Aurein 2.6-COOH and aurein 3.1-COOH were studied along with their naturally occurring C-terminally amidated analogues. Circular dichroism (CD) and molecular dynamic (MD) simulations were used to study the effects of amidation on the interaction of antimicrobial peptides (AMPs) with lipid bilayers. CD measurements and MD analysis suggested that both peptide analogues were predominantly random coil and adopted low levels of -helical structure in solution (<30 %) and in the presence of a lipid bilayer the peptides formed a stable -helical structure. In general, amidated analogues have a greater propensity than the non-amidated peptides to form a -helical structure. MD simulations predicted that aurein 2.6-COOH and aurein 3.1-CHOOH destabilised lipid bilayers from 1,2-dimyristoyl-sn-glycero-3-phosphocholine and 1,2-dimyristoyl-sn-glycero-3-phosphoserine via angled bilayer penetration. They also showed that aurein 2.6-CONH and aurein 3.1-CONH formed a helix horizontal to the plane of an asymmetric interface.Electronic supplementary materialThe online version of this article (doi:10.1007/s00249-015-1094-x) contains supplementary material, which is available to authorized users.

Using cell dynamics simulation we investigate the cubic gyroid morphology of block copolymer melts under simple shear flow and electric field. The electric field should be stronger than a certain critical value to induce transition to a cylindrical phase. In the case of simple steady shear the gyroid-to-cylinder transition was observed even for a very weak shear. Quantitative analysis of pathways of gyroid-to-cylinder transition is performed by means of Minkowski functionals. We found that the kinetics of the gyroid-to-cylinder transition are different under electric field and shear flow. Moreover, the gyroid structure under different strengths of electric field shows different pathways. Different types of intermediates such as five-, four-fold connections and "winding" cylinders are found for different pathways. This journal is © The Royal Society of Chemistry

Using cell dynamics computer simulation, we perform a systematic study of thin block copolymer films around a nanoparticle. Lamellar-, cylinder-, and sphere-forming block copolymers are investigated with respect to different film thicknesses, particle radii, and boundary conditions at the film interfaces. The obtained structures include standing lamellae and cylinders, "onions", cylinder "knitting balls", "golf ball", layered spherical, "virus"-like and mixed morphologies with T-junctions and U-type defects. The kinetics of the structure formation and difference with planar thin films are discussed. Our simulations suggest that novel porous nanocontainers can be formed by the coating of a sacrificial nanobead by a block copolymer layer with a well-controlled nanostructure. In addition, first scanning force microscopy experiments on a model system reveal surface structures similar to those predicted by our simulations.

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Cell dynamics simulation is used to investigate pathways of sphere-to-cylinder transition in block copolymer melt under applied simple shear flow and electric field. Both fields can induce the transition when their strength is above some critical value. At weak fields the spherical phase is preserved, with spheres being deformed into ellipsoids. Weak shear flow is found to improve order in the spherical phase. Observed sliding of layers of spheres under shear is very similar to the experimental finding by Hamley et al. [J. Chem. Phys. 108, 6929 (1998)]. The kinetic pathways are sensitive to the degree of microphase separation in the system and hence affected by temperature. The details of the pathways are described by means of Minkowski functionals.