriction endonuclease Cac824I was identified from the genome of C. acetobutylicum DSM1731, and disrupted using the ClosTron system based on group II intron insertion. The resulting strain SMB009 lost the type II restriction endonuclease activity, and can be transformed with unmethylated DNA as efficiently as with methylated DNA. The strategy reported here makes it easy to genetically modify the clostridial species using unmethylated DNA, which will help to advance the understanding of the clostridial physiology from the molecular level

Precise Particle Tracking Against a Complicated Background: Polynomial Fitting with Gaussian Weight

We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from the centre, and is especially suitable for tracking endogeneous particles in the cell, imaged with bright field, phase contrast or fluorescence optical microscopy. Furthermore, the method can simultaneously track particles of all different sizes, and allows significant freedom in their shape. The algorithm is evaluated using the quantitative measures of accuracy and precision of previous authors, using simulated images at variable signal-to-noise ratios. To these we add a new test of the error due to a non-uniform background. Finally the tracking of particles in real cell images is demonstrated. The method is made freely available for non-commencial use as a software package with a graphical user-inferface, which can be run within the Matlab programming environment

Acetoin Catabolism and Acetylbutanediol Formation by Bacillus pumilus in a Chemically Defined Medium

BACKGROUND: Most low molecular diols are highly water-soluble, hygroscopic, and reactive with many organic compounds. In the past decades, microbial research to produce diols, e.g. 1,3-propanediol and 2,3-butanediol, were considerably expanded due to their versatile usages especially in polymer synthesis and as possible alternatives to fossil based feedstocks from the bioconversion of renewable natural resources. This study aimed to provide a new way for bacterial production of an acetylated diol, i.e. acetylbutanediol (ABD, 3,4-dihydroxy-3-methylpentan-2-one), by acetoin metabolism. METHODOLOGY/PRINCIPAL FINDINGS: When Bacillus pumilus ATCC 14884 was aerobically cultured in a chemically defined medium with acetoin as the sole carbon and energy source, ABD was produced and identified by gas chromatography--chemical ionization mass spectrometry and NMR spectroscopy. CONCLUSIONS/SIGNIFICANCE: Although the key enzyme leading to ABD from acetoin has not been identified yet at this stage, this study proposed a new metabolic pathawy to produce ABD in vivo from using renewable resources--in this case acetoin, which could be reproduced from glucose in this study--making it the first facility in the world to prepare this new bio-based diol product

Flow separation control over a rounded ramp with spanwise alternating wall actuation

An implicit large-eddy simulation is carried out to study turbulent boundary-layer separation from a backward-facing rounded ramp with active wall actuation control. This method, called spanwise alternating distributed strips control, is imposed onto the flat plate surface upstream of a rounded ramp by alternatively applying out-of-phase control and in-phase control to the wall-normal velocity component in the spanwise direction. As a result, the local turbulence intensity is alternatively suppressed and enhanced, leading to the creation of vertical shear-layers, which is responsible for the presence of large-scale streamwise vortices. These vortices exert a predominant influence on the suppression of the flow separation. The interaction between the large-scale vortices and the downstream recirculation zone and free shear-layer is studied by examining flow statistics. It is found that in comparison with the non-controlled case the flow separation is delayed, the reattachment point is shifted upstream, and the length of the mean recirculation zone is reduced up to 8.49%. The optimal control case is achieved with narrow in-phase control strips. An in-depth analysis shows that the delay of the flow separation is attributed to the activation of the near-wall turbulence by the in-phase control strips and the improvement of the reattachment location is mainly due to the large-scale streamwise vortices, which enhance the momentum transport between the main flow and separated region

Raman Tweezers Spectroscopy of Live, Single Red and White Blood Cells

An optical trap has been combined with a Raman spectrometer to make high-resolution measurements of Raman spectra of optically-immobilized, single, live red (RBC) and white blood cells (WBC) under physiological conditions. Tightly-focused, near infrared wavelength light (1064 nm) is utilized for trapping of single cells and 785 nm light is used for Raman excitation at low levels of incident power (few mW). Raman spectra of RBC recorded using this high-sensitivity, dual-wavelength apparatus has enabled identification of several additional lines; the hitherto-unreported lines originate purely from hemoglobin molecules. Raman spectra of single granulocytes and lymphocytes are interpreted on the basis of standard protein and nucleic acid vibrational spectroscopy data. The richness of the measured spectrum illustrates that Raman studies of live cells in suspension are more informative than conventional micro-Raman studies where the cells are chemically bound to a glass cover slip

Graph Convolutional Neural Networks based on Quantum Vertex Saliency

This paper proposes a new Quantum Spatial Graph Convolutional Neural Network (QSGCNN) model that can directly learn a classification function for graphs of arbitrary sizes. Unlike state-of-the-art Graph Convolutional Neural Network (GCNN) models, the proposed QSGCNN model incorporates the process of identifying transitive aligned vertices between graphs, and transforms arbitrary sized graphs into fixed-sized aligned vertex grid structures. In order to learn representative graph characteristics, a new quantum spatial graph convolution is proposed and employed to extract multi-scale vertex features, in terms of quantum information propagation between grid vertices of each graph. Since the quantum spatial convolution preserves the grid structures of the input vertices (i.e., the convolution layer does not change the original spatial sequence of vertices), the proposed QSGCNN model allows to directly employ the traditional convolutional neural network architecture to further learn from the global graph topology, providing an end-to-end deep learning architecture that integrates the graph representation and learning in the quantum spatial graph convolution layer and the traditional convolutional layer for graph classifications. We demonstrate the effectiveness of the proposed QSGCNN model in relation to existing state-of-the-art methods. The proposed QSGCNN model addresses the shortcomings of information loss and imprecise information representation arising in existing GCN models associated with the use of SortPooling or SumPooling layers. Experiments on benchmark graph classification datasets demonstrate the effectiveness of the proposed QSGCNN model

Removal of phenanthrene from coastal waters by green tide algae Ulva prolifera

Ulva prolifera (U. prolifera) has been frequently involved in terrible algal proliferation in coastal areas. Although it is known to be associated with green tide, its contribution to the natural attenuation of the polycyclic aromatic hydrocarbons (PAHs) in seawater has not been evaluated. In this study, the removal of phenanthrene using U. prolifera collected from coastal water with green tide blooming was investigated. The results showed that phenanthrene could be removed efficiently in the presence of both the live and heat-killed U. prolifera. The phenanthrene concentrations of the live algae treatment decreased smoothly from 10.00 to 0.80 mu g L-1 through the whole process, while those of the heat-killed algae treatment decreased sharply from 10.0 to 2.71 mu g L-1 in one day and kept constantly after that. The in situ monitoring and visualizing using laser confocal scanning microscopy (LCSM) confirmed the accumulation of phenanthrene in U. prolifera. The increase in nutrient and temperature led to the increase of phenanthrene removal rate, while the salinity had less influence on the removal of phenanthrene. The removal efficiency by U. prolifera had a good linear relationship with phenanthrene initial concentration (r(2) = 0.999) even at 100 mu g L-1 which was higher than its environmentally relevant concentrations. High removal efficiency (91.3%) was observed when the initial phenanthrene concentration was set at environmental relevant concentration (5 mu g L-1). Results of this study demonstrate a potential new natural attenuation process for typical PAHs in coastal water during the outbreak of green tide. These findings indicate that the outbreak of harmful green tide algae may bring positive environmental benefits in the terms of the removal of harmful organic pollutants from coastal waters. (C) 2017 Elsevier B.V. All rights reserved.</p