Fast lithium-ion conductivity in the 'empty-perovskite' n = 2 Ruddlesden–Popper-type oxysulphide Y₂Ti₂S₂O₅

Materials with Wadsley–Roth (W–R) crystallographic shear and bronze-type structures display fast lithium (Li)-ion diffusion and are of interest as anode materials for high-power Li-ion batteries. Here we use density-functional-theory calculations to investigate Y2Ti2S2O5, a Li-ion anode material that shares structural features with W–R phases. Y2Ti2S2O5 is a layered Ruddlesden–Popper-type oxysulphide displaying a reversible capacity of 128 mA h g−1, with 60% capacity-retention at a charge rate of 20C in micrometer-sized electrode particles. The crystal structure contains an empty central layer of corner-sharing [TiO5S] octahedra, equivalent to a (∞ × ∞ × 2) block of the ReO3-like units that form Wadsley–Roth type phases. Intercalated Li+ ions on this plane occupy distorted ‘rectangular-planar’ sites, and display 2D mobility with single-ion hopping barriers of 64 meV under dilute conditions. The insertion geometry of Li+ is highly frustrated, giving rise to a smooth potential energy surface for Li-hopping and exceptionally low activation barriers. The [TiO5S] units do not experience major distortions or correlated rotations during discharge, due to framework rigidity provided by [Y2S2]2+ rocksalt slabs, meaning the rectangular-planar-like geometry of Li+ is retained across all states of charge. A tetragonal to orthorhombic to tetragonal phase change occurs upon lithiation, with a stable Li+ ordering at x = 1.0 in LixY2Ti2S2O5. Li+–Li+ repulsion has a significant effect on the cation ordering at all Li intercalation levels. Na+ hopping barriers are >1.7 eV, while Mg2+ ions can move with barriers of ∼607 meV, illustrating the how diffusion behaviour varies for ions of different size and charge within W–R-type frameworks. The exceptionally low activation barriers for Li-hopping and well-defined, rigid 2D diffusion plane makes Y2Ti2S2O5 a valuable model system within which to understand Li+ behaviour in high-rate electrode materials, such as the related Wadsley–Roth phases

Influence of Dispersion Interactions on the Polymorphic Stability of Crystalline Oxides

The accurate determination of relative phase stabilities using DFT methods is a significant challenge when some of these can vary by only a few kJ/mol. Here, we demonstrate that for a selection of oxides (TiO2, MnO2, and ZnO) the inclusion of dispersion interactions, accomplished using the DFT-D3 correction scheme, allows for the correct ordering and an improved calculation of the energy differences between polymorphic phases. The energetic correction provided is of the same order of magnitude as the energy difference between phases. D3-corrected hybrid functionals systematically yield results closest to experiment. We propose that the inclusion of dispersion interactions makes a significant contribution to the relative energetics of polymorphic phases, especially those with different densities, and should therefore be included for calculations of relative energies using DFT methods

Gene autoregulation via intronic microRNAs and its functions

Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human diseases. This paper focus on a minimal microRNA-mediated regulatory circuit, in which a protein-coding gene (host gene) is targeted by a microRNA located inside one of its introns. Results: Autoregulation via intronic microRNAs is widespread in the human regulatory network, as confirmed by our bioinformatic analysis, and can perform several regulatory tasks despite its simple topology. Our analysis, based on analytical calculations and simulations, indicates that this circuitry alters the dynamics of the host gene expression, can induce complex responses implementing adaptation and Weber's law, and efficiently filters fluctuations propagating from the upstream network to the host gene. A fine-tuning of the circuit parameters can optimize each of these functions. Interestingly, they are all related to gene expression homeostasis, in agreement with the increasing evidence suggesting a role of microRNA regulation in conferring robustness to biological processes. In addition to model analysis, we present a list of bioinformatically predicted candidate circuits in human for future experimental tests. Conclusions: The results presented here suggest a potentially relevant functional role for negative self-regulation via intronic microRNAs, in particular as a homeostatic control mechanism of gene expression. Moreover, the map of circuit functions in terms of experimentally measurable parameters, resulting from our analysis, can be a useful guideline for possible applications in synthetic biology.Comment: 29 pages and 7 figures in the main text, 18 pages of Supporting Informatio

Thermodynamics and defect chemistry of substitutional and interstitial cation doping in layered α-V2O5

A systematic study of the location and energetics of cation dopants in α-V2O5 has been conducted using pair-potential methods, supplemented by first-principles calculations. The consequences of doping on intrinsic defect equilibria have been discussed and the effects of selected dopants on Li+ and Mg2+ diffusion energy barriers have been investigated

Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail.Comment: 51 pages, 5 figures, 4 tables. Supporting information included. Accepted for publication in Molecular BioSystem

Em busca do sagrado. O ritual da criação poética em “Cara-de-Bronze”

ENThe present reflection, that takes JoãoGuimarães Rosa’s narrative “Cara-de-Bronze” as its corpus, exposes the issue of transforming the symbolic Middle Age into a literary mythic Outback, whose discursive articulation, understood as a symbolic level, describes the search of sacred as the poetic creation’s ritual. When this creation is built in two possible levels of fiction, it generates a mythic-symbolic scene, whose structure is presented in the text as the ritual of going back to sacred origins, which is an endless ritual. Such an aspect can be situated in both human and discursive instances. Keywords: Culture. Guimarães Rosa. Symbolic level. Poetry.PTEsta reflexão, que toma como corpusa narrativa “Cara-de-Bronze, de João Guimarães Rosa, evidencia a questão da transubstanciação da Idade Média simbólica em Sertão mítico literário, cuja articulação discursiva, entendida como plano simbólico, delineia a busca do sagrado como ritual de criação poética. Tal criação, ao se edificar em dois níveis ficcionais possíveis, deflagra uma encenação mítico-simbólica, cuja estrutura inscreve o ritual de eterno retorno às origens sagradas, seja na instância do humano, seja na do discurso.Palavras-chave: Cultura. Guimarães Rosa. Plano simbólico. Poesia

Identification of new pillared-layered carbon nitride materials at high pressure

The compression of the layered carbon nitride C6N9H3·HCl was studied experimentally and with density functional theory (DFT) methods. This material has a polytriazine imide structure with Cl(-) ions contained within C12N12 voids in the layers. The data indicate the onset of layer buckling accompanied by movement of the Cl(-) ions out of the planes beginning above 10-20 GPa followed by an abrupt change in the diffraction pattern and c axis spacing associated with formation of a new interlayer bonded phase. The transition pressure is calculated to be 47 GPa for the ideal structures. The new material has mixed sp(2)-sp(3) hybridization among the C and N atoms and it provides the first example of a pillared-layered carbon nitride material that combines the functional properties of the graphitic-like form with improved mechanical strength. Similar behavior is predicted to occur for Cl-free structures at lower pressures

Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis

Background: Common fragile sites (cfs) are specific regions in the human genome that are particularly prone to genomic instability under conditions of replicative stress. Several investigations support the view that common fragile sites play a role in carcinogenesis. We discuss a genome-wide approach based on graph theory and Gene Ontology vocabulary for the functional characterization of common fragile sites and for the identification of genes that contribute to tumour cell biology. Results: Common fragile sites were assembled in a network based on a simple measure of correlation among common fragile site patterns of expression. By applying robust measurements to capture in quantitative terms the non triviality of the network, we identified several topological features clearly indicating departure from the Erdos-Renyi random graph model. The most important outcome was the presence of an unexpected large connected component far below the percolation threshold. Most of the best characterized common fragile sites belonged to this connected component. By filtering this connected component with Gene Ontology, statistically significant shared functional features were detected. Common fragile sites were found to be enriched for genes associated to the immune response and to mechanisms involved in tumour progression such as extracellular space remodeling and angiogenesis. Moreover we showed how the internal organization of the graph in communities and even in very simple subgraphs can be a starting point for the identification of new factors of instability at common fragile sites. Conclusion: We developed a computational method addressing the fundamental issue of studying the functional content of common fragile sites. Our analysis integrated two different approaches. First, data on common fragile site expression were analyzed in a complex networks framework. Second, outcomes of the network statistical description served as sources for the functional annotation of genes at common fragile sites by means of the Gene Ontology vocabulary. Our results support the hypothesis that fragile sites serve a function; we propose that fragility is linked to a coordinated regulation of fragile genes expression

Identification of new pillared-layered carbon nitride materials at high pressure

The compression of the layered carbon nitride C6N9H3·HCl was studied experimentally and with density functional theory (DFT) methods. This material has a polytriazine imide structure with Cl− ions contained within C12N12 voids in the layers. The data indicate the onset of layer buckling accompanied by movement of the Cl− ions out of the planes beginning above 10–20 GPa followed by an abrupt change in the diffraction pattern and c axis spacing associated with formation of a new interlayer bonded phase. The transition pressure is calculated to be 47 GPa for the ideal structures. The new material has mixed sp2–sp3 hybridization among the C and N atoms and it provides the first example of a pillared-layered carbon nitride material that combines the functional properties of the graphitic-like form with improved mechanical strength. Similar behavior is predicted to occur for Cl-free structures at lower pressures

Mg²⁺ storage and mobility in anatase TiO₂: the role of frustrated coordination

Anatase TiO₂ is a candidate high-power electrode material in Li-ion and Na-ion batteries and has been explored as a Mg battery cathode material, although Mg capacity in undoped anatase is limited. Here we use hybrid-exchange density functional theory calculations to investigate the underlying factors affecting Mg intercalation and mobility in anatase. We find that at the dilute limit, Mg ions have 5-fold coordinated insertion sites, and activation barriers for migration are a surprisingly low 537 meV. As the concentration of Mg inserted into the structure is increased, a cooperative distortion of the lattice occurs, contracting the c lattice parameter. The distortion results in stable orderings of Mg ions in sites which are 6-fold coordinated, but also results in migration barriers that exceed 1500 meV in Mg₀.₅ TiO₂ due to a collective relaxation of the host lattice. The total increase in barrier is predominantly a result of the stabilisation of the insertion sites, as opposed to a destabilisation of the activated sites along the migration pathway. The insertion sites in the dilute limit can be described as frustrated, and it is this unfavourable insertion geometry under dilute conditions that allows the Mg ions to migrate with low activation barriers. The limited performance for Mg²⁺ storage can therefore be attributed to the loss of frustrated coordination at high Mg concentration, which restricts Mg mobility and therefore capacity. Strategies to enhance the capacity of Mg in anatase should therefore aim to inhibit the c lattice parameter contraction or otherwise destabilise stable orderings of Mg in Mg₀.₅ TiO₂ to retain the frustrated coordination of Mg ions at high Mg concentrations