Anisotropic intrinsic lattice thermal conductivity of phosphorene from first principles

Phosphorene, the single layer counterpart of black phosphorus, is a novel two-dimensional semiconductor with high carrier mobility and a large fundamental direct band gap, which has attracted tremendous interest recently. Its potential applications in nano-electronics and thermoelectrics call for a fundamental study of the phonon transport. Here, we calculate the intrinsic lattice thermal conductivity of phosphorene by solving the phonon Boltzmann transport equation (BTE) based on first-principles calculations. The thermal conductivity of phosphorene at $300\,\mathrm{K}$ is $30.15\,\mathrm{Wm^{-1}K^{-1}}$ (zigzag) and $13.65\,\mathrm{Wm^{-1}K^{-1}}$ (armchair), showing an obvious anisotropy along different directions. The calculated thermal conductivity fits perfectly to the inverse relation with temperature when the temperature is higher than Debye temperature ($\Theta_D = 278.66\,\mathrm{K}$). In comparison to graphene, the minor contribution around $5\%$ of the ZA mode is responsible for the low thermal conductivity of phosphorene. In addition, the representative mean free path (MFP), a critical size for phonon transport, is also obtained.Comment: 5 pages and 6 figures, Supplemental Material available as http://www.rsc.org/suppdata/cp/c4/c4cp04858j/c4cp04858j1.pd

General Dynamics of Topology and Traffic on Weighted Technological Networks

For most technical networks, the interplay of dynamics, traffic and topology is assumed crucial to their evolution. In this paper, we propose a traffic-driven evolution model of weighted technological networks. By introducing a general strength-coupling mechanism under which the traffic and topology mutually interact, the model gives power-law distributions of degree, weight and strength, as confirmed in many real networks. Particularly, depending on a parameter W that controls the total weight growth of the system, the nontrivial clustering coefficient C, degree assortativity coefficient r and degree-strength correlation are all in consistence with empirical evidences.Comment: 4 pages, 4 figure

Diverse anisotropy of phonon transport in two-dimensional IV-VI compounds: A comparative study

New classes two-dimensional (2D) materials beyond graphene, including layered and non-layered, and their heterostructures, are currently attracting increasing interest due to their promising applications in nanoelectronics, optoelectronics and clean energy, where thermal transport property is one of the fundamental physical parameters. In this paper, we systematically investigated the phonon transport properties of 2D orthorhombic group IV-VI compounds of $GeS$, $GeSe$, $SnS$ and $SnSe$ by solving the Boltzmann transport equation (BTE) based on first-principles calculations. Despite the similar puckered (hinge-like) structure along the armchair direction as phosphorene, the four monolayer compounds possess diverse anisotropic properties in many aspects, such as phonon group velocity, Young's modulus and lattice thermal conductivity ($\kappa$), etc. Especially, the $\kappa$ along the zigzag and armchair directions of monolayer $GeS$ shows the strongest anisotropy while monolayer $SnS$ and $SnSe$ shows an almost isotropy in phonon transport. The origin of the diverse anisotropy is fully studied and the underlying mechanism is discussed in detail. With limited size, the $\kappa$ could be effectively lowered, and the anisotropy could be effectively modulated by nanostructuring, which would extend the applications in nanoscale thermoelectrics and thermal management. Our study offers fundamental understanding of the anisotropic phonon transport properties of 2D materials, and would be of significance for further study, modulation and aplications in emerging technologies.Comment: 14 pages, 8 figures, 2 table

Genome reannotation of Escherichia coli CFT073 with new insights into virulence

BACKGROUND: As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome. RESULTS: The reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI) regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs). Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs), which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs) process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via http://mech.ctb.pku.edu.cn/CFT073/. CONCLUSION: As a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073. The new genes change the view of its uropathogenicity in many respects, particularly by new genes in GI regions and new virulence-associated factors. The reannotation thus functions as an important source by providing new information about genomic structure and organization, and gene function. Moreover, we expect that the detailed analysis will facilitate the studies for exploration of novel virulence mechanisms and help guide experimental design

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

BACKGROUND: Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. RESULTS: This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). The former is based on a linguistic "Entropy Density Profile" (EDP) model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED) algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. CONCLUSION: Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation

Computational evaluation of TIS annotation for prokaryotic genomes

<p>Abstract</p> <p>Background</p> <p>Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks.</p> <p>Results</p> <p>Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment of the reliability of TIS annotations for any prokaryotic genome. The method consists of modeling a positional weight matrix (PWM) of aligned sequences around predicted TISs in terms of a linear combination of three elementary PWMs, one for true TIS and the two others for false TISs. The three elementary PWMs are obtained using a reference set with highly reliable TIS predictions. A generalized least square estimator determines the weighting of the true TIS in the observed PWM, from which the accuracy of the prediction is derived. The validity of the method and the extent of the limitation of the assumptions are explicitly addressed by testing on experimentally verified TISs with variable accuracy of the reference sets. The method is applied to estimate the accuracy of TIS annotations that are provided on public databases such as RefSeq and ProTISA and by programs such as EasyGene, GeneMarkS, Glimmer 3 and TiCo. It is shown that RefSeq's TIS prediction is significantly less accurate than two recent predictors, Tico and ProTISA. With convincing proofs, we show two general preferential biases in the RefSeq annotation, <it>i.e</it>. over-annotating the longest open reading frame (LORF) and under-annotating ATG start codon. Finally, we have established a new TIS database, SupTISA, based on the best prediction of all the predictors; SupTISA has achieved an average accuracy of 92% over all 532 complete genomes.</p> <p>Conclusion</p> <p>Large-scale computational evaluation of TIS annotation has been achieved. A new TIS database much better than RefSeq has been constructed, and it provides a valuable resource for further TIS studies.</p

catena-Poly[diammonium [diaqua­bis(pyridine-2,4-dicarboxyl­ato-κ2 N,O 2)cuprate(II)] [[diaqua­copper(II)]-μ-pyridine-2,4-dicarboxyl­ato-κ3 N,O 2:O 2′-[tetra­aqua­cadmium(II)]-μ-pyridine-2,4-dicarboxyl­ato-κ3 O 2:N,O 2′] hexa­hydrate]

The title mixed-metal complex, {(NH4)2[Cu(C7H3NO4)2(H2O)2][CdCu(C7H3NO4)2(H2O)6]·6H2O}n, contains one octa­hedrally coordinated CdII center and two octa­hedrally coordinated CuII centers, each lying on an inversion center. The two CuII atoms are each coordinated by two O atoms and two N atoms from two 2,4-pydc (2,4-H2pydc = pyridine-2,4-dicarboxylic acid) ligands in the equatorial plane and two water mol­ecules at the axial sites, thus producing two crystallographically independent [Cu(2,4-pydc)2(H2O)2]2− metalloligands. One metalloligand exists as a discrete anion and the other connects the Cd(H2O)4 units, forming a neutral chain. O—H⋯O and N—H⋯O hydrogen bonds connects the polymeric chains, complex anions, ammonium cations and uncoordinated water mol­ecules into a three-dimensional supra­molecular network

HCN2 channels in the ventral tegmental area regulate behavioral responses to chronic stress

Dopamine neurons in the ventral tegmental area (VTA) are powerful regulators of depression-related behavior. Dopamine neuron activity is altered in chronic stress-based models of depression, but the underlying mechanisms remain incompletely understood. Here, we show that mice subject to chronic mild unpredictable stress (CMS) exhibit anxiety- and depressive-like behavior, which was associated with decreased VTA dopamine neuron firing in vivo and ex vivo. Dopamine neuron firing is governed by voltage-gated ion channels, in particular hyperpolarization- activated cyclic nucleotide-gated (HCN) channels. Following CMS, HCN-mediated currents were decreased in nucleus accumbens-projecting VTA dopamine neurons. Furthermore, shRNA-mediated HCN2 knockdown in the VTA was sufficient to recapitulate CMS-induced depressive- and anxiety- like behavior in stress-naı ̈ve mice, whereas VTA HCN2 overexpression largely prevented CMS- induced behavioral deficits. Together, these results reveal a critical role for HCN2 in regulating VTA dopamine neuronal activity and depressive-related behaviors