Density Functional Studies on Layered Perovskite Oxyhalide Bi₄MO₈X Photocatalysts (M = Nb and Ta, X = Cl, Br, and I)

Layered perovskite oxyhalides Bi₄MO₈X (M = Nb and Ta, X = Cl, Br, and I) have recently emerged as suitable photocatalysts for the photocatalytic water splitting reaction and degradation of organics. Here, we present a comparative study on the crystal structure, electronic structure, water adsorption, and oxygen evolution reaction of these systems. The calculated band gaps using hybrid density functional method HSE06 are smaller than 2.75 eV and increase with the increase of X atomic number, which is in excellent agreement with experimental data. All Bi₄MO₈X systems possess indirect band gaps, which benefits the separation of photogenerated electron–hole pairs. The density of states reveals that, for all the Bi₄MO₈X cases, the valence band maximum is mostly composed of O 2p states rather than X np states, which can explain the observed stability of these materials against photocorrosion. It is found that the molecular adsorption of water is energetically favorable on Bi₄MO₈X­(001) surfaces. As a result, the computed free energy changes for every step in the oxygen evolution reaction show that the rate-determining step is the first step of generating OH* species for all the cases. The computed overpotentials (0.69–0.77 V) of Bi₄MO₈X for the oxygen evolution reaction are comparable to and even lower than those of widely used photocatalysts for water oxidation, such as TiO₂, WO₃, BiVO₄, and α-Fe₂O₃. The calculations suggest that Bi₄MO₈X (M = Ta and Nb, X = Cl, Br, and I) are potential photocatalysts for overall water splitting in the visible light region, and we hope that the results reported in this work will stimulate experimental tests of our predictions

EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species-0

<p><b>Copyright information:</b></p><p>Taken from "EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species"</p><p>http://www.biomedcentral.com/1471-2164/8/246</p><p>BMC Genomics 2007;8():246-246.</p><p>Published online 24 Jul 2007</p><p>PMCID:PMC1940007.</p><p></p>ression change show a common trend during the six time points of the experiment. Figure 1b and 1c show analysis results of the case study in text and graphical forms

EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species-1

<p><b>Copyright information:</b></p><p>Taken from "EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species"</p><p>http://www.biomedcentral.com/1471-2164/8/246</p><p>BMC Genomics 2007;8():246-246.</p><p>Published online 24 Jul 2007</p><p>PMCID:PMC1940007.</p><p></p>ression change show a common trend during the six time points of the experiment. Figure 1b and 1c show analysis results of the case study in text and graphical forms

Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping

<div><p>Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.</p></div

Monitoring fractional nonconformance for short-run production

<p>Quality characteristics observed in industrial processes are not always free from measurement errors. The term <i>fractional nonconformance</i> refers to the probability of an error-prone observation breaching the specification limits. Four new control statistics based on the fractional nonconformance concept are defined for process monitoring purposes. This work, motivated by milk products manufacturing, is tailored for short-run productions in which only individual measurements are accumulated over time. The performance of the newly defined control statistics is evaluated using simulation for both independent and autocorrelated processes. The results show that fractional nonconformance charts can be useful to monitor short-run production process, and the choice of the monitoring scheme does not heavily depend on the distribution of the quality characteristics.</p

Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data

<p>Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.</p

Theoretical Study of Structure, Stability, and the Hydrolysis Reactions of Small Iridium Oxide Nanoclusters

The geometric structures and relative stabilities of small iridium oxide nanoclusters, Ir_<i>m</i>O_<i>n</i> (<i>m</i> = 1–5 and <i>n</i> = 1–2<i>m</i>), have been systematically investigated using density functional theory (DFT) calculations at the B3LYP level. Our results show that the lowest-energy structures of these clusters can be obtained by the sequential oxidation of small “core” iridium clusters. The iridium-monoxide-like clusters have relatively higher stability because of their relatively high binding energy and second difference in energies. On the basis of the optimized lowest-energy structures of neutral and cationic (IrO₂)_<i>n</i> (<i>n</i> = 1–5), DFT has been used to study the hydrolysis reaction of these clusters with water molecules. The calculated results show that the addition of water molecules to the cationic species is much easier than the neutral ones. The overall hydrolysis reaction energies are more exothermic for the cationic clusters than for the neutral clusters. Our calculations indicate that H₂O can be more easily split on the cationic iridium oxide clusters than on the neutral clusters

Comparison between <i>τ</i>_<i>life</i>, <i>τ</i> and <i>τ</i>_<i>eq</i>.

<p>The blue symbols (squares for the ones with error bar, stars for the ones without error bar) denote the estimated <i>τ</i>_<i>life</i> of the metastable states. The green crosses denote the identified timescale of the states. The red diamonds denote the estimated <i>τ</i>_<i>eq</i>. The error bars are estimated where possible. The dotted lines are just for aiding the inspection.</p

Deletion of the <i>trx2</i>⁺ gene enhanced Rst2 transcriptional activity.

<p>(A) The Δ<i>trx1</i> and Δ<i>trx2</i> cells showed H₂O₂-sensitive phenotype. Wild-type, Δ<i>trx1</i> and Δ<i>trx2</i> cells were streaked onto YES plates with or without 3 mM H₂O₂, and cultured at 30°C for 3 days. (B) Deletion of the <i>trx2</i>⁺ gene enhanced Rst2 transcriptional activity. Wild-type and Δ<i>trx2</i> cells harboring the reporter plasmid were cultured and assayed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078012#pone-0078012-g001" target="_blank">Figure 1A</a>. (C and D) Deletion of the <i>trx2</i>⁺ gene specifically enhanced Rst2 transcriptional activity. Wild-type, Δ<i>trx2</i>, Δ<i>tpx1</i> and Δ<i>pap1</i> cells harboring the reporter plasmid were cultured and assayed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078012#pone-0078012-g001" target="_blank">Figure 1A</a>. Error bars, mean ± S.D. (n ≥ 3).</p

Imaging Metastable States and Transitions in Proteins by Trajectory Map

It has been a long-standing and intriguing issue to develop robust methods to identify metastable states and interstate transitions from simulations or experimental data to understand the functional conformational changes of proteins. It is usually hard to define the complicated boundaries of the states in the conformational space using most of the existing methods, and they often lead to parameter-sensitive results. Here, we present a new approach, visualized Trajectory Map (vTM), to identify the metastable states and the rare interstate transitions, by considering both the conformational similarity and the temporal successiveness of conformations. The vTM is able to give a nonambiguous description of slow dynamics. The case study of a β-hairpin peptide shows that the vTM can reveal the states and transitions from all-atom MD trajectory data even when a single observable (i.e, one-dimensional reaction coordinate) is used. We also use the vTM to refine the folding/unfolding mechanism of HP35 in explicit water by analyzing a 125 μs all-atom MD trajectory and obtain folding/unfolding rates of about 1/μs, which are in good agreement with the experimental values