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Search for H I emission from superdisk candidates associated with radio galaxies
No full textGiant gaseous layers (termed ``superdisks'') have been hypothesized in the past to account for the strip-like radio emission gap (or straight-edged central brightness depression) observed between twin radio lobes, in over a dozen relatively nearby powerful Fanaroff-Riley Class II radio galaxies. They could also provide a plausible alternative explanation for a range of observations. Although a number of explanations have been proposed for the origin of the superdisks, little is known about their material content. Some X-ray observations of superdisk candidates indicate the presence of hot gas, but a cool dusty medium also seems to be common. If they are entirely or partly composed of neutral gas, then it may be directly detectable and we report here a first attempt to detect/image any neutral hydrogen gas present in the superdisks that are inferred to be present in four nearby radio galaxies. We have not found a positive H I signal in any of the four sources, resulting in tight upper limits on the H I number density in the postulated superdisks, estimated directly from the central rms noise values of the final radio continuum subtracted image. The estimated ranges of the upper limit on neutral hydrogen number density and column density are 10(-4) - 10(-3) atoms per cm(3) and 10(19) - 10(20) atoms per cm(2), respectively. No positive H I signal is detected even after combining all the four available H I images (with inverse variance weighting). This clearly rules out an H I dominated superdisk as a viable model to explain these structures, however, the possibility of a superdisk being composed of warm/hot gas still remains open
Dissection of Protonation Sites for Antibacterial Recognition and Transport in QacA, a Multi-Drug Efflux Transporter
No full textQacA is a drug:H+ antiporter with 14 transmembrane helices that confers antibacterial resistance to methicillin-resistant Staphylococcus aureus strains, with homologs in other pathogenic organisms. It is a highly promiscuous antiporter, capable of H+-driven efflux of a wide array of cationic antibacterial compounds and dyes. Our study, using a homology model of QacA, reveals a group of six protonatable residues in its vestibule. Systematic mutagenesis resulted in the identification of D34 (TM1), and a cluster of acidic residues in TM13 including E407 and D411 and D323 in TM10, as being crucial for substrate recognition and transport of monovalent and divalent cationic antibacterial compounds. The transport and binding properties of QacA and its mutants were explored using whole cells, inside-out vesicles, substrate-induced H+ release and microscale thermophoresis-based assays. The activity of purified QacA was also observed using proteoliposome-based substrate-induced H+ transport assay. Our results identify two sites, D34 and D411 as vital players in substrate recognition, while E407 facilitates substrate efflux as a protonation site. We also observe that E407 plays an additional role as a substrate recognition site for the transport of dequalinium, a divalent quaternary ammonium compound. These observations rationalize the promiscuity of QacA for diverse substrates. The study unravels the role of acidic residues in QacA with implications for substrate recognition, promiscuity and processive transport in multidrug efflux transporters, related to QacA
Simulations on ``Powder'' Samples for Better Agreement with Macroscopic Measurements
No full textDifferent experimental measurement techniques give widely differing values for diffusivity (D-s) and activation energy (E-a) for the same sample. Values from molecular dynamics simulations agree with quasi-elastic neutron scattering measurements and not with those obtained from macroscopic techniques, such as uptake or zero length column chromatography. We report molecular dynamics simulations on different zeolite samples with intercrystalline space along 0-, 1-, 2-, and 3-dimensions. The results on n-hexane in zeolite NaY samples with intercrystalline space along three-dimensions exhibit values of D-s and E-a in excellent agreement with macroscopic techniques, demonstrating the importance of ``powder'' samples in simulations
Engineering the tilt angle in quasi-perpendicularly magnetized Ta/Pt/CoFeB/Pt thin films
No full textKerr microscopy measurements of Ta/Pt/CoFeB/Pt thin films, with ferromagnetic (FM) CoFeB layer grown by oblique-angle sputter deposition, indicated a quasi-perpendicular magnetic anisotropy. In such a system, the anisotropy is slightly tilted from the normal to substrate plane. The effect of tilt was observed as shift in out-of-plane (OP) room-temperature hysteresis, in presence of in-plane (IP) bias field. Tilt angles were obtained by measuring the shifts in OP hysteresis for several magnitudes and relative azimuthal orientations of bias field with respect to IP projection of tilted anisotropy direction. We studied variation of tilt angle as function of FM layer thickness which was increased near to Spin Reorientation Transition (SRT) value for FM layer in corresponding system. We also studied this variation for different bottom Pt layer thicknesses. The results of our experiment show the variation to follow two different profiles - one monotonic and the other non-monotonic
Structure, dynamics and phase behavior of short rod inclusions dissolved in a colloidal membrane
No full textInclusions dissolved in an anisotropic quasi-2D membrane acquire new types of interactions that can drive assembly of complex structures and patterns. We study colloidal membranes composed of a binary mixture of long and short rods, such that the length ratio of the long to short rods is approximately two. At very low volume fractions, short rods dissolve in the membrane of long rods by strongly anchoring to the membrane polymer interface. At higher fractions, the dissolved short rods phase separate from the background membrane, creating a composite structure comprised of bilayer droplets enriched in short rods that coexist with the background monolayer membrane. These results demonstrate that colloidal membranes serve as a versatile platform for assembly of soft materials, while simultaneously providing new insight into universal membrane-mediated interactions
Modifications of amino acids using arenediazonium salts
No full textAryl transfer reactions from arenediazonium salts have started to make their impact in chemical biology with initial forays in the arena of arylative modifications and bio-conjugations of amino acids, peptides and proteins. The unique multimodal reactivity of arenediazonium salts, ranging from thermal or photochemical radical chain reactions, Pd-catalyzed coupling to arylazo-coupling reactions, all under distinct but mild conditions, provides multiple options for side chain modifications of amino acids and peptides and in addition, site-selective protein conjugation and labelling, protein immobilization, azo-bridged macrocyclization, etc. under bio-ambient conditions. The purpose of this review is to highlight these recent advances and to stimulate interest towards broader applications of arenediazonium salts as aryl transfer agents in bioconjugation reactions
Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum
No full textAutophagy is a degradative pathway associated with many pathological and physiological processes crucial for cell survival. During ER stress, while selective autophagy occurs via ER-phagy, the re-establishment of physiologic ER homeostasis upon resolution of a transient ER stress is mediated by recovER-phagy. Recent studies demonstrated that recovER-phagy is governed via association of Sec62 as an ER-resident autophagy receptor through its autophagy interacting motifs (AIM)/LC3-interacting region (LIR) toAtg8/LC3. Atg8 is an autophagy protein, which is central to autophagosome formation and maturation. Plasmodium falciparum Atg8 (PfAtg8) has both autophagic and non-autophagic functions critical for parasite survival. Since Plasmodium also has Sec62 in the ER membrane and is prone to ER stress due to drastic transformation during their complex intraerythrocytic cycle; hence, we initiated the studies to check whether recovER-phagy occurs in the parasite. To achieve this, a comprehensive study based on the computational approaches was carried out. This study embarks upon identification of AIM sequences in PfSec62 by carrying out peptide-protein docking simulations and comparing the interactions of these AIMs with PfAtg8, based on the molecular dynamic simulations. Detailed analysis is based on electrostatic surface complementarity, peptide-protein interaction strength, mapping of non-covalent bond interactions and rupture force calculated from steered MD simulations. Potential mean forces and unbinding free energies (AGdissociation) using Jarzynski's equality were also computed for the AIM/LIR motif complexes with PfAtg8/HsLC3 autophagy proteins to understand their dissociation free energy profiles and thereby their binding affinities and stability of the peptide-protein complexes. Through this study, we predict Sec62 mediated recovER-phagy in Plasmodium falciparum, which might open new avenues to explore novel drug targets for antimalarial drug discovery
From natural language text to rules: knowledge acquisition from formal documents for aircraft assembly
No full textKnowledge acquisition is a well-acknowledged bottleneck in the building of knowledge-based systems. Documents are a useful source of knowledge from experts. This paper targets the reuse of knowledge from the assembly phase of a product in the design and planning phases. Issues, their causes and the parameters involved are necessary to be acquired for reusing the knowledge so acquired. This paper discusses a method for knowledge acquisition, as a pipeline of existing tools in natural language understanding and processing. The acquired knowledge is expected to help in the decision making for a smart manufacturing system. The process of knowledge acquisition involves recognising the presence of issues and their causes using a combination of sentiment analysis and text patterns. The causes are then dissected to identify the constraints and constituent parameters. These pieces of knowledge are then reconstructed to form rules in a knowledge base. This paper demonstrates progress towards realising the method, by developing the cause dissection and rule-writing components, and validation of the issue-cause acquisition component with human subjects. A discussion is then presented on the potential integration and validation of the overall knowledge acquisition pipeline with a smart manufacturing system
Annealing induced transformations in structural and optical properties of Ge30Se70-xBix thin films
No full textThin films of Ge30Se70-xBix (x = 5, 15, 20) were prepared by thermal evaporation method on glass substrates with thickness 800 nm. The films were annealed at 250 degrees C and 320 degrees C for 2 h to study the annealing-induced structural and optical change. The X-ray diffraction characterization revealed the amorphous to crystalline phase transformation with annealing. The indirect optical band gap decreased with annealing which is explained on the basis of phase transformation and density of localized states. The formation of surface dangling bonds around the crystallites during crystallization process reduced the band gap. The Tauc parameter and Urbach energy change show the degree of chemical disorderness in the films. The transmitivity decreased while the absorption coefficient increased with the annealing process. The microstructural study done by Field emission scanning electron microscopy shows the formation of crystallites upon annealing. Atomic force microscopy investigation on these films shows the influence of annealing on surface topography
A numerical study of an acoustic-hydrodynamic system exhibiting an intermittent prelude to instability
No full textA model problem comprising two subsytems (acoustic and hydrodynamic), both admitting unsteady flows, has been studied using numerical simulations. Simulations capture all key features observed in an experiment with a similar configuration, and reveal the differences in flow field evolution that manifest as an intermittent prelude to instability in this nonlinear system, coupling acoustic and hydrodynamic phenomena. The system consists of a uniform flow that enters a long duct and leaves through an orifice into the atmosphere. The duct supports acoustic modes, while the shear layer at the boundary of the jet emerging from the orifice can develop into a train of vortices. Over some range of inflow velocities that support a stable operation, duct acoustic modes and shear layer breakup result in aperiodic, small amplitude pressure fluctuations. As the flow rate is increased, fluctuations become essentially periodic and have much larger amplitudes. This transition from a quiescent to a (so-called) whistling state occurs over a range of flow rates and is characterized by intermittent, moderately large, aperiodic fluctuations. As in the experiment, the aperiodic time series from the quiescent state is found to be multifractal; multifractality is then lost as the flow transitions to whistling. Simulation flow fields reveal differences in the development of vortices in the bounding shear layer, and near the orifice walls, that give rise to the large changes in pressure fluctuations, as well as the intermittent behavior that precedes whistling