Off-lattice pattern recognition scheme for kinetic Monte Carlo simulations

We report the development of a pattern-recognition scheme for the off-lattice self-learning kinetic Monte Carlo (KMC) method, one that is simple and flexible enough that it can be applied to all types of surfaces. In this scheme, to uniquely identify the local environment and associated processes involving three-dimensional (3D) motion of an atom or atoms, space around a central atom is divided into 3D rectangular boxes. The dimensions and the number of 3D boxes are determined by the accuracy with which a process needs to be identified and a process is described as the central atom moving to a neighboring vacant box accompanied by the motion of any other atom or atoms in its surrounding boxes. As a test of this method to we apply it to examine the decay of 3D Cu islands on the Cu(100) and to the surface diffusion of a Cu monomer and a dimer on Cu(111) and compare the results and computational efficiency to those available in the literature.     

Non-singular coordinates for circularly symmetric black holes in 2 + 1 dimensions

In this paper we present non-singular coordinates for the rotating BTZ (Banados–Teitelboim–Zanelli) black hole. The approach is further extended to construct non-singular coordinates for different cases of general circularly symmetric black holes in 2 + 1 dimensions.     

A liquid lens-based broadband variable fiber optical attenuator

To the best of our knowledge, proposed is the first variable fiber optical attenuator (VFOA) using an electronically controlled variable focus liquid lens. The approach uses the changes in the radius of curvature of the liquid lens edge to enable an electronically controlled optical wedge that produces a varying beam tilt angle. In effect, changing beam tilt within a single mode fiber (SMF) lens free space coupling assembly leads to a polarization independent broadband VFOA design. The demonstrated VFOA experiment shows broadband operation over the 1530-1560 nm C-Band with a 40 dB dynamic range, <0.5 dB resolution, 0.3 dB polarization dependant loss, 4.3 dB fiber-to-fiber optical loss, 3 dB optical bandwidth from 1510 nm to 1700 nm, and switching time of <100 ms. Applications for this VFOA include use in hand held test and measurement equipment.     

On the electron transfer through Geobacter sulfurreducens PilA protein

Geobacter sulfurreducens pili composed of the Type IV pili structural peptide PilA have been implicated as efficient electronic conductors. Though investigated experimentally, no detailed theoretical studies have been performed to date that provide quantitative estimation of the transmission spectrum, electron transfer (ET) paths, efficiency of current generation, and other factors needed for understanding possible mechanisms of conductivity. In the present work, we calculate from first principles the possibilities of electron tunneling through 3 PilA fragments which structure was identified recently by NMR. The results indicate that positively charged amino acids, arginines and lysines form electrostatic traps in the middle of the peptide preventing ET at low bias voltages (<～6 V). At higher biases the traps are filled with electrons making possible sequential electron tunneling through the central part of the protein. In addition, leucines and phenylalanines form ET loops facilitating electron stabilization within the protein and sequential ET. Our results indicate that ET through the PilA protein cannot occur by coherent ET, but suggest a sequential (incoherent) mechanism. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1706–1717     

Random mutagenesis and media optimisation for hyperproduction of cellulase from Bacillus species using proximally analysed Saccharum spontaneum in submerged fermentation

This study deals with the isolation of novel mutant of Bacillus and optimisation of media for the hyperproduction of cellulase. Cellulase-producing Bacillus PC-BC6 was subjected to physical and chemical mutagenesis to enhance the cellulolytic potential. Later, mutagenesis isolates were screened both qualitatively and quantitatively. Among all the tested isolates, Bacillus N3 yielded maximum (CMCase 1250 IU/mL/min and FPase 629 IU/mL/min) activity. The Bacillus N3 strain exhibited 1.7-fold more enzyme production as compared with the parental strain. Proximate analysis of untreated and pretreated Saccharum spontaneum was carried out to improve cellulase production. Three different media were tested for the production of cellulase, among which M2 medium containing MgSO₄, pretreated S. spontaneum, K₂HPO₄, (NH₄)₂SO₄ and peptone was found to be the best for maximum enzyme production by mutant Bacillus N3.     

Spectrophotometric determination of Fe(III) by using casein-functionalized gold nanoparticles

The preparation and application of casein-capped gold nanoparticles (AuNPs) as a specific probe for ferric ions Fe(III) is reported. The functionalized AuNPs exhibit narrow size distribution and form stable dispersions in water of different ionic strengths and basicity. The presence of diverse functional groups from the side chain of peptides warrants colloidal stability of AuNPs and also assists recognition of Fe(III) in versatile conditions. Fe(III) ion reportedly causes the aggregation of AuNPs and a red-shift in absorbance toward longer wavelength (660 nm). A spectrophotometric method is appropriate for selective detection of Fe(III) and the spectral shift is also accompanied by a color change from red to blue. The aggregation of AuNPs is not suppressed after the addition of NaOH or at moderate ionic strength. The resulting spectrophotometric method works for Fe(III) in the concentration range of 0.1 to 0.9 μM and has a detection limit of 450 nM. The AuNP probe can also detect Fe(III) ion content in real samples at the same detection limit, which is much lower than the maximum contaminant level allowed for Fe(III) in drinking water (5.37 μM) by the U.S. Environmental Protection Agency.

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Graphical abstract Casein peptide functionalized gold nanoparticles: synthesis, characterization, and their application to the visual detection of Fe(III).