Mode-locked 2 μm fiber laser with a multi-walled carbon nanotube as a saturable absorber

We propose and demonstrate a passively mode-locked fiber laser operating at 1951.8 nm using a commercial thulium-doped fiber(TDF) laser, a homemade double-clad thulium–ytterbium co-doped fiber(TYDF)as the gain media, and a multi-walled carbon nanotube(MWCNT) based saturable absorber(SA). We prepare the MWCNT composite by mixing a homogeneous solution of MWCNTs with a diluted polyvinyl alcohol(PVA) polymer solution and then drying it at room temperature to form a film. The film is placed between two fiber connectors as a SA before it is integrated into a laser ring cavity. The cavity consists of a 2 m long TDF pumped by a 800 nm laser diode and a 15 m long homemade TYDF pumped by a 905 nm multimode laser diode. A stable mode-locking pulse with a repetition rate of 34.6 MHz and a pulse width of 10.79 ps is obtained when the 905 nm multimode pump power reaches 1.8–2.2 W, while the single-mode 800 nm pump power is fixed at 141.5 m W at all times. To the best of our knowledge, this is the first reported mode-locked fiber laser using a MWCNT-based SA.     

Spatial distribution of uranium and chemo-radiological assessment in Hamirpur district,Himachal Pradesh,India

Monitoring of radioactivity in an environment is an important step towards establishing the baseline for environment protection. This work highlights the spatial distribution of uranium (U); assessment of physico-chemical parameters and radiological assessment in groundwater of Hamirpur district, HP, India. The concentration of U ranges from 0.15 to 18.92 μg l^?1. High correlation of U is observed with TDS, Chloride and Nitrate. Major concentration of U is present along the NW–SE trend-line following the Siwalik in the areas where mineralisation is prevalent and is of geogenic source derived from granitic and volcanic rock fragments present in conglomerates. The water-quality-index indicates that the water is suitable for drinking purpose.

     

D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors

The Drug Design Data Resource (D3R) Grand Challenges present an opportunity to assess, in the context of a blind predictive challenge, the accuracy and the limits of tools and methodologies designed to help guide pharmaceutical drug discovery projects. Here, we report the results of our participation in the D3R Grand Challenge 4 (GC4), which focused on predicting the binding poses and affinity ranking for compounds targeting the $$\beta$$-amyloid precursor protein (BACE-1). Our ligand similarity-based protocol using HYBRID (OpenEye Scientific Software) successfully identified poses close to the native binding mode for most of the ligands with less than 2 Å RMSD accuracy. Furthermore, we compared the performance of our HYBRID-based approach to that of AutoDock Vina and DOCK 6 and found that using a reference ligand to guide the docking process is a better strategy for pose prediction and helped HYBRID to perform better here. We also conducted end-point free energy estimates on molecules dynamics based ensembles of protein-ligand complexes using molecular mechanics combined with generalized Born surface area method (MM-GBSA). We found that the binding affinity ranking based on MM-GBSA scores have poor correlation with the experimental values. Finally, the main lessons from our participation in D3R GC4 are: (i) the generation of the macrocyclic conformers is a key step for successful pose prediction, (ii) the protonation states of the BACE-1 binding site should be treated carefully, (iii) the MM-GBSA method could not discriminate well between different predicted binding poses, and (iv) the MM-GBSA method does not perform well at predicting protein–ligand binding affinities here.     

Analysis of stacking overlap in nucleic acid structures: algorithm and application

RNA contains different secondary structural motifs like pseudo-helices, hairpin loops, internal loops, etc. in addition to anti-parallel double helices and random coils. The secondary structures are mainly stabilized by base-pairing and stacking interactions between the planar aromatic bases. The hydrogen bonding strength and geometries of base pairs are characterized by six intra-base pair parameters. Similarly, stacking can be represented by six local doublet parameters. These dinucleotide step parameters can describe the quality of stacking between Watson–Crick base pairs very effectively. However, it is quite difficult to understand the stacking pattern for dinucleotides consisting of non canonical base pairs from these parameters. Stacking interaction is a manifestation of the interaction between two aromatic bases or base pairs and thus can be estimated best by the overlap area between the planar aromatic moieties. We have calculated base pair overlap between two consecutive base pairs as the buried van der Waals surface between them. In general, overlap values show normal distribution for the Watson–Crick base pairs in most double helices within a range from 45 to 50 Å² irrespective of base sequence. The dinucleotide steps with non-canonical base pairs also are seen to have high overlap value, although their twist and few other parameters are rather unusual. We have analyzed hairpin loops of different length, bulges within double helical structures and pseudo-continuous helices using our algorithm. The overlap area analyses indicate good stacking between few looped out bases especially in GNRA tetraloop, which was difficult to quantitatively characterise from analysis of the base pair or dinucleotide step parameters. This parameter is also seen to be capable to distinguish pseudo-continuous helices from kinked helix junctions.     

SURFACE PROPERTIES OF SOME LOW MOLECULAR WEIGHT PROTEINS

Surface properties of four proteins having molecular weights less than 5,000 are reported at air/water and alumina/water interface at pH 7.0. Reversibility in the adsorption of these proteins at the alumina/water interface is tested. The adsorption on alumina/water interface has been found to be controlled by electrostatic interaction. Positive adsorption was obtained when protein and alumina surface had opposite charges and negative adsorption was obtained when both protein and surface had same charges. Of the four proteins reversibility in adsorption was observed with the one having the lowest molecular weight of 3100. The adsorption behavior apparently had no correlation with their surface hydrophobic!ty. Time dependent changes in air/water interfacial tension was observed for all the four proteins indicating time dependent loosening of compact protein structure and surface unfolding.     

Dimension der Bahnen lokal kompakter Gruppen

Ohne Zusammenfassung     

Dehydration of the nanoporous coordination framework ErIII[CoIII(CN)6].4(H2O): single crystal to single crystal transformation and negative thermal expansion in ErIII[CoIII(CN)6

Desorption of bound and unbound water molecules from the nanoporous coordination framework ErIII[CoIII(CN)6].4(H2O) to form the apohost, ErIII[CoIII(CN)6], proceeds via a single crystal to single crystal transformation in which the Er(III) cations change from 8- to 6-coordinate; dehydration results in a striking change in the thermal expansion properties.     

Gold nanostructures from cube-shaped crystalline intermediates

Conventional bottom-up approaches for building nanostructures rely on the ability to synthesize nanoparticles of different shapes and sizes in a controlled manner that are then assembled to produce useful structures. Here, we present an alternate approach for producing nanostructures based on the formation of a crystalline intermediate in which the metal ion can be reduced in a controlled manner. Partial reduction of HAuCl4 by a long-chain amine results in the formation of a cube-shaped crystalline intermediate in which Au is present in a +1 oxidation state. By control of the nucleation of the metal in the intermediate, a variety of nanostructures can be synthesized. Here, we present results on the formation of superlattices, hollow cubes, nanotubes, and extended hollow structures starting from the intermediate. Direct evidence for the formation of metal within the intermediate by in situ electron-beam-induced reduction in the transmission electron microscope is presented.     

Comparison of single-layer and bilayer InAs/GaAs quantum dots with a higher InAs coverage

Epitaxially grown self-assembled InAs quantum dots (QDs) have found applications in optoelectronics. Efforts are being made to obtain efficient quantum-dot lasers operating at longer telecommunication wavelengths, specifically 1.3 μm and 1.55 μm. This requires narrow emission linewidth from the quantum dots at these wavelengths. In InAs/GaAs single layer quantum dot (SQD) structure, higher InAs monolayer coverage for the QDs gives rise to larger dots emitting at longer wavelengths but results in inhomogeneous dot-size distribution. The bilayer quantum dot (BQD) can be used as an alternative to SQDs, which can emit at longer wavelengths (1.229 μm at 8 K) with significantly narrow linewidth (∼16.7 meV). Here, we compare the properties of single layer and bilayer quantum dots grown with higher InAs monolayer coverage. In the BQD structure, only the top QD layer is covered with increased (3.2 ML) InAs monolayer coverage. The emission line width of our BQD sample is found to be insensitive towards post growth treatments.     

A novel approach to increase emission wavelength of InAs/GaAs quantum dots by using a quaternary capping layer

In this paper, we present a new approach to obtain large size dots in an MBE grown InAs/GaAs multilayer quantum dot system. This is achieved by adding an InAlGaAs quaternary capping layer in addition to a high growth temperature (590°C) GaAs capping layer with the view to tune the emission wavelength of these QDs towards the 1.3 μm/0.95 eV region important for communication devices. Strain driven migration of In atoms from InAlGaAs alloy to the InAs QDs effectively increases the size of QDs. Microscopic investigations were carried out to study the dot size and morphology in the different layers of the grown samples. Methods to reduce structural defects like threading dislocations in multilayer quantum dot samples are also studied.