Effect of functional groups on separating carbon dioxide from CO2/N-2 gas mixtures using edge functionalized graphene nanoribbons

Development of microporous adsorbents for separation and sequestration of carbon dioxide from flue gas streams is an area of active research. In this study, we assess the influence of specific functional groups on the adsorption selectivity of CO2/N-2 mixtures through Grand Canonical Monte Carlo (GCMC) simulations. Our model system consists of a bilayer graphene nanoribbon that has been edge functionalized with OH, NH2, NO2, CH3 and COOH. Ab initio Moller-Plesset (MP2) calculations with functionalized benzenes are used to obtain binding energies and optimized geometries for CO2 and N-2. This information is used to validate the choice classical forcefields in GCMC simulations. In addition to simulations of adsorption from binary mixtures of CO2 and N-2, the ideal adsorbed solution theory (IAST) is used to predict mixture isotherms. Our study reveals that functionalization always leads to an increase in the adsorption of both CO2 and N-2 with the highest for COOH. However, significant enhancement in the selectivity for CO2 is only seen with COOH functionalized nanoribbons. The COOH functionalization gives a 28% increase in selectivity compared to H terminated nanoribbons, whereas the improvement in the selectivity for other functional groups are much Enure modest. Our study suggests that specific functionalization with COOH groups can provide a material's design strategy to improve CO2 selectivity in microporous adsorbents. Synthesis of graphene nanoplatelets with edge functionalized COOH, which has the potential for large scale production, has recently been reported (Jeon el, al., 2012). (C) 2014 Elsevier Ltd. All rights reserved,

Dendritic atrophy constricts functional maps in resonance and impedance properties of hippocampal model neurons

A gradient in the density of hyperpolarization-activated cyclic-nucleotide gated (HCN) channels is necessary for the emergence of several functional maps within hippocampal pyramidal neurons. Here, we systematically analyzed the impact of dendritic atrophy on nine such functional maps, related to input resistance and local/transfer impedance properties, using conductance-based models of hippocampal pyramidal neurons. We introduced progressive dendritic atrophy in a CA1 pyramidal neuron reconstruction through a pruning algorithm, measured all functional maps in each pruned reconstruction, and arrived at functional forms for the dependence of underlying measurements on dendritic length. We found that, across frequencies, atrophied neurons responded with higher efficiency to incoming inputs, and the transfer of signals across the dendritic tree was more effective in an atrophied reconstruction. Importantly, despite the presence of identical HCN-channel density gradients, spatial gradients in input resistance, local/transfer resonance frequencies and impedance profiles were significantly constricted in reconstructions with dendrite atrophy, where these physiological measurements across dendritic locations converged to similar values. These results revealed that, in atrophied dendritic structures, the presence of an ion channel density gradient alone was insufficient to sustain homologous functional maps along the same neuronal topograph. We assessed the biophysical basis for these conclusions and found that this atrophy-induced constriction of functional maps was mediated by an enhanced spatial spread of the influence of an HCN-channel cluster in atrophied trees. These results demonstrated that the influence fields of ion channel conductances need to be localized for channel gradients to express themselves as homologous functional maps, suggesting that ion channel gradients are necessary but not sufficient for the emergence of functional maps within single neurons.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

An Improved Outer Bound on the Storage-Repair-Bandwidth Tradeoff of Exact-Repair Regenerating Codes

While the tradeoff between the amount of data stored and the repair bandwidth of an (n, k, d) regenerating code has been characterized under functional repair (FR), the case of exact repair (ER) remains unresolved. It is known that there do not exist ER codes which lie on the FR tradeoff at most of the points. The question as to whether one can asymptotically approach the FR tradeoff was settled recently by Tian who showed that in the (4, 3, 3) case, the ER region is bounded away from the FR region. The FR tradeoff serves as a trivial outer bound on the ER tradeoff. In this paper, we extend Tian's results by establishing an improved outer bound on the ER tradeoff which shows that the ER region is bounded away from the FR region, for any (n; k; d). Our approach is analytical and builds upon the framework introduced earlier by Shah et. al. Interestingly, a recently-constructed, layered regenerating code is shown to achieve a point on this outer bound for the (5, 4, 4) case. This represents the first-known instance of an optimal ER code that does not correspond to a point on the FR tradeoff.

Quantification of the Particle Size and Stability of Graphene Oxide in a Variety of Solvents

The exceptional solution processing potential of graphene oxide (GO) is always one of its main advantages over graphene in terms of its industrial relevance in coatings, electronics, and energy storage. However, the presence of a variety of functional groups on the basal plane and edges of GO makes understanding suspension behavior in aqueous and organic solvents, a major challenge. Acoustic spectroscopy can also measure zeta potential to provide unique insight into flocculating, meta-stable, and stable suspensions of GO in deionized water and a variety of organic solvents (including ethanol, ethylene glycol, and mineral oil). As expected, a match between solvent polarity and the polar functional groups on the GO surface favors stable colloidal suspensions accompanied by a smaller aggregate size tending toward disperse individual flakes of GO. This work is significant since it describes the characteristics of GO in solution and its ability to act as a precursor for graphene-based materials.

Spatial modulation of the composition of a binary liquid near a repulsive wall

When a binary liquid is confined by a strongly repulsive wall, the local density is depleted near the wall and an interface similar to that between the liquid and its vapor is formed. This analogy suggests that the composition of the binary liquid near this interface should exhibit spatial modulation similar to that near a liquid-vapor interface even if the interactions of the wall with the two components of the liquid are the same. The Guggenheim adsorption relation quantifies the concentrations of two components of a binary mixture near a liquid-vapor interface and qualitatively states that the majority (minority) component enriches the interface for negative (positive) mixing energy if the surface tensions of the two components are not very different. From molecular dynamics simulations of binary mixtures with different compositions and interactions we find that the Guggenheim relation is qualitatively satisfied at wall-induced interfaces for systems with negative mixing energy at all state points considered. For systems with positive mixing energy, this relation is found to be qualitatively valid at low densities, while it is violated at state points with high density where correlations in the liquid are strong. This observation is validated by a calculation of the density profiles of the two components of the mixture using density functional theory with the Ramakrishnan-Yussouff free-energy functional. Possible reasons for the violation of the Guggenheim relation are discussed.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

The Asian elephant is amongst the top three frugivores of two tree species with easily edible fruit

Large animal species are prone to local extirpation, but ecologists cannot yet predict how the loss of megaherbivores affects ecosystem processes such as seed dispersal. Few studies have compared the quantity and quality of seed dispersal by megaherbivores versus alternative frugivores in the wild, particularly for plant species with fruit easily consumed by many frugivorous species. In a disturbed tropical moist forest in India, we examine whether megaherbivores are a major frugivore of two tree species with easily edible, mammal-dispersed fruit. We quantify the relative fruit removal rates of Artocarpus chaplasha and Careya arborea, by the Asian elephant (Elephas maximus) and alternative dispersers. Through focal watches and camera trapping, we found the elephant to be amongst the top three frugivores for each tree species. Furthermore, seed transects under A. chaplasha show that arboreal frugivores discard seeds only a short distance from the parental tree, underscoring the elephant's role as a long-distance disperser. Our data provide unprecedented support for an old notion: megaherbivores may be key dispersers for a broad set of mammal-dispersed fruiting species, and not just fruit inaccessible to smaller frugivores. As such, the elephant may be particularly important for the functional ecology of the disturbed forests it still inhabits across tropical Asia.

Probing the role of highly conserved residues in triosephosphate isomerase-analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme

Highly conserved residues in enzymes are often found to be clustered close to active sites, suggesting that functional constraints dictate the nature of amino acid residues accommodated at these sites. Using the Plasmodiumfalciparum triosephosphate isomerase (PfTIM) enzyme () as a template, we have examined the effects of mutations at positions 64 and 75, which are not directly involved in the proton transfer cycle. Thr (T) occurring at position 75 is completely conserved, whereas only Gln (Q) and Glu (E) are accommodated at position 64. Biophysical and kinetic data are reported for four T75 (T75S/V/C/N) and two Q64 (Q64N/E) mutants. The dimeric structure is weakened in the Q64E and Q64N mutants, whereas dimer integrity is unimpaired in all four T75 mutants. Measurement of the concentration dependence of enzyme activity permits an estimate of K-d values for dimer dissociation (Q64N=73.79.2nm and Q64E=44.6 +/- 8.4nm). The T75S/V/C mutants have activities comparable to the wild-type enzyme, whereas a fourfold drop is observed for T75N. All four T75 mutants show a dramatic fall in activity between 35 degrees C and 45 degrees C. Crystal structure determination of the T75S/V/N mutants provides insights into the variations in local interactions, with the T75N mutant showing the largest changes. Hydrogen-bond interactions determine dimer stability restricting the choice of residues at position 64 to Gln (Q) and Glu (E). At position 75, the overwhelming preference for Thr (T) may be dictated by the imperative of maintaining temperature stability of enzyme activity.

The putative role of some conserved water molecules in the structure and function of human transthyretin

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.

Roles for Transcription Factors Sp1, NF-kappa B, IRF3, and IRF7 in Expression of the Human IFNL4 Gene

The expression of a biologically active human IFN4 depends on the presence of a frameshift deletion polymorphism within the first exon of the interferon lambda 4 (IFNL4) gene. In this report, we use the lung carcinoma-derived cell line, A549, which is genetically viable to express a functional IFN4, to address transcriptional requirements of the IFNL4 gene. We show that the GC-rich DNA-binding transcription factor (TF) specificity protein 1 (Sp1) is recruited to the IFNL4 promoter and has a role in induction of gene expression upon stimulation with viral RNA mimic poly(I:C). By using RNAi and overexpression strategies, we also show key roles in IFNL4 gene expression for the virus-inducible TFs, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-B), IFN regulatory factor 3 (IRF3), and IRF7. Interestingly, we also observe that overexpression of IFN4 influences IFNL4 promoter activity, which may further be dependent on the retinoic acid-inducible gene-I (RIG-I)-like receptor pathway. Together, our work for the first time reports on the functional characterization of the human IFNL4 promoter.

Optimizing Photovoltaic Response by Tuning Light-Harvesting Nanocrystal Shape Synthesized Using a Quick Liquid-Gas Phase Reaction

The electron recombination lifetime in a sensitized semiconductor assembly is greatly influenced by the crystal structure and geometric form of the light-harvesting semiconductor nanocrystal. When such light harvesters with varying structural characteristics are configured in a photoanode, its interface with the electrolyte becomes equally important and directly influences the photovoltaic efficiency. We have systematically probed here the influence of nanocrystal crystallographic structure and shape on the electron recombination lifetime and its eventual influence on the light to electricity conversion efficiency of a liquid junction semiconductor sensitized solar cell. The light-harvesting cadmium sulfide (CdS) nanocrystals of distinctly different and controlled shapes are obtained using a novel and simple liquid gas phase synthesis method performed at different temperatures involving very short reaction times. High resolution synchrotron X-ray diffraction and spectroscopic studies respectively exhibit different crystallographic phase content and optical properties. When assembled on a mesoscopic TiO2 film by a linker molecule, they exhibit remarkable variation in electron recombination lifetime by 1 order of magnitude, as determined by ac-impedance spectroscopy. This also drastically affects the photovoltaic efficiency of the differently shaped nanocrystal sensitized solar cells.

Optimizing Photovoltaic Response by Tuning Light-Harvesting Nanocrystal Shape Synthesized Using a Quick Liquid-Gas Phase Reaction

The electron recombination lifetime in a sensitized semiconductor assembly is greatly influenced by the crystal structure and geometric form of the light-harvesting semiconductor nanocrystal. When such light harvesters with varying structural characteristics are configured in a photoanode, its interface with the electrolyte becomes equally important and directly influences the photovoltaic efficiency. We have systematically probed here the influence of nanocrystal crystallographic structure and shape on the electron recombination lifetime and its eventual influence on the light to electricity conversion efficiency of a liquid junction semiconductor sensitized solar cell. The light-harvesting cadmium sulfide (CdS) nanocrystals of distinctly different and controlled shapes are obtained using a novel and simple liquid gas phase synthesis method performed at different temperatures involving very short reaction times. High resolution synchrotron X-ray diffraction and spectroscopic studies respectively exhibit different crystallographic phase content and optical properties. When assembled on a mesoscopic TiO2 film by a linker molecule, they exhibit remarkable variation in electron recombination lifetime by 1 order of magnitude, as determined by ac-impedance spectroscopy. This also drastically affects the photovoltaic efficiency of the differently shaped nanocrystal sensitized solar cells.