FDserver: A web service for protein folding research

*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.
*Availability:* http://sdbi.sdut.edu.cn/FDserve

On the cyclic bending behaviour of a hard coating on a ductile substrate with periodic surface hardened regions

AbstractA cyclic bending experiment is designed to investigate the interface fracture behaviour of a hard chromium coating on a ductile substrate with periodic surface hardened regions. The unique deflection pattern of the vertical cracks after they run through the coating and impinge at the interface is revealed experimentally. A simple double-layer elastic beam model is adopted to investigate the interfacial shear stresses analytically. A FE model is employed to compute the stresses of the tri-phase structure under a single round of bending, and to investigate the effect of the loading conditions on the deflection pattern of the vertical cracks at the interface

Probing Transverse Momentum Broadening via Dihadron and Hadron-jet Angular Correlations in Relativistic Heavy-ion Collisions

Dijet, dihadron, hadron-jet angular correlations have been reckoned as important probes of the transverse momentum broadening effects in relativistic nuclear collisions. When a pair of high-energy jets created in hard collisions traverse the quark-gluon plasma produced in heavy-ion collisions, they become de-correlated due to the vacuum soft gluon radiation associated with the Sudakov logarithms and the medium-induced transverse momentum broadening. For the first time, we employ the systematical resummation formalism and establish a baseline calculation to describe the dihadron and hadron-jet angular correlation data in $pp$ and peripheral $AA$ collisions where the medium effect is negligible. We demonstrate that the medium-induced broadening $\langle p_\perp^2\rangle$ and the so-called jet quenching parameter $\hat q$ can be extracted from the angular de-correlations observed in $AA$ collisions. A global $\chi^2$ analysis of dihadron and hadron-jet angular correlation data renders the best fit $\langle p_\perp^2 \rangle \sim 13~\textrm{GeV}^2$ for a quark jet at RHIC top energy. Further experimental and theoretical efforts along the direction of this work shall significantly advance the quantitative understanding of transverse momentum broadening and help us acquire unprecedented knowledge of jet quenching parameter in relativistic heavy-ion collisions.Comment: 6 pages, 3 figure

Numerical investigations of flow around subsea covers at high Reynolds numbers

Two-dimensional (2D) numerical simulations of flow over wall-mounted rectangular and trapezoidal ribs subjected to a turbulent boundary layer flow with the normalized boundary layer thickness of δ/D = 0.73,1.96,2.52 (D is the height of the ribs) have been carried out by using the Reynolds-averaged Navier-Stokes (RANS) equations combined with the k – ω SST (Shear Stress Transport) turbulence model. The angles of the two side slopes of trapezoidal rib varies from 0° to 60°. The Reynolds number based on the free-stream velocity U∞ and D are 1 × 106 and 2 × 106. The results obtained from the present numerical simulations are in good agreement with the published experimental data. Furthermore, the effects of the angle of the two side slopes of the trapezoidal ribs, the Reynolds number and the boundary layer thickness on the hydrodynamic quantities are discussed.publishedVersio

Polymer materials for high‐performance triboelectric nanogenerators

As an emerging branch of energy conversion technologies, the triboelectric nanogenerator (TENG) pioneers a brand‐new path to effectively harness varieties of mechanical energies for the purpose of powering and/or sensing. Since its invention in 2012, the TENG has experienced a booming and revolutionary development in every respect, ranging from materials synthesis and modification, architecture design to performance optimization, power management, and application exploration. In comparison to the organic solar cell and organic light‐emitting diodes, TENG is a unique technique that opens the venue of using polymer materials (PMs) for harvesting mechanical energy. So far, by virtue of superior charge transfer and capturing capabilities during friction, various kinds of PMs have been developed and used as triboelectric materials in order to achieve high‐performance TENGs. Here, this work focuses on the utilization and development of PMs for the TENGs technology and first gives a summary of main PMs that are frequently adopted in currently reported energy‐harvesting TENGs. Second, several kinds of PMs used lately in a few novel TENGs for special or specific energy‐harvesting circumstances are introduced and highlighted. Finally, the perspectives on and challenges in developing high‐performance PMs toward TENGs technology are conceived and expected to be instructive to future research

Spatial clustering and common regulatory elements correlate with coordinated gene expression

Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression. In eukaryotic cells, transcriptional activity of a gene is affected by not only transcription factors but also the epigenetic modifications and three-dimensional chromosome structure of the gene. To examine how local gene environment and transcription factor regulation are coupled, we performed a combined analysis of time-course RNA-seq data of TGF-\b{eta} treated MCF10A cells and related epigenomic and Hi-C data. Using Dynamic Regulatory Events Miner (DREM), we clustered differentially expressed genes based on gene expression profiles and associated transcription factors. Genes in each class have similar temporal gene expression patterns and share common transcription factors. Next, we defined a set of linear and radial distribution functions, as used in statistical physics, to measure the distributions of genes within a class both spatially and linearly along the genomic sequence. Remarkably, genes within the same class despite sometimes being separated by tens of million bases (Mb) along genomic sequence show a significantly higher tendency to be spatially close despite sometimes being separated by tens of Mb along the genomic sequence than those belonging to different classes do. Analyses extended to the process of mouse nervous system development arrived at similar conclusions. Future studies will be able to test whether this spatial organization of chromosomes contributes to concerted gene expression.Comment: 30 pages, 9 figures, accepted in PLoS Computational Biolog

Myeloid-Derived Suppressor Cells Impair Alveolar Macrophages through PD-1 Receptor Ligation during Pneumocystis Pneumonia

Myeloid-derived suppressor cells (MDSCs) were recently found to accumulate in the lungs during Pneumocystis pneumonia (PcP). Adoptive transfer of these cells caused lung damage in recipient mice, suggesting that MDSC accumulation is a mechanism of pathogenesis in PcP. In this study, the phagocytic activity of alveolar macrophages (AMs) was found to decrease by 40% when they were incubated with MDSCs from Pneumocystis-infected mice compared to those incubated with Gr-1+ cells from the bone marrow of uninfected mice. The expression of the PU.1 gene in AMs incubated with MDSCs also was decreased. This PU.1 downregulation was due mainly to decreased histone 3 acetylation and increased DNA methylation caused by MDSCs. MDSCs were found to express high levels of PD-L1, and alveolar macrophages (AMs) were found to express high levels of PD-1 during PcP. Furthermore, PD-1 expression in AMs from uninfected mice was increased by 18-fold when they were incubated with MDSCs compared to those incubated with Gr-1+ cells from the bone marrow of uninfected mice. The adverse effects of MDSCs on AMs were diminished when the MDSCs were pretreated with anti-PD-L1 antibody, suggesting that MDSCs disable AMs through PD-1/PD-L1 ligation during PcP