Tethering preferences of domain families co-occurring in multi-domain proteins

Genomic data of several organisms have revealed the presence of a vast repertoire of multi-domain proteins. The role played by individual domains in a multi-domain protein has a profound influence on the overall function of the protein. In the present analysis an attempt has been made to better understand the tethering preferences of domain families that occur in multi-domain proteins. The analysis has been carried out on an exhaustive dataset of 2 961 898 sequences of proteins from 930 organisms, where 741 274 proteins are comprised of at least two domain families. For every domain family, the number of other domain families with which it co-occurs within a protein in this dataset has been enumerated and is referred to as the tethering number of the domain family. It was found that, in the general dataset, the AAA ATPase family and the family of Ser/Thr kinases have the highest tethering numbers of 450 and 444 respectively. Further analysis reveals significant correlation between the number of members in a family and its tethering number. Positive correlation was also observed for the extent of a sequence and functional diversity within a family and the tethering numbers of domain families. Domain families that are present ubiquitously in diverse organisms tend to have large tethering numbers, while organism/kingdom-specific families have low tethering numbers. Thus, the analysis uncovers how domain families recombine and evolve to give rise to multi-domain proteins.

Structural and magnetic properties of SmCo5/Co exchange coupled nanocomposite thin films

We investigated the structural and magnetic properties of SmCo5/Co exchange coupled nanocomposite thin films grown by magnetron sputtering from Sm and Co multitargets successively. The growth of the films was carried out at elevated substrate temperature followed by in situ annealing. On Si (100) substrate, X-ray diffraction confirms the formation of textured (110) SmCo5 hard phase, whereas on MgO (110) substrate, the diffraction pattern shows the epitaxial growth of SmCo5 phase with crystalline orientation along 100] direction. Secondary Ion Mass Spectroscopy reveals the structural transformation from multilayered (Sm/Co) to SmCo5/Co nano-composite films due to high reactivity of Sm at elevated temperature. Transmission electron microscopy indicates the existence of nanocrystalline phase of SmCo5 along with unreacted Co. Observed single phase behavior in magnetic hysteresis measurements indicates well exchange coupling between the soft and the hard phases in these nano-composite films. For samples with samarium layer thickness, t(sm)=3.2 nm and cobalt layer thickness, t(Co)= 11.4 nm, the values of (BH)(max) were obtained as 20.1 MGOe and 12.38 MGOe with H-c value similar to 3.0 kOe grown on MgO and Si substrates, respectively.

DRIFTS studies on CO and NO adsorption and NO plus CO reaction over Pd2+-substituted CeO2 and Ce0.75Sn0.25O2 catalysts

Sequential adsorption of CO and NO as well as equimolar NO + CO reaction with variation of temperature over Pd2+ ion-substituted CeO2 and Ce0.75Sn0.25O2 supports has been studied by DRIFTS technique. The results are compared with 2 at.% Pd/Al2O3 containing Pd-0. Both linear and bridging Pd-0-CO bands are observed over 2 at.% Pd/Al2O3. But, band positions are shifted to higher frequencies in Ce0.98Pd0.02O2-delta and Ce0.73Sn0.25Pd0.02O2-delta catalysts that could be associated with Pd delta+-CO species. In contrast, a Pd2+-CO band at 2160 cm(-1) is observed upon CO adsorption over Ce0.98Pd0.02O2-delta and Ce0.73Sn0.25Pd0.02O2-delta catalysts pre-adsorbed with NO and a Pd+-CO band at 2120 cm(-1) is slowly developed on Ce(0.73)Srl(0.25)Pd(0.02)O(2-delta) over time. An intense linear Pd-0-NO band at 1750 cm(-1) found upon NO exposure to CO pre-adsorbed 2 at.% Pd/Al2O3 indicates molecular adsorption of NO. On the other hand, a weak Pd2+-NO band at 1850 cm(-1) is noticed after NO exposure to Ce0.98Pd0.02O2-delta catalyst pre-adsorbed with CO indicating dissociative adsorption of NO which is crucial for NO reduction. Pd-0-NO band is initially formed over CO pre-adsorbed Ce0.73Sn0.25Pd0.02O2-delta which is red-shifted over time along with formation of Pd2+-NO band. Several intense bands related to nitrates and nitrites are observed after exposure of NO to fresh as well as CO pre-adsorbed Ce0.98Pd0.02O2-delta and Ce0.73Sn0.25Pd0.02O2-delta catalysts. Ramping the temperature in a DRIFTS cell upon NO and CO adsorption shows the formation of N2O and NCO surface species, and N2O-formation temperature is comparable with the reaction done in a reactor.

Interdiffusion and solid solution strengthening in Ni-Co-Pt and Ni-Co-Fe ternary systems

Diffusion couple experiments are conducted in Co-Ni-Pt system at 1200 degrees C and in Co-Ni-Fe system at 1150 degrees C, by coupling binary alloys with the third element. Uphill diffusion is observed for both Co and Ni in Pt rich corner of the Co-Ni-Pt system, whereas in the Co-Ni-Fe system, it is observed for Co. Main and cross interdiffusion coefficients are calculated at the composition of intersection of two independent diffusion profiles. In both the systems, the main interdiffusion coefficients are positive over the whole composition range and the cross interdiffusion coefficients show both positive and negative values at different regions. Hardness measured by performing the nanoindentations on diffusion couples of both the systems shows the higher values at intermediate compositions.

Interfacial growth as a model of tube-width heterogeneities in concentrated solutions of stiff polymers

Recent experimental measurements of the distribution P(w) of transverse chain fluctuations w in concentrated solutions of F-actin filaments B. Wang, J Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010); J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchgessner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)] are shown to be well-fit to an expression derived from a model of the conformations of a single harmonically confined weakly bendable rod. The calculation of P(w) is carried out essentially exactly within a path integral approach that was originally applied to the study of one-dimensional randomly growing interfaces. Our results are generally as successful in reproducing experimental trends as earlier approximate results obtained from more elaborate many-chain treatments of the confining tube potential.

Flexible poly(vinyl alcohol-co-ethylene)/modified MMT moisture barrier composite for encapsulating organic devices

Flexible, nano-composite moisture barrier films of poly(vinyl alcohol-co-ethylene) with surface modified montmorillonite fabricated by solution casting were used to encapsulate organic devices. The composite films were characterized by FTIR, UV-visible spectroscopy and SEM imaging. Thermal and mechanical properties of the composite films were studied by DSC and UTM. Calcium degradation test was used to determine the transmission rate of water vapour through the composite films, which showed a gradual reduction from similar to 0.1 g m(-2) day(-1) to 0.0001 g m(-2) day(-1) with increasing modified montmorillonite loading in the neat copolymer. The increase in moisture barrier performance is attributed to the decreased water vapour diffusivity due to matrix-filler interactions in the composite. The accelerated aging test was carried out for non-encapsulated and encapsulated devices to evaluate the efficiency of the encapsulants. The encapsulated devices exhibited longer lifetimes indicating the efficacy of the encapsulant.

Aza-induced cardiomyocyte differentiation of P19 EC-cells by epigenetic co-regulation and ERK signaling

Stem cells in cell based therapy for cardiac injury is being potentially considered. However, genetic regulatory networks involved in cardiac differentiation are not clearly understood. Among stem cell differentiation models, mouse P19 embryonic carcinoma (EC) cells, are employed for studying (epi)genetic regulation of cardiomyocyte differentiation. Here, we comprehensively assessed cardiogenic differentiation potential of 5-azacytidine (Aza) on P19 EC-cells, associated gene expression profiles and the changes in DNA methylation, histone acetylation and activated-ERK signaling status during differentiation. Initial exposure of Aza to cultured EC-cells leads to an efficient (55%) differentiation to cardiomyocyte-rich embryoid bodies with a threefold (16.8%) increase in the cTnI(+) cardiomyocytes. Expression levels of cardiac-specific gene markers i.e., Isl-1, BMP-2, GATA-4, and alpha-MHC were up-regulated following Aza induction, accompanied by differential changes in their methylation status particularly that of BMP-2 and alpha-MHC. Additionally, increases in the levels of acetylated-H3 and pERK were observed during Aza-induced cardiac differentiation. These studies demonstrate that Aza is a potent cardiac inducer when treated during the initial phase of differentiation of mouse P19 EC-cells and its effect is brought about epigenetically and co-ordinatedly by hypo-methylation and histone acetylation-mediated hyper-expression of cardiogenesis-associated genes and involving activation of ERK signaling.

Li3MRuO5 (M = Co, Ni), new lithium-rich layered oxides related to LiCoO2: promising electrochemical performance for possible application as cathode materials in lithium ion batteries

We describe the synthesis and crystal structure of Li3MRuO5 (M = Co and Ni), new rock salt related oxides. Both the oxides crystallize in the layered LiCoO2 (alpha-NaFeO2) structure, as revealed by powder XRD data. Magnetic susceptibility data suggest that the oxidation states of transition metals are Li3Co3+(ls)Ru4+(ls) O-5 (ls = low spin) for the M = Co compound and Li3Ni2+Ru5+O5 for the M = Ni compound. Electrochemical investigations of lithium deintercalation-intercalation behaviour reveal that both Co and Ni phases exhibit attractive specific capacities of ca. 200 mA h g(-1) at an average voltage of 4 V that has been interpreted as due to the oxidation of Co3+ and Ru4+ in Li3CoRuO5 and Ni2+ to Ni4+ in the case of Li3NiRuO5. Thus, a different role of Ru ions is played in the isostructural oxides. Finally, in both cases evidence of irreversible behaviour above 4.2 V is observed and interpreted as formation of high valent ions or alternatively oxidation of oxide ions.

Novel co-evaporation approach for the growth of Sb doped SnO2 nanowires

Antimony doped tin oxide (Sb:SnO2) nanowires were grown by thermal and e-beam assisted co-evaporation of Sb and Sn in the presence of oxygen at a low substrate temperature of 450 degrees C. The field emission scanning electron microscopy study revealed that the nanowires had a length and diameter of 2-4 mu m and 20-60 nm respectively. Transmission electron microscopy study revealed the single crystalline nature of the nanowires; energy dispersive X-ray spectroscopy (EDS) and EDS mapping on the nanowires confirmed the presence of Sb doping in the nanowires. UV light detection study on the doped SnO2 nanowire films exhibited fast response and recovery time compared to undoped SnO2 nanowire films. This is an innovative and simple method to grow doped SnO2 nanowires.

Near-infrared photoactive Cu2ZnSnS4 thin films by co-sputtering

The thin films of Cu2ZnSnS4 (CZTS) were grown by co-sputtering further the structural, optical and electrical properties were analyzed and confirmed the CZTS phase formation. The photo response of CZTS in near IR photodectection has been demonstrated. The detector response was measured employing both the IR lamp and IR laser illuminations. The calculated growth and decay constants were 130 m sec and 700 m sec followed by the slower components upon lamp illumination. The external quantum efficiency of 15%, responsivity of 13 AW(-1) makes CZTS a suitable candidate for the IR photodectection.

Transition and acoustic response of recirculation structures in an unconfined co-axial isothermal swirling flow

This paper reports the first observations of transition from a pre-vortex breakdown (Pre-VB) flowreversal to a fully developed central toroidal recirculation zone in a non-reacting, double-concentric swirling jet configuration and its response to longitudinal acoustic excitation. This transition proceeds with the formation of two intermediate, critical flow regimes. First, a partially penetrated vortex breakdown bubble (VBB) is formed that indicates the first occurrence of an enclosed structure as the centre jet penetration is suppressed by the growing outer roll-up eddy; resulting in an opposed flow stagnation region. Second, a metastable transition structure is formed that marks the collapse of inner mixing vortices. In this study, the time-averaged topological changes in the coherent recirculation structures are discussed based on the non-dimensional modified Rossby number (Ro(m)) which appears to describe the spreading of the zone of swirl influence in different flow regimes. Further, the time-mean global acoustic response of pre-VB and VBB is measured as a function of pulsing frequency using the relative aerodynamic blockage factor (i.e., maximum radial width of the inner recirculation zone). It is observed that all flow modes except VBB are structurally unstable as they exhibit severe transverse radial shrinkage (similar to 20%) at the burner Helmholtz resonant modes (100-110 Hz). In contrast, all flow regimes show positional instability as seen by the large-scale, asymmetric spatial shifting of the vortex core centres. Finally, the mixing transfer function M (f) and magnitude squared coherence lambda(2)(f) analysis is presented to determine the natural couplingmodes of the system dynamic parameters (u', p'), i.e., local acoustic response. It is seen that the pre-VB flow mode exhibits a narrow-band, low pass filter behavior with a linear response window of 100-105 Hz. However, in the VBB structure, presence of critical regions such as the opposed flow stagnation region alters the linearity range with the structure showing a response even at higher pulsing frequencies (100-300 Hz). (C) 2013 AIP Publishing LLC.

Fe as Hydrogen/Halogen Bond Acceptor in Square Pyramidal Fe(CO)(5)

Hydrogen bonded complexes formed between the square pyramidal Fe(CO)(5) with HX (X = F, Cl, Br), showing X-H center dot center dot center dot Fe interactions, have been investigated theoretically using density functional theory (DFT) including dispersion correction. Geometry, interaction energy, and large red shift of about 400 cm(-1) in the FIX stretching frequency confirm X-H center dot center dot center dot Fe hydrogen bond formation. In the (CO)(5)Fe center dot center dot center dot HBr complex, following the significant red shift, the HBr stretching mode is coupled with the carbonyl stretching modes. This clearly affects the correlation between frequency shift and binding energy, which is a hallmark of hydrogen bonds. Atoms in Molecule (AIM) theoretical analyses show the presence of a bond critical point between the iron and the hydrogen of FIX and significant mutual penetration. These X-H center dot center dot center dot Fe hydrogen bonds follow most but not all of the eight criteria proposed by Koch and Popelier (J. Phys. Chem. 1995, 99, 9747) based on their investigations on C-H center dot center dot center dot O hydrogen bonds. Natural bond orbital (NBO) analysis indicates charge transfer from the organometallic system to the hydrogen bond donor. However, there is no correlation between the extent of charge transfer and interaction,energy, contrary to what is proposed in the recent IUPAC recommendation (Pure Appl.. Chem. 2011, 83, 1637). The ``hydrogen bond radius'' for iron has been determined to be 1.60 +/- 0.02 angstrom, and not surprisingly it is between the covalent (127 angstrom) and van der Waals (2.0) radii of Fe. DFT and AIM theoretical studies reveal that Fe in square pyramidal Fe(CO)(5) can also form halogen bond with CIF and ClH as ``halogen bond donor''. Both these complexes show mutual penetration as well, though the Fe center dot center dot center dot Cl distance is closer to the sum of van der Waals radii of Fe and Cl in (CO)5Fe center dot center dot center dot ClH, and it is about 1 angstrom less in (CO)(5)Fe center dot center dot center dot ClF.

Interfacial growth as a model of tube-width heterogeneities in concentrated solutions of stiff polymers

Recent experimental measurements of the distribution P(w) of transverse chain fluctuations w in concentrated solutions of F-actin filaments B. Wang, J Guan, S. M. Anthony, S. C. Bae, K. S. Schweizer, and S. Granick, Phys. Rev. Lett. 104, 118301 (2010); J. Glaser, D. Chakraborty, K. Kroy, I. Lauter, M. Degawa, N. Kirchgessner, B. Hoffmann, R. Merkel, and M. Giesen, Phys. Rev. Lett. 105, 037801 (2010)] are shown to be well-fit to an expression derived from a model of the conformations of a single harmonically confined weakly bendable rod. The calculation of P(w) is carried out essentially exactly within a path integral approach that was originally applied to the study of one-dimensional randomly growing interfaces. Our results are generally as successful in reproducing experimental trends as earlier approximate results obtained from more elaborate many-chain treatments of the confining tube potential. (C) 2013 AIP Publishing LLC.

New rock salt-related oxides Li3M2RuO6 (M=Co, Ni): Synthesis, structure, magnetism and electrochemistry

We describe the synthesis, crystal structure, magnetic and electrochemical characterization of new rock salt-related oxides of formula, Li3M2RuO6 (M=Co, Ni). The M=Co oxide adopts the LiCoO2 (R-3m) structure, where sheets of LiO6 and (Co-2/Ru)O-6 octahedra are alternately stacked along the c-direction. The M=Ni oxide also adopts a similar layered structure related to Li2TiO3, where partial mixing of Li and Ni/Ru atoms lowers the symmetry to monoclinic (C2/c). Magnetic susceptibility measurements reveal that in Li3Co2RuO6, the oxidation states of transition metal ions are Co3+ (S=0), Co2+ (S=1/2) and Ru4+ (S=1), all of them in low-spin configuration and at 10 K, the material orders antiferromagnetically. Analogous Li3Ni2RuO6 presents a ferrimagnetic behavior with a Curie temperature of 100 K. The differences in the magnetic behavior have been explained in terms of differences in the crystal structure. Electrochemical studies correlate well with both magnetic properties and crystal structure. Li-transition metal intermixing may be at the origin of the more impeded oxidation of Li3Ni2RuO6 when compared to Li3CO2RuO6. Interestingly high first charge capacities (between ca. 160 and 180 mAh g(-1)) corresponding to ca. 2/3 of theoretical capacity are reached albeit, in both cases, capacity retention and cyclability are not satisfactory enough to consider these materials as alternatives to LiCoO2. (C) 2013 Elsevier Inc. All rights reserved.

Influence of CeO2 morphology on the catalytic activity of CeO2-Pt hybrids for CO oxidation

Ceria, because of its excellent redox behavior and oxygen storage capacity, is used as a catalyst for several technologically important reactions. In the present study, different morphologies of nano-CeO2 (rods, cubes, octahedra) were synthesized using the hydrothermal route. An ultrafast microwave-assisted method was used to efficiently attach Pt particles to the CeO2 polyhedra. These nanohybrids were tested as catalysts for the CO oxidation reaction. The CeO2/Pt catalyst with nanorods as the support was found to be the most active catalyst. XPS and IR spectroscopy measurements were carried out in order to obtain a mechanistic understanding and it was observed that the adsorbed carbonates with lower stability on the reactive planes of nanorods and cubes are the major contributor to this enhanced catalytic activity.