Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Diketopyrrolopyrrole-Based Conjugated Polymers and Small Molecules for Organic Ambipolar Transistors and Solar Cells

The present highlight discusses major work in the synthesis of low bandgap diketopyrrolopyrrole (DPP)-based polymers with donor-acceptor-donor (D-A-D) approach and their application in organic electronics. It examines the past and recent significant advances which have led to development of low bandgap DPP-based materials with phenyl and thiophene as donors. (c) 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4241-4260

Anthracene-Containing Conjugated Polymer Showing Four Optical Transitions Upon Doping: A Spectroscopic Study

An anthracene-containing poly(arylene-ethynylene)-alt-poly(arylene-vinylene) (PAE-PAV) of general constitutional unit (PhCCAnthrCCPhCHCHAnthrCHCH)(n) bearing two 2-ethylhexyloxy solubilizing side chains on each phenylene (Ph) unit has been synthesized and characterized. The basic electrochemical characterization was done, showing the existence of two non-reversible oxidation and one reversible reduction peaks. The optical properties, the real and imaginary part of the dielectric function, were probed using spectroscopic ellipsometry (SE). The vibrational structure of the undoped/doped polymer was investigated using Fourier transformed infrared spectroscopy. A strong change in the polaronic absorption was observed during the doping, which after modeling revealed the existence of two separated transitions. The optical changes upon doping were additionally recorded using the SE technique. Similar to the results from FT-IR spectroscopy, two new in-the-gap absorptions were found. Moreover, the electrical conductivity as well as the mobility of positive carriers were measured. In the undoped state, the conductivity of the polymer was found to be below the detection limit (Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 338-346

Better early osteogenesis of electroconductive hydroxyapatite-calcium titanate composites in a rabbit animal model

In view of the fact that bone healing can be enhanced due to external electric field application, it is important to assess the influence of the implant conductivity on the bone regeneration in vivo. To address this issue, this study reports the in vivo biocompatibility property of multistage spark plasma sintered hydroxyapatite (HA)-80 wt % calcium titanate (CaTiO3) composites and monolithic HA, which have widely different conductivity property (14 orders of magnitude difference). The ability of bone regeneration was assessed by implantation in cylindrical femoral bone defects of rabbit animal model for varying time period of 1, 4, and 12 weeks. The overall assessment of the histology results suggests that the progressive healing of bone defects around HA-80 wt % CaTiO3 is associated with a better efficacy with respect to (w.r.t) early stage neobone formation, which is histomorphometrically around 140% higher than monolithic HA. Overall, this study demonstrates that the in vivo biocompatibility property of HA-80 wt % CaTiO3 with respect to local effects after 12 weeks of implantation is not compromised both qualitatively and quantitatively, and a comparison with control implant (HA) points toward the critical role of electrical conductivity on better early stage bone regeneration. (c) 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 842-851, 2014.

MRT Letter: Experimental Verification of Vectorial Theory to Determine Field at the Geometrical Focus of a Cylindrical Lens

We provide experimental evidence supporting the vectorial theory for determining electric field at and near the geometrical focus of a cylindrical lens. This theory provides precise distribution of field and its polarization effects. Experimental results show a close match (approximate to 95% using (2)-test) with the simulation results (obtained using vectorial theory). Light-sheet generated both at low and high NA cylindrical lens shows the importance of vectorial theory for further development of light-sheet techniques. Potential applications are in planar imaging systems (such as, SPIM, IML-SPIM, imaging cytometry) and spectroscopy. Microsc. Res. Tech. 77:105-109, 2014. (c) 2014 Wiley Periodicals, Inc.

Synergistic effect of static magnetic field and HA-Fe3O4 magnetic composites on viability of S. aureus and E. coli bacteria

In addressing the issue of prosthetic infection, this work demonstrated the synergistic effect of the application of static magnetic field (SMF) and ferrimagnetic substrate properties on the bactericidal property in vitro. This aspect was studied using hydroxyapatite (HA)-xFe(3)O(4) (x=10, 20, and 40 wt.%) substrates, which have different saturation magnetization properties. During bacteria culture experiments, 100 mT SMF was applied to growth medium (with HA-xFe(3)O(4) substrate) in vitro for 30, 120, and 240 min. A combination of MTT assay, membrane rupture assays, live/dead assay, and fluorescence microscopic analysis showed that the bactericidal effect of SMF increases with the exposure duration as well as increasing Fe3O4 content in biomaterial substrates. Importantly, the synergistic bactericidal effect was found to be independent of bacterial cell type, as similar qualitative trend is measured with both gram negative Escherichia coli (E. coli) and gram positive Staphylococcus aureus (S. aureus) strains. The reduction in E. coli viability was 83% higher on HA-40 Wt % Fe3O4 composite after 4 h exposure to SMF as compared to nonexposed control. Interestingly, any statistically significant difference in ROS was not observed in bacterial growth medium after magnetic field exposure, indicating the absence of ROS enhancement due to magnetic field. Overall, this study illustrates significant role being played by magnetic substrate compositions towards bactericidal property than by magnetic field exposure alone. (c) 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 102B: 524-532, 2014.

Toward Real-Time Availability of 3D Temperature Maps Created with Temporally Constrained Reconstruction

PurposeTo extend the previously developed temporally constrained reconstruction (TCR) algorithm to allow for real-time availability of three-dimensional (3D) temperature maps capable of monitoring MR-guided high intensity focused ultrasound applications. MethodsA real-time TCR (RT-TCR) algorithm is developed that only uses current and previously acquired undersampled k-space data from a 3D segmented EPI pulse sequence, with the image reconstruction done in a graphics processing unit implementation to overcome computation burden. Simulated and experimental data sets of HIFU heating are used to evaluate the performance of the RT-TCR algorithm. ResultsThe simulation studies demonstrate that the RT-TCR algorithm has subsecond reconstruction time and can accurately measure HIFU-induced temperature rises of 20 degrees C in 15 s for 3D volumes of 16 slices (RMSE = 0.1 degrees C), 24 slices (RMSE = 0.2 degrees C), and 32 slices (RMSE = 0.3 degrees C). Experimental results in ex vivo porcine muscle demonstrate that the RT-TCR approach can reconstruct temperature maps with 192 x 162 x 66 mm 3D volume coverage, 1.5 x 1.5 x 3.0 mm resolution, and 1.2-s scan time with an accuracy of 0.5 degrees C. ConclusionThe RT-TCR algorithm offers an approach to obtaining large coverage 3D temperature maps in real-time for monitoring MR-guided high intensity focused ultrasound treatments. Magn Reson Med 71:1394-1404, 2014. (c) 2013 Wiley Periodicals, Inc.

A Thiol- ene Clickable Hyperbranched Polyester via a Simple Single- Step Melt Trans- Esterification Process

Self-condensation of AB(2) type monomers (containing one A-type and two B-type functional groups) generates hyperbranched (HB) polymers that carry numerous B-type end-groups at their molecular periphery; thus, development of synthetic methods that directly provide quantitatively transformable peripheral B groups would be of immense value as this would provide easy access to multiply functionalized HB systems. A readily accessible AB(2) monomer, namely diallyl, 5-(4-hydroxybutoxy)isophthalate was synthesized, which on polymerization under standard melt-transesterfication conditions yielded a peripherally clickable HB polyester in a single step; the allyl groups were quantitatively reacted with a variety of thiols using the facile photoinitiated thiol-ene reaction to generate a wide range of derivatives, with varying solubility and thermal properties. Furthermore, it is shown that the peripheral allyl double bonds can also be readily epoxidized using meta-chloroperoxybenzoic acid to yield interesting HB systems, which could potentially serve as a multifunctional cross-linking agent in epoxy formulations. (c) 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40248.

Division of Labor in Hand Usage in Free- Ranging Bonnet Macaques, Macaca radiata

Primates exhibit laterality in hand usage either in terms of (a) hand with which an individual solves a task or while solving a task that requires both hands, executes the most complex action, that is, hand preference, or (b) hand with which an individual executes actions most efficiently, that is, hand performance. Observations from previous studies indicate that laterality in hand usage might reflect specialization of the two hands for accomplishing tasks that require maneuvering dexterity or physical strength. However, no existing study has investigated handedness with regard to this possibility. In this study, we examined laterality in hand usage in urban free-ranging bonnet macaques, Macaca radiata with regard to the above possibility. While solving four distinct food extraction tasks which varied in the number of steps involved in the food extraction process and the dexterity required in executing the individual steps, the macaques consistently used one hand for extracting food (i.e., task requiring maneuvering dexterity)the maneuvering hand, and the other hand for supporting the body (i.e., task requiring physical strength)the supporting hand. Analogously, the macaques used the maneuvering hand for the spontaneous routine activities that involved maneuvering in three-dimensional space, such as grooming, and hitting an opponent during an agonistic interaction, and the supporting hand for those that required physical strength, such as pulling the body up while climbing. Moreover, while solving a task that ergonomically forced the usage of a particular hand, the macaques extracted food faster with the maneuvering hand as compared to the supporting hand, demonstrating the higher maneuvering dexterity of the maneuvering hand. As opposed to the conventional ideas of handedness in non-human primates, these observations demonstrate division of labor between the two hands marked by their consistent usage across spontaneous and experimental tasks requiring maneuvering in three-dimensional space or those requiring physical strength. Am. J. Primatol. 76:576-585, 2014. (c) 2013 Wiley Periodicals, Inc.

Modeling of Bubble-Size Distribution in Water and Freon Co-Blown Free Rise Polyurethane Foams

A model has been developed to simulate the foam characteristics obtained, when chemical (water) and physical (Freon) blowing agents are used together for the formation of polyurethane foams. The model considers the rate of reaction, the consequent rise in temperature of the reaction mixture, nucleation of bubbles, and mass transfer of CO2 and Freon to them till the time of gelation. The model is able to explain the experimental results available in literature. It further predicts that the nucleation period gets reduced with increase in water (at constant Freon content), whereas with increase in Freon (at constant water) concentration nucleation period decreases marginally leading to narrower bubble-size distribution. By the use of uniform sized nuclei added initially, the model predicts that the bubble-size distribution can be made independent of the rate of homogeneous nucleation and can, thus, offer an extra parameter for its control. (C) 2014 Wiley Periodicals, Inc.

Specroelectrochemical, Switching Kinetics, and Chronoamperometric Studies of Dibenzyl Derivative of Poly(3,4-propylenedioxythiophene) Thin-Film-Based Electrochromic Device

The dibenzyl derivative of poly(3,4-propylenedioxythiophene) (PProDOT-Bz(2)) thin film is deposited onto ITO-coated glass substrate by electropolymerization technique. The electropolymerization of ProDOT-Bz(2) is carried out by a three-electrode electrochemical cell. The cyclic voltammogram shows the redox properties of electrochemically prepared films deposited at different scan rates. The thin films prepared were characterized for its morphological properties to study the homogeniety. Classic six-layer structure of PProDOT-Bz(2) electrochromic device using this material was fabricated and reported for the first and its characterizations such as spectroelectrochemical, switching kinetics, and chronoamperometric studies are performed. The color contrast of the thin film and the device achieved are 64 and 40%, respectively, at lambda(max) (628 nm). The switching time is recorded and the observed values are 5 s from the coloring state to the bleaching state and vice versa. The chronoamperometry shows that the device performed up to 400 cycles, and it is capable of working up to 35 cycles without any degradation. (C) 2014 Wiley Periodicals, Inc.

Sparsely populated residue conformations in protein structures: Revisiting ``experimental'' Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (phi-) space for amino acid residues in proteins. Experimental distributions of phi, values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely arid, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of phi- space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in hairpins. The strand-helix motif with the Type II turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101-1112. (c) 2013 Wiley Periodicals, Inc.

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: Implications for three-dimensional modeling

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naive Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (approximate to 85%) and specific (approximate to 95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. Proteins 2014; 82:1219-1234. (c) 2013 Wiley Periodicals, Inc.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

Nanostructured electrode materials for electrochemical energy storage and conversion

Manipulation of matter at the nanoscale is a way forward to move beyond our current choices in electrochemical energy storage and conversion technologies with promise of higher efficiency, environmental benignity, and cost-effectiveness. Electrochemical processes being basically surface phenomena, tailored multifunctional nanoarchitecturing can lead to improvements in terms of electronic and ionic conductivities, diffusion and mass transport, and electron transfer and electrocatalysis. The nanoscale is also a domain in which queer properties surface: those associated with conversion electrodes, ceramic particles enhancing the conductivity of polymer electrolytes, and transition metal oxide powders catalyzing fuel cell reactions, to cite a few. Although this review attempts to present a bird's eye view of the vast literature that has accumulated in this rather infant field, it also lists a few representative studies that establish the beneficial effects of going `nano'. Investigations on nanostructuring and use of nanoparticles and nanoarchitectures related to lithium-ion batteries (active materials and electrolytes), supercapacitors (electrical double-layer capacitors, supercapacitors based on pseudo-capacitance, and hybrid supercapacitors), and fuel cells (electrocatalysts, membranes and hydrogen storage materials) are highlighted. (C) 2012 John Wiley & Sons, Ltd.