203 research outputs found
Spin states of zigzag-edged Mobius graphene nanoribbons from first principles
Mobius graphene nanoribbons have only one edge topologically. How the
magnetic structures, previously associated with the two edges of zigzag-edged
flat nanoribbons or cyclic nanorings, would change for their Mobius
counterparts is an intriguing question. Using spin-polarized density functional
theory, we shed light on this question. We examine spin states of zigzag-edged
Mobius graphene nanoribbons (ZMGNRs) with different widths and lengths. We find
a triplet ground state for a Mobius cyclacene, while the corresponding
two-edged cyclacene has an open-shell singlet ground state. For wider ZMGNRs,
the total magnetization of the ground state is found to increase with the
ribbon length. For example, a quintet ground state is found for a ZMGNR. Local
magnetic moments on the edge carbon atoms form domains of majority and minor
spins along the edge. Spins at the domain boundaries are found to be
frustrated. Our findings show that the Mobius topology (i.e., only one edge)
causes ZMGNRs to favor one spin over the other, leading to a ground state with
non-zero total magnetization.Comment: 17 pages, 4 figure
Entanglement Measures for Single- and Multi-Reference Correlation Effects
Electron correlation effects are essential for an accurate ab initio
description of molecules. A quantitative a priori knowledge of the single- or
multi-reference nature of electronic structures as well as of the dominant
contributions to the correlation energy can facilitate the decision regarding
the optimum quantum chemical method of choice. We propose concepts from quantum
information theory as orbital entanglement measures that allow us to evaluate
the single- and multi-reference character of any molecular structure in a given
orbital basis set. By studying these measures we can detect possible artifacts
of small active spaces.Comment: 14 pages, 4 figure
Anomalous Optoelectronic Properties of Chiral Carbon Nanorings...and One Ring to Rule Them All
Carbon nanorings are hoop-shaped, {\pi}-conjugated macrocycles which form the
fundamental annular segments of single-walled carbon nanotubes (SWNTs). In a
very recent report, the structures of chiral carbon nanorings (which may serve
as chemical templates for synthesizing chiral nanotubes) were experimentally
synthesized and characterized for the first time. Here, in our communication,
we show that the excited-state properties of these unique chiral nanorings
exhibit anomalous and extremely interesting optoelectronic properties, with
excitation energies growing larger as a function of size (in contradiction with
typical quantum confinement effects). While the first electronic excitation in
armchair nanorings is forbidden with a weak oscillator strength, we find that
the same excitation in chiral nanorings is allowed due to a strong geometric
symmetry breaking. Most importantly, among all the possible nanorings
synthesized in this fashion, we show that only one ring, corresponding to a
SWNT with chiral indices (n+3,n+1), is extremely special with large
photoinduced transitions that are most readily observable in spectroscopic
experiments.Comment: Accepted by the Journal of Physical Chemistry Letter
Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of Staphylococcus aureus
Background: Daptomycin remains one of our last-line anti-staphylococcal agents. This study aims to characterize the genetic evolution to daptomycin resistance in S. aureus. Methods: Whole genome sequencing was performed on a unique collection of isogenic, clinical (21 strains) and laboratory (12 strains) derived strains that had been exposed to daptomycin and developed daptomycin-nonsusceptibility. Electron microscopy (EM) and lipid membrane studies were performed on selected isolates. Results: On average, six coding region mutations were observed across the genome in the clinical daptomycin exposed strains, whereas only two mutations on average were seen in the laboratory exposed pairs. All daptomycin-nonsusceptible strains had a mutation in a phospholipid biosynthesis gene. This included mutations in the previously described mprF gene, but also in other phospholipid biosynthesis genes, including cardiolipin synthase (cls2) and CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (pgsA). EM and lipid membrane composition analyses on two clinical pairs showed that the daptomycin-nonsusceptible strains had a thicker cell wall and an increase in membrane lysyl-phosphatidylglycerol. Conclusion: Point mutations in genes coding for membrane phospholipids are associated with the development of reduced susceptibility to daptomycin in S. aureus. Mutations in cls2 and pgsA appear to be new genetic mechanisms affecting daptomycin susceptibility in S. aureus
Photoinduced Structural Phase Transitions in Polyacene
There exist two types of structural instability in polyacene: double bonds in
a cis pattern and those in a trans pattern. They are isoenergetic but
spectroscopically distinct. We demonstrate optical characterization and
manipulation of Peierls-distorted polyacene employing both correlated and
uncorrelated Hamiltonians. We clarify the phase boundaries of the cis- and
trans-distorted isomers, elucidate their optical-conductivity spectra, and then
explore their photoresponses. There occurs a photoinduced transformation in the
polyacene structure, but it is one-way switching: The trans configuration is
well convertible into the cis one, whereas the reverse conversion is much less
feasible. Even the weakest light irradiation can cause a transition of
uncorrelated electrons, while correlated electrons have a transition threshold
against light irradiation.Comment: 14 pages with 15 figures embedde
Estimatation of evapotranspiration and crop coefficient of melon cultivated in protected environment
The power of the Mediator complex-Expanding the genetic architecture and phenotypic spectrum of MED12 -related disorders
MED12 is a member of the large Mediator complex that controls cell growth, development, and differentiation. Mutations in MED12 disrupt neuronal gene expression and lead to at least three distinct X-linked intellectual disability (XLID) syndromes (FG, Lujan-Fryns, and Ohdo). Here we describe six families with missense variants in MED12 (p.(Arg815Gln), p.(Val954Gly), p.(Glu1091Lys),p.(Arg1295Cys), p.(Pro1371Ser) and p.(Arg1148His), the latter being firstly reported in affected females) associated with a continuum of symptoms rather than distinct syndromes. The variants expanded the genetic architecture and phenotypic
spectrum of MED12-related disorders. New clinical symptoms included brachycephaly, anteverted nares, bulbous nasal tip, prognathism, deep set eyes, and single palmar crease. We
showed that MED12 variants, initially implicated in X-linked recessive disorders in males, may predict a potential risk for phenotypic expression in females, with no correlation of the X chromosome inactivation pattern in blood cells. Molecular modeling (Yasara Structure) performed to model the functional effects of the variants strongly supported the pathogenic character of the variants examined. We demonstrated that molecular modeling is a useful method for in silico testing of potential functional effects of MED12 variants and thus can be a valuable addition to the interpretation of the clinical and genetic findings
Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli
Although co-translational biological processes attract much attention, no general and easy method has been available to detect cellular nascent polypeptide chains, which we propose to call collectively a “nascentome.” We developed a method to selectively detect polypeptide portions of cellular polypeptidyl-tRNAs and used it to study the generality of the quality control reactions that rescue dead-end translation complexes. To detect nascent polypeptides, having their growing ends covalently attached to a tRNA, cellular extracts are separated by SDS-PAGE in two dimensions, first with the peptidyl-tRNA ester bonds preserved and subsequently after their in-gel cleavage. Pulse-labeled nascent polypeptides of Escherichia coli form a characteristic line below the main diagonal line, because each of them had contained a tRNA of nearly uniform size in the first-dimension electrophoresis but not in the second-dimension. The detection of nascent polypeptides, separately from any translation-completed polypeptides or degradation products thereof, allows us to follow their fates to gain deeper insights into protein biogenesis and quality control pathways. It was revealed that polypeptidyl-tRNAs were significantly stabilized in E. coli upon dysfunction of the tmRNA-ArfA ribosome-rescuing system, whose function had only been studied previously using model constructs. Our results suggest that E. coli cells are intrinsically producing aberrant translation products, which are normally eliminated by the ribosome-rescuing mechanisms
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