Artefacts in geometric phase analysis of compound materials

The geometric phase analysis (GPA) algorithm is known as a robust and straightforward technique that can be used to measure lattice strains in high resolution transmission electron microscope (TEM) images. It is also attractive for analysis of aberration-corrected scanning TEM (ac-STEM) images that resolve every atom column, since it uses Fourier transforms and does not require real-space peak detection and assignment to appropriate sublattices. Here it is demonstrated that in ac-STEM images of compound materials (i.e. with more than one atom per unit cell) an additional phase is present in the Fourier transform. If the structure changes from one area to another in the image (e.g. across an interface), the change in this additional phase will appear as a strain in conventional GPA, even if there is no lattice strain. Strategies to avoid this pitfall are outlined.Comment: 9 pages, 7 figures, Preprint before review, submitted to Ultramicroscopy 7 April 201

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

<p>Abstract</p> <p>Background</p> <p>Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom) pairs in the non-interaction state.</p> <p>Results</p> <p>The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK) potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the D<smcaps>OCKGROUND</smcaps> resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results.</p> <p>Conclusions</p> <p>A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of the potentials.</p

On-surface synthesis of graphene nanoribbons with zigzag edge topology

Graphene-based nanostructures exhibit a vast range of exciting electronic properties that are absent in extended graphene. For example, quantum confinement in carbon nanotubes and armchair graphene nanoribbons (AGNRs) leads to the opening of substantial electronic band gaps that are directly linked to their structural boundary conditions. Even more intriguing are nanostructures with zigzag edges, which are expected to host spin-polarized electronic edge states and can thus serve as key elements for graphene-based spintronics. The most prominent example is zigzag graphene nanoribbons (ZGNRs) for which the edge states are predicted to couple ferromagnetically along the edge and antiferromagnetically between them. So far, a direct observation of the spin-polarized edge states for specifically designed and controlled zigzag edge topologies has not been achieved. This is mainly due to the limited precision of current top-down approaches, which results in poorly defined edge structures. Bottom-up fabrication approaches, on the other hand, were so far only successfully applied to the growth of AGNRs and related structures. Here, we describe the successful bottom-up synthesis of ZGNRs, which are fabricated by the surface-assisted colligation and cyclodehydrogenation of specifically designed precursor monomers including carbon groups that yield atomically precise zigzag edges. Using scanning tunnelling spectroscopy we prove the existence of edge-localized states with large energy splittings. We expect that the availability of ZGNRs will finally allow the characterization of their predicted spin-related properties such as spin confinement and filtering, and ultimately add the spin degree of freedom to graphene-based circuitry.Comment: 15 pages, 4 figure

Controlled Release from Cleavable Polymerized Liposomes upon Redox and pH Stimulation

A gallate derivative with three propargyl groups was coupled to palmitoyl oleoyl phosphoethanolamine (POPE). The resulting anionic lipid was formulated with common lipids such as palmitoyl oleoyl phosphatidyl choline (POPC) to form large unilamellar vesicles (LUVs). Polymerization of the LUVs was accomplished by the Cu(I)-catalyzed click reaction between the propargyl groups and the azide groups in the cross-linker. When the cross-linker contained a disulfide or ketal group, the resulting polymerized liposomes depolymerized and released entrapped contents upon the addition of a reducing thiol or under weakly acidic conditions. The click reaction allowed simultaneous multivalent surface functionalization during cross-linking, making these cleavable polymerized liposomes (CPLs) potentially very useful in the delivery and controlled release of pharmaceutical agents

Facile Preparation of Organic Nanoparticles by Interfacial Cross-Linking of Reverse Micelles and Template Synthesis of Subnanometer Au−Pt Nanoparticles

A single- and a double-tailed cationic surfactant with the triallylammonium headgroup formed reverse micelles (RMs) in heptane/chloroform containing a small amount of water. The reverse micelles were cross-linked at the interface upon UV irradiation in the presence of a water-soluble dithiol cross-linker and a photoinitiator. The resulting interfacially cross-linked reverse micelles (ICRMs) of the single-tailed surfactant aggregated in a solvent-dependent fashion, whereas those of the double-tailed were identical in size as the corresponding RMs. The ICRMs could extract anionic metal salts, such as AuCl4− and PtCl62−, from water into the organic phase. Au and Pt metal nanoparticles were produced upon reduction of metal salts. The covalent nature of the ICRMs made the template synthesis highly predictable, with the size of the metal particles controlled by the amount of the metal salt and the method of reduction. Nanoalloys were obtained by combining two metal precursors in the same reaction. Reduction of the ICRM-entrapped aurate also occurred without any external reducing agents, and the gold nanoparticles differed dramatically from those obtained through sodium borohydride reduction. The same template allowed the preparation of luminescent Au4, Au8, and Au13−Au23 clusters, as well as gold nanoparticles several nanometers in size, simply by using different amounts of gold precursor and reducing conditions

Characterization and modelling the mechanical behaviour of poly (l-lactic acid) for the manufacture of bioresorbable vascular scaffolds by stretch blow moulding

Bioresorbable Vascular Scaffolds (BVS) manufactured from poly (l-lactic acid) (PLLA) offer an alternative to metal scaffolds for the treatment of coronary heart disease. One of the key steps in the manufacture of these scaffolds is the stretch blow moulding process where the PLLA is biaxially stretched above glass transition temperature (Tg), inducing biaxial orientation and thus increasing ductility, strength and stiffness. To optimise the manufacture and performance of these scaffolds it is important to understand the influence of temperature and strain rate on the constitutive behaviour of PLLA in the blow moulding process. Experiments have been performed on samples of PLLA on a custom built biaxial stretch testing machine to replicate conditions typically experienced during blow moulding i.e. in a temperature range from 70 °C to 100 °C and at strain rates of 1 s−1, 4 s−1 and 16 s−1 respectively. The data is subsequently used to calibrate a nonlinear viscoelastic material model to represent the deformation behaviour of PLLA in the blow moulding process. The results highlight the significance of temperature and strain rate on the yielding and strain hardening behaviour of PLLA and the ability of the selected model to capture it