Gap renormalization of molecular crystals from density-functional theory

Fundamental gap renormalization due to electronic polarization is a basic phenomenon in molecular crystals. Despite its ubiquity and importance, all conventional approaches within density-functional theory completely fail to capture it, even qualitatively. Here, we present a new screened range-separated hybrid functional, which, through judicious introduction of the scalar dielectric constant, quantitatively captures polarization-induced gap renormalization, as demonstrated on the prototypical organic molecular crystals of benzene, pentacene, and C-60. This functional is predictive, as it contains system-specific adjustable parameters that are determined from first principles, rather than from empirical considerations.

Species importance in a heterospecific foraging association network

There is a growing recognition of the need to integrate non-trophic interactions into ecological networks for a better understanding of whole-community organization. To achieve this, the first step is to build networks of individual non-trophic interactions. In this study, we analyzed a network of interdependencies among bird species that participated in heterospecific foraging associations (flocks) in an evergreen forest site in the Western Ghats, India. We found the flock network to contain a small core of highly important species that other species are strongly dependent on, a pattern seen in many other biological networks. Further, we found that structural importance of species in the network was strongly correlated to functional importance of species at the individual flock level. Finally, comparisons with flock networks from other Asian forests showed that the same taxonomic groups were important in general, suggesting that species importance was an intrinsic trait and not dependent on local ecological conditions. Hence, given a list of species in an area, it may be possible to predict which ones are likely to be important. Our study provides a framework for the investigation of other heterospecific foraging associations and associations among species in other non-trophic contexts.

Large-area Piezoceramic Coating with IDT Electrodes for Ultrasonic Sensing Applications

In the present paper, the ultrasonic strain sensing performance of large-area piezoceramic coating with Inter Digital Transducer (IDT) electrodes is studied. The piezoceramic coating is prepared using slurry coating technique and the piezoelectric phase is achieved by poling under DC field. To study the sensing performance of the piezoceramic coating with IDT electrodes for strain induced by the guided waves, the piezoceramic coating is fabricated on the surface of a beam specimen at one end and the ultrasonic guided waves are launched with a piezoelectric wafer bonded on another end. Often a wider frequency band of operation is needed for the effective implementation of the sensors in the Structural Health Monitoring (SHM) of various structures, for different types of damages. A wider frequency band of operation is achieved in the present study by considering the variation in the number of IDT electrodes in the contribution of voltage for the induced dynamic strain. In the present work, the fabricated piezoceramic coatings with IDT electrodes have been characterized for dynamic strain sensing applications using guided wave technique at various different frequencies. Strain levels of the launched guided wave are varied by varying the magnitude of the input voltage sent to the actuator. Sensitivity variation with the variation in the strain levels of guided wave is studied for the combination of different number of IDT electrodes. Piezoelectric coefficient e(11) is determined at different frequencies and at different strain levels using the guided wave technique.

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.

Polymer template-assisted microemulsion synthesis of large surface area, porous Li2MnO3 and its characterization as a positive electrode material of Li-ion cells

Lithium-rich manganese oxide (Li2MnO3) is prepared by reverse microemulsion method employing Pluronic acid (P123) as a soft template and studied as a positive electrode material. The as-prepared sample possesses good crystalline structure with a broadly distributed mesoporosity but low surface area. As expected, cyclic voltammetry and charge-discharge data indicate poor electrochemical activity. However, the sample gains surface area with narrowly distributed mesoporosity and also electrochemical activity after treating in 4 M H2SO4. A discharge capacity of about 160 mAh g(-1) is obtained. When the acid-treated sample is heated at 300 A degrees C, the resulting porous sample with a large surface area and dual porosity provides a discharge capacity of 240 mAh g(-1). The rate capability study suggests that the sample provides about 150 mAh g(-1) at a specific discharge current of 1.25 A g(-1). Although the cycling stability is poor, the high rate capability is attributed to porous nature of the material.

Highly photoactive heterostructures of PbO quantum dots on TiO2

We present a non-hydrolytic sol-gel combustion method for synthesizing nanocomposites of PbO quantum dots on anatase TiO2 with a high surface area. XRD, electron microscopy, DRS, cathodoluminescence and BET were employed for structural, microstructural and optical characterization of the composites. The photocatalytic activity of TiO2 and PbO/TiO2 was investigated and compared with Degussa P-25. The results indicate that the photocatalytic activity of quantum dot dispersed TiO2 is higher than that of bare TiO2 and much higher than that of commercial Degussa P-25. The origin of enhanced photoreactivity of the synthesized material can be assigned to a synergetic effect of high surface area, higher number of active sites and an engineered band structure in the heterostructure. The mechanisms for photocatalytic activity are discussed based on production of photogenerated reactive species. The knowledge gained through this report open up ideal synthesis routes for designing advanced functional heterostructures with engineered band structure and has important implications in solar energy based applications.

Functional specificity among yeast mitochondrial Hsp70s paralogs and orthologs

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can “make or break” mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: An exploration involving mutants

Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.

Functional analysis of ultra high information rates conveyed by rat vibrissal primary afferents

Sensory receptors determine the type and the quantity of information available for perception. Here, we quantified and characterized the information transferred by primary afferents in the rat whisker system using neural system identification. Quantification of ``how much'' information is conveyed by primary afferents, using the direct method (DM), a classical information theoretic tool, revealed that primary afferents transfer huge amounts of information (up to 529 bits/s). Information theoretic analysis of instantaneous spike-triggered kinematic stimulus features was used to gain functional insight on ``what'' is coded by primary afferents. Amongst the kinematic variables tested-position, velocity, and acceleration-primary afferent spikes encoded velocity best. The other two variables contributed to information transfer, but only if combined with velocity. We further revealed three additional characteristics that play a role in information transfer by primary afferents. Firstly, primary afferent spikes show preference for well separated multiple stimuli (i.e., well separated sets of combinations of the three instantaneous kinematic variables). Secondly, neurons are sensitive to short strips of the stimulus trajectory (up to 10 ms pre-spike time), and thirdly, they show spike patterns (precise doublet and triplet spiking). In order to deal with these complexities, we used a flexible probabilistic neuron model fitting mixtures of Gaussians to the spike triggered stimulus distributions, which quantitatively captured the contribution of the mentioned features and allowed us to achieve a full functional analysis of the total information rate indicated by the DM. We found that instantaneous position, velocity, and acceleration explained about 50% of the total information rate. Adding a 10 ms pre-spike interval of stimulus trajectory achieved 80-90%. The final 10-20% were found to be due to non-linear coding by spike bursts.

Protumorigenic actions of S100A2 involve regulation of PI3/Akt signaling and functional interaction with Smad3

S100 family of calcium-binding proteins is commonly upregulated in a variety of tumor types and is often associated with tumor progression. Among several S100 members, altered expression of S100A2 is a potential diagnostic and prognostic marker in cancer. Several reports suggest a role for S100A2 in metastasis. Earlier, our studies established regulation of S100A2 by transforming growth factor- (TGF-) and its involvement in TGF--mediated cancer cell invasion and migration. However, the molecular mechanisms of S100A2 protumorigenic actions remain unexplored. In the present study, we demonstrate that overexpression of S100A2 in A549 lung cancer cells induced epithelialmesenchymal transition (EMT) followed by increased invasion, loose colony morphology in soft agar and enhanced Akt phosphorylation (Ser-473). Furthermore, overexpression of S100A2 led to increased tumor growth in immunocompromised mice. In agreement, immunohistochemical examination of resected xenograft tumors established inverse correlation between S100A2 and E-cadherin expression together with activated Akt signaling. Interestingly, our study demonstrates a strong dependence of S100A2 and Smad3 in TGF--induced Hep3B cell EMT and invasion. Most importantly, we demonstrate that these effects of S100A2 are manifested through functional interaction with Smad3, which is enhanced in the presence of high calcium and TGF-. S100A2 stabilizes Smad3 and binds to its C-terminal MH2 domain. Additionally, loss of S100A2 attenuates the transcription of TGF-/Smad3 target genes involved in tumor promotion, such as PA1-1 and vimentin. Collectively, our findings present the first mechanistic details of S100A2 protumorigenic actions and its involvement in TGF--mediated cancer cell invasion and EMT.

STOKES' SYSTEM IN A DOMAIN WITH OSCILLATING BOUNDARY: HOMOGENIZATION AND ERROR ANALYSIS OF AN INTERIOR OPTIMAL CONTROL PROBLEM

Homogenization and error analysis of an optimal interior control problem in the framework of Stokes' system, on a domain with rapidly oscillating boundary, are the subject matters of this article. We consider a three dimensional domain constituted of a parallelepiped with a large number of rectangular cylinders at the top of it. An interior control is applied in a proper subdomain of the parallelepiped, away from the oscillating volume. We consider two types of functionals, namely a functional involving the L-2-norm of the state variable and another one involving its H-1-norm. The asymptotic analysis of optimality systems for both cases, when the cross sectional area of the rectangular cylinders tends to zero, is done here. Our major contribution is to derive error estimates for the state, the co-state and the associated pressures, in appropriate functional spaces.

A Networked Control Systems Perspective for Wide-Area Monitoring Control of Smart Power Grids

This paper presents a networked control systems (NCS) framework for wide area monitoring control of smart power grids. We consider a scenario in which wide area measurements are transmitted to controllers at remote locations. We model the effects of delays and packet dropouts due to limited communication capabilities in the grid. We also design a robust networked controller to damp wide-area oscillations based on information obtained from Wide Area Monitoring Systems (WAMS), and analyze the improvement in system stability due to networked control. With communication integration being an important feature of the smart grid, detailed consideration of the effects of communication is essential in the control design for future power systems. We believe that this work is an essential step in this direction.

Functional Corannulene: Diverse Structures, Enhanced Charge Transport, and Tunable Optoelectronic Properties

Chemical functionalization of various hydrocarbons, such as coronene, corannulene, and so forth, shows good promise in electronics applications because of their tunable optoelectronic properties. By using quantum chemical calculations, we have investigated the changes in the corannulene buckybowl structure, which greatly affect its electronic and optical properties when functionalized with different electron-withdrawing imide groups. We find that the chemical nature and position of functional groups strongly regulate the stacking geometry, -stacking interactions, and electronic structure. Herein, a range of optoelectronic properties and structure-property relationships of various imide-functionalized corannulenes are explored and rationalized in detail. In terms of carrier mobility, we find that the functionalization strongly affects the reorganization energy of corannulene, while the enhanced stacking improves hopping integrals, favoring the carrier mobility of crystals of pentafluorophenylcorannulene-5-monoimide. The study shows a host of emerging optoelectronic properties and enhancements in the charge-transport characteristics of functionalized corannulene, which may find possible semiconductor and electronics applications.