Charge Transfer Excitations with Range Separated Functionals Using Improved Virtual Orbitals

We present an implementation of range separated functionals utilizing the Slater function on grids in real space in the projector augmented waves method. The screened Poisson equation is solved to evaluate the necessary screened exchange integrals on Cartesian grids. The implementation is verified against existing literature and applied to the description of charge transfer excitations. We find very slow convergence for calculations within linear response time-dependent density functional theory and unoccupied orbitals of the canonical Fock operator. Convergence can be severely improved by using Huzinaga’s virtual orbitals instead. This combination furthermore enables an accurate determination of long-range charge transfer excitations by means of ground-state calculations

Conformer Ring Flip Enhances Mechanochromic Performance of <i>ansa</i>-Donor–Acceptor–Donor Mechanochromic Torsional Springs

Mechanochromophores based on conformational changes of donor–acceptor–donor (DAD) springs allow sensing of forces acting on polymer chains by monotonic changes of absorbance or photoluminescence (PL) wavelength. Here, we identify a series of thiophene (D)-flanked quinoxalines (A) as molecular torsional springs for force sensing in bulk polymers at room temperature. The mode of DAD linkage to the polymer matrix and linker rigidity are key parameters that influence the efficacy of force transduction to the DAD spring and thus mechanochromic response, as probed by in situ PL spectroscopy of bulk films during stress–strain experiments. The largest shift of the PL maximum, and thus the highest sensitivity, is obtained from an ansa-DAD spring exhibiting bridged D units and a stiff A linker. Using detailed spectroscopy and density functional theory calculations, we reveal conformer redistribution in the form of a thiophene ring flip as the major part of the overall mechanochromic response. At forces as low as 27 pN at early stages of deformation, the ring flip precedes mechanically induced planarization of the ansa-DAD spring, the latter process producing a PL shift of 21 nm nN–1. Within the stress–strain diagram, the thiophene ring flip and DAD planarization are thus two separated processes that also cause irreversible and reversible mechanochromic responses, respectively, upon sample failure. As the thiophene ring flip requires much smaller forces than planarization of the DAD spring, such micromechanical motion gives access to sensing of tiny forces and expands both sensitivity and the force range of conformational mechanochromophores

1,3-Diketone Fluids and Their Complexes with Iron

Tribological experiments with 1,3-diketone fluids in contact with iron surfaces show ultralow friction, which was suggested to be connected to the formation of iron complexes. In order to support this assumption, we calculate infrared and optical spectra of various substituted 1,3-diketones and their iron complexes using gradient-corrected density functional theory (DFT). The description of the complexes requires the application of the DFT+U scheme for a correct prediction of the high spin state on the central iron atom. With this approach, we obtain excellent agreement between experiment and simulation in infrared and optical spectra, allowing for the determination of 1,3-diketone tautomeric forms. The match in the spectra of the complex strongly supports the assumption of iron complex formation by these lubricants

Ultralow Friction Induced by Tribochemical Reactions: A Novel Mechanism of Lubrication on Steel Surfaces

The tribological properties of two steel surfaces rubbing against each other are measured while they are in contact with 1,3-diketones of varying structure. Such systems show after a short running-in period ultralow friction properties with a coefficient of friction of as low as μ = 0.005. It is suggested that the extremely favorable friction properties are caused by a tribochemical reaction between the 1,3-diketones and the steel surfaces, leading to formation of a chelated iron–diketo complex. The influence of temperature and the molecular structure of the 1,3 diketo-lubricants onto the friction properties of the system is elucidated under both static and dynamic conditions. With progression of the tribochemical reaction, the sliding surfaces become very conformal and smooth, so that the pressure is greatly reduced and further wear is strongly reduced. All iron particles potentially generated by wear during the initial running-in period are completely dissolved through complex formation. It is proposed that the tribochemical polishing reaction causes a transition from boundary lubrication to fluid lubrication

Numbers of reads and identified miRNAs obtained by deep sequencing.

<p>Numbers of unfiltered and filtered reads, percentage of filtered reads and numbers of miRNA reads with indication of percentage as well as numbers of different miRNAs identified are depicted for each sample applied to deep sequencing.</p><p>Numbers of reads and identified miRNAs obtained by deep sequencing.</p

Deregulated miRNAs involved in the immune response in ALK+ALCL.

<p>MiRNAs with known functions in the immune response [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117780#pone.0117780.ref062" target="_blank">62</a>] and deregulated in ALK+ ALCLs in our study are shown (red: downregulated miRNAs in ALK+ ALCL, green: upregulated miRNAs in ALK+ ALCL). The miR-17~92 cluster comprises the 6 miRNAs 17, 18a, 19a, 20a, 19b and 92a. The table shows the deep sequencing results of these miRNAs as base mean values from triplicates. CLP, common lymphocyte progenitor; CMP, common myeloid progenitor; DC, dentritic cell; DP, double positive T cell; DN, double negative T cell; GMP, granulocyte monocytic progenitor; HSC, hematopoietic stem cell; MDP, myeloid dendritic progenitor.</p

Principal Component Analysis.

<p>2D scatter plot shows principal component analysis (PCA) of miRNA deep sequencing data. The two axes represent the first two principal components (PCs) from the principal component analysis. The values in brackets indicate the amount of variation in the data that can be explained by the PC. The percent of variation given by a particular PC is indicated in the axis label. Points are colored by sample type. Samples were analyzed in triplicates. The graph shows a clear separation by principal component 1 between normal T cells (grey) and ALCL cells. The principal component 2 separates ALK+ and ALK- ALCL (light blue).</p

Analysis of C/EBPβ regulated miRNAs.

<p>(<b>A</b>) Western Blot analysis of the C/EBPβ isoforms LAP* and LAP in the transduced SR786 cells three days after infection. Each lane of the Western Blot contains 20 μg protein extract. Tubulin was used as loading control. SR786 = uninfected cells, pRRL = empty virus, pRRL-LAP* = virus containing the C/EBPβ isoform LAP* sequence, pRRL-LAP = virus containing the C/EBPβ isoform LAP sequence. (<b>B</b>) RT-qPCR analysis of miRNAs 146b-5p, 203, 181a* and 181a in untreated, mock-treated and pRRL.PPT.SF.i2GFPp (containing LAP and LAP* isoforms) transduced ALK+ ALCL cell line SR-786. Values were normalized to miR-106b and data were analysed according to the 2^-ΔΔCp method. Results are depicted as miRNA levels relative to untreated SR-786 cells. (<b>C</b>) RT-qPCR analysis of miRNAs 146b-5p, 203, 181a* and 181a in primary ALCL cases (4 ALK+ and 5 ALK- ALCL cases). For RT-qPCR quantification values were normalized to miR-106b and data were analysed according to the 2^-ΔΔCp method. Results are depicted as miRNA levels relative to mean value of ALK+ ALCL levels. For statistical analysis of RT-qPCR results a Wilcoxon rank-sum test was used (*p<0.05).</p

Additional file 1: of Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data

Supplemental material and method. (DOCX 10269 kb

Comparative relative miRNA expression of miRNAs miR-146b-5p, miR-203, miR-181a* and miR-181a after C/EBPβ down-regulation—deep sequencing and RT-qPCR of ALK+ ALCL cell lines.

<p>Quantification of three by C/EBPβ knockdown significantly regulated miRNAs miR-146b-5p (upper panel), miR-203 (second panel), miR-181a* (third panel) and additionally miR-181a (lower panel), in ALK+ ALCL cell lines. (<b>A</b>) Deep sequencing results of ALK+ ALCL cell lines transduced with pF or pF-C/EBPβ shRNA. Results are depicted as base mean values from triplicates. (<b>B</b>) RT-qPCR analysis of miRNAs 146b-5p, 203, 181a* and 181a in pF and pF-C/EBPβ (shaded) transduced ALK+ ALCL cells four days after infection. Values were normalized to RNU6B and data were analysed according to the 2^-ΔΔCp method. Results are depicted as miRNA levels relative to untreated SUDHL-1 cells. Error bars indicate standard deviation of triplicates.</p