DNA Assisted Self-Assembly of PAMAM Dendrimers

We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391-397). We have used single stranded DNA (ssDNA) to direct the self-assembly process. To explore the effect of pH on this mechanism, we have used both the protonated (low pH) and nonprotonated (high pH) dendrimers. In all cases studied here, we observe that the DNA strand on one dendrimer unit drives self-assembly as it binds to the complementary DNA strand present on the other dendrimer unit, leading to the formation of a DNA-linked dendrimer dimeric complex. However, this binding process strongly depends on the charge of the dendrimer and length of the ssDNA. We observe that the complex with a nonprotonated dendrimer can maintain a DNA length dependent inter-dendrimer distance. In contrast, for complexes with a protonated dendrimer, the inter-dendrimer distance is independent of the DNA length. We attribute this observation to the electrostatic complexation of a negatively charged DNA strand with the positively charged protonated dendrimer.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Transverse orthotropic elastic moduli of bundled coated thin elliptical tubes

Light weight structures with tailored mechanical properties have evolved beyond regular hexagonal/circular honeycomb topology. For applications which demand anisotropic mechanical properties, elliptical-celled structures offer interesting features. This paper characterizes the anisotropic in-plane elastic response of coated thin elliptical tubes in different array patterns viz, close-packed, diagonal and rectangular patterns under compression. This paper also extends earlier works on elliptical close-packed structure to a more general case of coated tubes. Theoretical framework using thin ring theory provides formulae in terms of geometric and material parameters. These are compared with a series of FE simulations using contact elements. The FE results are presented as graphs to aid in design. (C) 2014 Elsevier Ltd. All rights reserved.

The X-C center dot center dot center dot pi (X = F, Cl, Br, CN) Carbon Bond

High-level ab initio calculations have been used to study the interactions between the CH3 group of CH3X (X = F, Cl, Br, CN) molecules and pi-electrons. These interactions are important because of the abundance of both the CH3 groups and pi-electrons in biological systems. Complexes between C2H4/C2H2 and CH3X molecules have been used as model systems. Various theoretical methods such as atoms in molecules theory, reduced density gradient analysis, and natural bond orbital analysis have been used to discern these interactions. These analyses show that the interaction of the p-electrons with the CH3X molecules leads to the formation of X-C...p carbon bonds. Similar complexes with other tetrel molecules, SiH3X and GeH3X, have also been considered.

Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Heterogeneity in Dye-TiO2 Interactions Dictate Charge Transfer Efficiencies for Diketopyrrolopyrrole-Based Polymer Sensitized Solar Cells

Power conversion efficiency of a solar cell is a complex parameter which usually hides the molecular details of the charge generation process. For rationally tailoring the overall device efficiency of the dye-sensitized solar cell, detailed molecular understanding of photoinduced reactions at the dye-TiO2 interface has to be achieved. Recently, near-IR absorbing diketopyrrolopyrrole-based (DPP) low bandgap polymeric dyes with enhanced photostabilities have been used for TiO2 sensitization with moderate efficiencies. To improve the reported device performances, a critical analysis of the polymerTiO(2) interaction and electron transfer dynamics is imperative. Employing a combination of time-resolved optical measurements complemented by low temperature EPR and steady-state Raman spectroscopy on polymerTiO(2) conjugates, we provide direct evidence for photoinduced electron injection from the TDPP-BBT polymer singlet state into TiO2 through the C-O group of the DPP-core. A detailed excited state description of the electron transfer process in films reveals instrument response function (IRF) limited (<110 fs) charge injection from a minor polymer fraction followed by a picosecond recombination. The major fraction of photoexcited polymers, however, does not show injection indicating pronounced ground state heterogeneity induced due to nonspecific polymerTiO(2) interactions. Our work therefore underscores the importance of gathering molecular-level insight into the competitive pathways of ultrafast charge generation along with probing the chemical heterogeneity at the nanoscale within the polymerTiO2 films for optimizing photovoltaic device efficiencies.

Synergistic Effect of Mo plus Cu Codoping on the Photocatalytic Behavior of Metastable TiO2 Solid Solutions

Codoping with Cu and Mo is shown to have a synergistic effect on the photocatalytic activity of TiO2. The enhancement in activity is observed only if the synthesis route results in TiO2 in which (Cu, Mo) codopants are forced into the TiO2 lattice. Using X-ray photoelectron spectroscopy, Cu and Mo are shown to be present in the +2 and +6 oxidation states, respectively. A systematic study of the ternary system shows that TiO2 containing 6 mol % CuO and 1.5 mol % MoO3 is the most active ternary composition. Ab initio calculations show that codoping of TiO2 using (Mo, Cu) introduces levels above the valence band, and below the conduction band, resulting in a significant reduction in the band gap (similar to 0.8 eV). However, codoping also introduces deep defect states, which can have a deleterious impact on photoactivity. This helps rationalize the narrow compositional window over which the enhancement in photocatalytic activity is observed.

Ionic Bonding between Artificial Atoms

Conventional solids are prepared from building blocks that are conceptually no larger than a hundred atoms. While van der Waals and dipole-dipole interactions also influence the formation of these materials, stronger interactions, referred to as chemical bonds, play a more decisive role in determining the structures of most solids. Chemical bonds that hold such materials together are said to be ionic, covalent, metallic, dative, or otherwise a combination of these. Solids that utilize semiconductor nanocrystal quantum dots as building units have been demonstrated to exist; however, the interparticle forces in such materials are decidedly not chemical. Here we demonstrate the formation of charge transfer states in a binary quantum dot mixture. Charge is observed to reside in quantum confined states of one of the participating quantum dots. These interactions lead to materials that may be regarded as the nanoscale analog of an ionic solid. The process by which these materials form has interesting parallels to chemical reactions in conventional chemistry.

Why is the influence of soil macrofauna on soil structure only considered by soil ecologists?

These last twenty years have seen the development of an abundant literature on the influence of soil macrofauna on soil structure. Amongst these organisms, earthworms, termites and ants are considered to play a key role in regulating the physical, chemical and microbiological properties of soils. Due to these influential impacts, soil ecologists consider these soil macro-invertebrates as `soil engineers' and their diversity and abundance are nowadays considered as relevant bioindicators of soil quality by many scientists and policy makers. Despite this abundant literature, the soil engineering concept remains a `preach to the choir' and bioturbation only perceived as important for soil ecologists. We discussed in this article the main mechanisms by which soil engineers impact soil structure and proposed to classify soil engineers with respect to their capacity to produce biostructures and modify them. We underlined the lack of studies considering biostructure dynamics and presented recent techniques in this purpose. We discussed why soil engineering concept is mainly considered by soil ecologists and call for a better collaboration between soil ecologists and soil physicists. Finally, we summarized main challenges and questions that need to be answered to integrate soil engineers activities in soil structure studies. (C) 2014 Elsevier B.V. All rights reserved.

An alluaudite Na-2+Fe-2x(2-x)(SO4)(3)(x=0.2) derivative phase as insertion host for lithium battery

A new desodiated derivative compound, Na0.89Fe1.8(SO4)(3), was prepared by the chemical oxidation of alluaudite Na2.4Fe1.8(SO4)(3) Phase using NOBF4 as oxidant. The structure and valency of Fe were characterized by X-ray diffraction (XRD) and Fe-57 Mossbauer spectroscopy. Intercalation behavior of lithium ions in the structure of Na0.89Fe1.8(SO4)(3) was gauged by electrochemical analyses and ex-situ X-ray diffraction. A high capacity of 110 mAh g(-1) at 0.1 C was obtained with a good rate kinetics within a range of 0.1-10 C(1 C = 118 mAh g-1) involving a high Fe3+/Fe2+ redox potential of 3.75 V (vs. Li/Li+). These results confirmed that the Na2.4-delta Fe1.8(SO4)(3) framework was stable even after oxidation and forms a new competitive cathode for the reversible intercalation of lithium ions. (C) 2014 Elsevier B.V. All rights reserved.

Lizards of the Thar Desert - Resource partitioning and community composition

How similar species co-exist in nature is a fundamental question in community ecology. Resource partitioning has been studied in desert lizard communities across four continents, but data from South Asia is lacking. We used area-constrained visual encounter surveys to study community composition and spatial and temporal resource partitioning in a lizard community during summer in the Thar Desert, western India, addressing an important biogeographic gap in knowledge. Twelve one-hectare grids divided into 25 m x 25 m plots were placed across four habitats barren dunes, stabilized dunes, grassland, and rocky hills. We recorded 1039 sightings of 12 species during 84 sampling sessions. Lizard abundance decreased in the order stabilized dunes > grassland > barren dunes > rocky hills; richness was in roughly the opposite order. Resource partitioning was examined for the seven commonest species. Overall spatial overlap was low (<0.6) between species pairs. Overlap was higher within habitats, but species showed finer separation through use of different microhabitat categories and specific spatial resources, as well as by positioning at different distances to vegetation. Diurnal species were also separated by peak time of activity. Space appears to be an important resource dimension facilitating coexistence in this desert lizard community. (C) 2015 Elsevier Ltd. All rights reserved.

Challenges in the quantification and interpretation of spike-LFP relationships

Brain signals often show fluctuations in particular frequency bands, which are highly conserved across species and are associated with specific behavioural states. Such rhythmic patterns can be captured in the local field potential (LFP), which is obtained by low-pass filtering the extracellular signal recorded from microelectrodes. However, LFP also captures other neural processes that are associated with spikes, such as synaptic events preceding a spike, low-frequency component of the action potential (spike bleed-through'') and spike afterhyperpolarization, which pose difficulties in the estimation of the amplitude and phase of the rhythm with respect to spikes. Here we discuss these issues and different techniques that have been used to dissociate the rhythm from other neural events in the LFP.

Spontaneous Lorentz violation: the case of infrared QED

It is by now clear that the infrared sector of quantum electrodynamics (QED) has an intriguingly complex structure. Based on earlier pioneering work on this subject, two of us recently proposed a simple modification of QED by constructing a generalization of the U(1) charge group of QED to the ``Sky'' group incorporating the well-known spontaneous Lorentz violation due to infrared photons, but still compatible in particular with locality (Balachandran and Vaidya, Eur Phys J Plus 128:118, 2013). It was shown that the ``Sky'' group is generated by the algebra of angle-dependent charges and a study of its superselection sectors has revealed a manifest description of spontaneous breaking of the Lorentz symmetry. We further elaborate this approach here and investigate in some detail the properties of charged particles dressed by the infrared photons. We find that Lorentz violation due to soft photons may be manifestly codified in an angle-dependent fermion mass, modifying therefore the fermion dispersion relations. The fact that the masses of the charged particles are not Lorentz invariant affects their spin content, and time dilation formulas for decays should also get corrections.

NUMERICAL STUDIES OF DYNAMO ACTION IN A TURBULENT SHEAR FLOW. I.

We perform numerical experiments to study the shear dynamo problem where we look for the growth of a large-scale magnetic field due to non-helical stirring at small scales in a background linear shear flow in previously unexplored parameter regimes. We demonstrate the large-scale dynamo action in the limit where the fluid Reynolds number (Re) is below unity while the magnetic Reynolds number (Rm) is above unity; the exponential growth rate scales linearly with shear, which is consistent with earlier numerical works. The limit of low Re is particularly interesting, as seeing the dynamo action in this limit would provide enough motivation for further theoretical investigations, which may focus attention on this analytically more tractable limit of Re < 1 compared to the more formidable limit of Re > 1. We also perform simulations in the regimes where (i) both (Re, Rm) < 1, and (ii) Re > 1 and Rm < 1, and compute all of the components of the turbulent transport coefficients (alpha(ij) and alpha(ij)) using the test-field method. A reasonably good agreement is observed between our results and the results of earlier analytical works in similar parameter regimes.

Trap modulated photoresponse of InGaN/Si isotype heterojunction at zero-bias

n-n isotype heterojunction of InGaN and bare Si (111) was formed by plasma assisted molecular beam epitaxy without nitridation steps or buffer layers. High resolution X-ray diffraction studies were carried out to confirm the formation of epilayers on Si (111). X-ray rocking curves revealed the presence of large number of edge threading dislocations at the interface. Room temperature photoluminescence studies were carried out to confirm the bandgap and the presence of defects. Temperature dependent I-V measurements of Al/InGaN/Si (111)/Al taken in dark confirm the rectifying nature of the device. I-V characteristics under UV illumination, showed modest rectification and was operated at zero bias making it a self-powered device. A band diagram of the heterojunction is proposed to understand the transport mechanism for self-powered functioning of the device. (c) 2015 AIP Publishing LLC.