Structural properties of amorphous hydrogenated carbon. IV. A molecular-dynamics investigation and comparison to experiments

Hydrogenated amorphous carbon structures, a-C:H, with densities of 1.8 and 2.0 g/cm3, have been generated by semiempirical density-functions (DF) molecular-dynamics (MD) rapid cooling of a liquid phase of 128 carbon and 64 hydrogen atoms within periodically arranged cubic supercells. The electronic bonding properties of the model structures are analyzed within a local-orbital description. The structural properties are compared to relevant statistical and diffraction data obtained by neutron scattering and NMR in order to achieve a fundamental understanding of structure-related properties on the molecular level of chemical bonding

Exciton tuning in monolayer WSe2_2 via substrate induced electron doping

We report on large exciton tuning in WSe$_2$ monolayers via substrate induced non-degenerate doping. We observe a redshift of $\sim$62 meV for the $A$ exciton together with a 1-2 orders of magnitude photoluminescence (PL) quenching when the monolayer WSe$_2$ is brought in contact with highly oriented pyrolytic graphite (HOPG) compared to the dielectric substrates such as hBN and SiO$_2$. As the evidence of doping from HOPG to WSe$_2$, a drastic increase of the trion emission intensity was observed. Using a systematic PL and Kelvin probe force microscopy (KPFM) investigation on WSe$_2$/HOPG, WSe$_2$/hBN, and WSe$_2$/graphene, we conclude that this unique excitonic behavior is induced by electron doping from the substrate. Our results propose a simple yet efficient way for exciton tuning in monolayer WSe$_2$, which plays a central role in the fundamental understanding and further device development.Comment: 14 pages, 10 figure

Identification and assignment of porphyrin-CdSe Hetero-nanoassemblies

Hetero-nanoassemblies in toluene solution are formed via anchoring pyridyl substituted free base porphyrin molecules on the colloidal core-shell semiconductor nanocrystals CdSe/ZnS. The formation can be identified via quenching of semiconductor photoluminescence and followed via spectral changes of porphyrin spectral properties such as fluorescence, fluorescence decay and absorption. Interpreting these changes we estimate that even at high molar ratios on average only one molecule is anchored on one nanocrystal. Experimentally determined complexation constants are comparable to those observed for multi-porphyrin complexes. © 2007 Elsevier B.V. All rights reserved

Large scale quantum simulations: C_60 impacts on a semiconducting surface

We present tight binding molecular dynamics simulations of C_60 collisions on the reconstructed diamond(111) surface, carried out with an O(N) method and with cells containing 1140 atoms. The results of our simulations are in very good agreement with experiments performed under the same impact conditions. Furthermore our calculations provide a detailed characterization of the microscopic processes occuring during the collision, and allow the identification of three impact regimes, as a function of the fullerene incident energy. Finally, the study of the reactivity between the cluster and the surface gives insight into the deposition mechanisms of C_60 on semiconducting substrates

Flanking signal and mature peptide residues influence signal peptide cleavage

<p>Abstract</p> <p>Background</p> <p>Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I), and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i) eukaryotes (Euk) (ii) Gram-positive (Gram+) bacteria, and (iii) Gram-negative (Gram-) bacteria.</p> <p>Results</p> <p>In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as p<it>I</it>, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups.</p> <p>Conclusion</p> <p>We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.</p

Transport of Folded Proteins by the Tat System

The twin-arginine protein translocation (Tat) system has been characterized in bacteria, archaea and the chloroplast thylakoidal membrane. This system is distinct from other protein transport systems with respect to two key features. Firstly, it accepts cargo proteins with an N-terminal signal peptide that carries the canonical twin-arginine motif, which is essential for transport. Second, the Tat system only accepts and translocates fully folded cargo proteins across the respective membrane. Here, we review the core essential features of folded protein transport via the bacterial Tat system, using the three-component TatABC system of Escherichia coli and the two-component TatAC systems of Bacillus subtilis as the main examples. In particular, we address features of twin-arginine signal peptides, the essential Tat components and how they assemble into different complexes, mechanistic features and energetics of Tat-dependent protein translocation, cytoplasmic chaperoning of Tat cargo proteins, and the remarkable proofreading capabilities of the Tat system. In doing so, we present the current state of our understanding of Tat-dependent protein translocation across biological membranes, which may serve as a lead for future investigations

Specificity of signal peptide recognition in Tat-dependent bacterial protein translocation

The bacterial twin arginine translocation (Tat) pathway translocates across the cytoplasmic membrane folded proteins which, in most cases, contain a tightly bound cofactor. Specific amino-terminal signal peptides that exhibit a conserved amino acid consensus motif, S/T-R-R-X-F-L-K, direct these proteins to the Tat translocon. The glucose-fructose oxidoreductase (GFOR) of Zymomonas mobilis is a periplasmic enzyme with tightly bound NADP as a cofactor. It is synthesized as a cytoplasmic precursor with an amino-terminal signal peptide that shows all of the characteristics of a typical twin arginine signal peptide. However, GFOR is not exported to the periplasm when expressed in the heterologous host Escherichia coli, and enzymatically active pre-GFOR is found in the cytoplasm. A precise replacement of the pre-GFOR signal peptide by an authentic E. coli Tat signal peptide, which is derived from pre-trimethylamine N-oxide (TMAO) reductase (TorA), allowed export of GFOR, together with its bound cofactor, to the E. coli periplasm. This export was inhibited by carbonyl cyanide m-chlorophenylhydrazone, but not by sodium azide, and was blocked in E. coli tatC and tatAE mutant strains, showing that membrane translocation of the TorA-GFOR fusion protein occurred via the Tat pathway and not via the Sec pathway. Furthermore, tight cofactor binding (and therefore correct folding) was found to be a prerequisite for proper translocation of the fusion protein. These results strongly suggest that Tat signal peptides are not universally recognized by different Tat translocases, implying that the signal peptides of Tat-dependent precursor proteins are optimally adapted only to their cognate export apparatus. Such a situation is in marked contrast to the situation that is known to exist for Sec-dependent protein translocation

Self-assembly of spherical colloidal photonic crystals inside inkjet-printed droplets

The manufacturing of three-dimensional colloidal structures on solid substrates is an important topic of applied research, aiming for photonic components especially in photovoltaic and sensor applications. Whereas conventional techniques such as wet self-assembly are based on engineering of the substrate surface energy, alternative strategies envisage the independence of the interfacial conditions. We report on inkjet printing of colloidal suspensions of monodisperse silica or polystyrene nanoparticles or both and their self-assembly to spherical colloidal photonic crystals. The formation process of the colloidal nanoparticles into stable spherical colloidal assemblies (SCAs) is achieved by a self-assembly process inside tiny droplets of a stochastic mist generated intentionally instead of a jet of individual single droplets using inkjet printing. The mist jetted, shrinking droplets serve as confined geometries for the solidification of the nanoparticles during the evaporation; thus the particles are packed into stable ball-shaped assemblies. We show how fine-tuning of the jetting parameters allows the reliable generation and deposition of three-dimensional (3D) spherical colloidal assemblies of nanoparticles variable in size and with a high packing order. Microreflectance spectroscopy proves that the degree of order in the SCA is such that photonic stop bands occur inherent for photonic crystals