Optical nonlinearity in lead sulfide microtowers

Lead sulfide (PbS) microtowers on silicon substrates, having the physical properties of bulk PbS, have been synthesized. Optical nonlinearity studies using the open aperture z-scan technique employing 5 ns and 100 fs laser pulses reveal effective two-photon type absorption. For nanosecond excitation the nonlinear absorption coefficients (beta(eff)) are in the order of 10(-11) m W-1, two orders of magnitude less than the values reported for quantum confined PbS nanocrystals. For femtosecond excitation beta(eff) is of the order of 10(-14) m W-1. These results obtained in bulk PbS experimentally confirm the importance of quantum confinement in the enhancement of optical nonlinearities in semiconductor materials.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Visualizing lone pairs in compounds containing heavier congeners of the carbon and nitrogen group elements

In this mini-review, I discuss some recent work on the stereochemistry and bonding of lone pairs of electrons in divalent compounds of the heavier carbon group elements (SnII, PbII) and in trivalent compounds of the heavier nitrogen group elements (BiIII). Recently developed methods that permit the real-space visualization of bonding patterns on the basis of density functional calculations of electronic structure, reveal details of the nature of s electron lone pairs in compounds of the heavier main group elements – their stereochemistry and their inertness (or lack thereof). An examination of tetragonal P4/nmm SnO, a-PbO and BiOF, and cubic Fm3m PbS provides a segue into perovskite phases of technological significance, including ferroelectric PbTiO3 and antiferroelectric/piezoelectric PbZrO3, in both of which the lone pairs on Pb atoms play a pivotal rôle.

Synthesis, characterization, degradation of biodegradable castor oil based polyesters

A new family of castor oil based biodegradable polyesters was synthesized by catalyst free melt condensation reaction between two different diacids and castor oil with D-mannitol. The polymers synthesized were characterized by NMR spectroscopy, FF-IR and the thermal properties were analysed by DSC. The results of DSC show that the polymer is rubbery in physiological conditions. The contact angle measurement and hydration test results indicate that the surface of the polymer is hydrophilic. The mechanical properties, evaluated in the tensile mode, shows that the polymer has characteristics of a soft material. In vitro degradation of polymer in PBS solution carried out at physiological conditions indicates that the degradation goes to completion within 21 days and it was also found that the rate of degradation can be tuned by varying the curing conditions. (C) 2011 Elsevier Ltd. All rights reserved.

Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBS) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. (C) 2011 Elsevier Masson SAS. All rights reserved.

Synthesis, Characterization, and Degradation of Biodegradable Poly(mannitol citric dicarboxylate) Copolyesters

Three groups of poly(mannitol citric dicarboxylate) [p(MCD)] copolyesters were synthesized by catalyst-free melt condensation of mannitol with acids. The resulting copolyesters were designated as poly(mannitol citric succinate) [p(MCSu)], poly(mannitol citric adipate) [p(MCA)], poly(mannitol citric sebacate) [p(MCS)]. The polymers were characterized by FTIR, (1)H NMR, and DSC analysis. The synthesized p(MCD) polymers exhibit glass transition temperatures ranging from 16.5 to 58.58 degrees C. The mechanical, degradation properties, and the drug-releasing characteristics of these polymers were investigated. It was observed that the mechanical properties of the p(MCD) polymers cover a wide range with Young's modulus of the polymer varying from 12.25 to 660 MPa. Hydrolytic degradation of all polymers was investigated by incubating polymer discs in PBS and the hydrolytic degradation of p(MCD) polymers followed the order, p(MCSu) > p(MCA) > p(MCS). This was attributed to the number of -CH(2)(units in the dicarboxylic monomers. The release of model drug compounds from the p(MCD) polymer discs was also studied. POLYM. ENG. SCI., 51:2035-2043, 2011. (C) 2011 Society of Plastics Engineers

Solubilities of Pb+2, Bi+3, Sb+3 and Cu+1 sulphides in (NaCl KCl Na2S) melts

Solubilities of common metal sulfides have been determined in the (NaCl+KCl) eutectic melt with and without Na2S. A novel gas-phase equilibrium technique has been used for PbS, Bi2S3, and So2S3, and an improved liquid phase equilibrium technique for Cu2S, which eliminates the errors due to physical entrapment of the sulfide phase and segregation on quenching, enabling precise measurements to be made. Solubilities in the (NaCl+KCl) eutectic melt were determined as a function of temperature in the rante 700° to 950°C, and were found to be small. The partial molar heats of mixing of the sulfides in the eutectic melt have been calculated from the solubility measurements, to be 13.3, 31.4, 37.1, and 49.0 kcal for PbSs), Sb2S2(l), and Cu2S(s), respectively. Sodium sulfide addition was observed to enhance these solubilities, the effect being largest for Cu2S followed by Sb2S3, Bi2S3, and PbS. This effect is explained qualitatively. It was observed that PbS and Sb2S3 obey Henry's law up to saturation in (NaCl+KCl+Na2S) melts.

Investigation of biodegradable and biocompatible castor oil poly(mannitol-citric-sebacate) polyester as a drug carrier

Castor oil-based poly(mannitol-citric sebacate) was synthesized by simple, catalyst-free melt condensation process using monomers having potential to be metabolized in vivo. The polymer was characterized using various techniques and the tensile and hydration properties of the polymers were also determined. The biocompatibility of the polymer was tested using human foreskin fibroblasts cells. The in vitro degradation studies show that the time for complete degradation of the polymer was more than 21 days. The usage of castor oil polyester as a drug carrier was analysed by doping the polymer with 5-fluorouracil model drug and the release rate was studied by varying the percentage loading of drugs and the pH of the PBS solution medium. The cumulative drug-release profiles exhibited a biphasic release with an initial burst release and cumulative 100% release within 42 h. To understand the role of the polymer as a drug carrier in the release behaviour, drug-release studies were conducted with another drug, isoniazid. The release behaviour of isoniazid drug from the same polymer matrix followed an nth order kinetic model and 100% cumulative release was achieved after 12 days. The variation in the release behaviour for two model drugs from the same polymer matrix suggests a strong interaction between the polymer and the drug molecule.

Thermal instability and the feedback regulation of hot haloes in clusters, groups and galaxies

We present global multidimensional numerical simulations of the plasma that pervades the dark matter haloes of clusters, groups and massive galaxies (the intracluster medium; ICM). Observations of clusters and groups imply that such haloes are roughly in global thermal equilibrium, with heating balancing cooling when averaged over sufficiently long time- and length-scales; the ICM is, however, very likely to be locally thermally unstable. Using simple observationally motivated heating prescriptions, we show that local thermal instability (TI) can produce a multiphase medium with similar to 104 K cold filaments condensing out of the hot ICM only when the ratio of the TI time-scale in the hot plasma (tTI) to the free-fall time-scale (tff) satisfies tTI/tff? 10. This criterion quantitatively explains why cold gas and star formation are preferentially observed in low-entropy clusters and groups. In addition, the interplay among heating, cooling and TI reduces the net cooling rate and the mass accretion rate at small radii by factors of similar to 100 relative to cooling-flow models. This dramatic reduction is in line with observations. The feedback efficiency required to prevent a cooling flow is similar to 10-3 for clusters and decreases for lower mass haloes; supernova heating may be energetically sufficient to balance cooling in galactic haloes. We further argue that the ICM self-adjusts so that tTI/tff? 10 at all radii. When this criterion is not satisfied, cold filaments condense out of the hot phase and reduce the density of the ICM. These cold filaments can power the black hole and/or stellar feedback required for global thermal balance, which drives tTI/tff? 10. In comparison to clusters, groups have central cores with lower densities and larger radii. This can account for the deviations from self-similarity in the X-ray luminositytemperature () relation. The high-velocity clouds observed in the Galactic halo can be due to local TI producing multiphase gas close to the virial radius if the density of the hot plasma in the Galactic halo is >rsim 10-5 cm-3 at large radii.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Zinc Oxide Modified Au Electrode as Sensor for an Efficient Detection of Hydrazine

ZnO nanoparticles (ZnO NPs) prepared by microwave heating technique are used to modify a gold electrode (ZnO/Au) for the hydrazine detection study. The synthesized product is well characterized by various techniques. Detailed electrochemical investigation of the oxidation of hydrazine on the ZnO/Au electrode in 0.02 M phosphate buffer solution (PBS) of pH 7.4 was carried out. A very low detection limit of 66 nM (S/N=4) and a wide linearity in current for a concentration range from 66.0X10-3 to 415 mu M was achieved by amperometry. The electrode was found to be stable for over a month when preserved in PBS.

Structure, tensile properties and cytotoxicity assessment of sebacic acid based biodegradable polyesters with ricinoleic acid

A new family of ricinoleic acid based polyesters was synthesized using catalyst free melt-condensation polymerization with sebacic acid, citric acid, mannitol and ricinoleic acid as precursors. The use of FT-IR and NMR characterisation techniques confirms the presence of ester linkages in the as-synthesized polymers. Depending on the precursor combination, their relative amount and the degree of curing, a broad range of elastic modulus (22-327 MPa) and tensile strength (0.7-12.7 MPa) can be obtained in the newly synthesized biopolymers. The polymers show rubbery behaviour at a physiological temperature (37 degrees C) and the contact angles of the synthesized polymers fall in the range of 42 degrees to 71 degrees, making them ideal substrates to study delivery of drugs through polymer scaffolds. The cytocompatibility assessment of the cured polymers confirmed good cell attachment and growth of smooth muscle cells (C2C12 myoblast cells). Importantly, oriented cell growth was observed after culturing myoblast cells for 3 days. The in vitro degradation in PBS indicates that the mild cured polymers follow a first order reaction kinetics and have degradation rate constants in the range of 0.009-0.038 h(-1), depending on the relative proportions of monomers. Overall, the results of our study indicate that the physical properties can be tailored by varying the composition of the monomers and curing conditions in the newly developed polyesters. Hence, they may be used as potential substrates for tissue engineering scaffolds and for localized drug delivery.

Precoder optimization in cognitive radio with interference constraints

We consider precoding strategies at the secondary base station (SBS) in a cognitive radio network with interference constraints at the primary users (PUs). Precoding strategies at the SBS which satisfy interference constraints at the PUs in cognitive radio networks have not been adequately addressed in the literature so far. In this paper, we consider two scenarios: i) when the primary base station (PBS) data is not available at SBS, and ii) when the PBS data is made available at the SBS. We derive the optimum MMSE and Tomlinson-Harashima precoding (THP) matrix Alters at the SBS which satisfy the interference constraints at the PUs for the former case. For the latter case, we propose a precoding scheme at the SBS which performs pre-cancellation of the PBS data, followed by THP on the pre-cancelled data. The optimum precoding matrix filters are computed through an iterative search. To illustrate the robustness of the proposed approach against imperfect CSI at the SBS, we then derive robust precoding filters under imperfect CSI for the latter case. Simulation results show that the proposed optimum precoders achieve good bit error performance at the secondary users while meeting the interference constraints at the PUs.

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a-p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and beta-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.

Clusters, asters, and collective oscillations in chemotactic colloids

The creation of synthetic systems that emulate the defining properties of living matter, such as motility, gradient-sensing, signaling, and replication, is a grand challenge of biomimetics. Such imitations of life crucially contain active components that transform chemical energy into directed motion. These artificial realizations of motility point in the direction of a new paradigm in engineering, through the design of emergent behavior by manipulating properties at the scale of the individual components. Catalytic colloidal swimmers are a particularly promising example of such systems. Here we present a comprehensive theoretical description of gradient-sensing of an individual swimmer, leading controllably to chemotactic or anti-chemotactic behavior, and use it to construct a framework for studying their collective behavior. We find that both the positional and the orientational degrees of freedom of the active colloids can exhibit condensation, signaling formation of clusters and asters. The kinetics of catalysis introduces a natural control parameter for the range of the interaction mediated by the diffusing chemical species. For various regimes in parameter space in the long-ranged limit our system displays precise analogs to gravitational collapse, plasma oscillations, and electrostatic screening. We present prescriptions for how to tune the surface properties of the colloids during fabrication to achieve each type of behavior.