Voronoi, Delaunay, and Block-Structured Mesh Refinement for Solution of the Shallow-Water Equations on the Sphere

Alternative meshes of the sphere and adaptive mesh refinement could be immensely beneficial for weather and climate forecasts, but it is not clear how mesh refinement should be achieved. A finite-volume model that solves the shallow-water equations on any mesh of the surface of the sphere is presented. The accuracy and cost effectiveness of four quasi-uniform meshes of the sphere are compared: a cubed sphere, reduced latitude–longitude, hexagonal–icosahedral, and triangular–icosahedral. On some standard shallow-water tests, the hexagonal–icosahedral mesh performs best and the reduced latitude–longitude mesh performs well only when the flow is aligned with the mesh. The inclusion of a refined mesh over a disc-shaped region is achieved using either gradual Delaunay, gradual Voronoi, or abrupt 2:1 block-structured refinement. These refined regions can actually degrade global accuracy, presumably because of changes in wave dispersion where the mesh is highly nonuniform. However, using gradual refinement to resolve a mountain in an otherwise coarse mesh can improve accuracy for the same cost. The model prognostic variables are height and momentum collocated at cell centers, and (to remove grid-scale oscillations of the A grid) the mass flux between cells is advanced from the old momentum using the momentum equation. Quadratic and upwind biased cubic differencing methods are used as explicit corrections to a fast implicit solution that uses linear differencing.

Undulation instability in block-copolymer lamellae subjected to a perpendicular electric field

We examine the stability of lamellar stacks in the presence of an electric field, E-0, applied normal to the lamellae. Calculations are performed with self-consistent field theory (SCFT) supplemented by an exact treatment of the electrostatic energy for linear dielectric materials. The calculations identify a critical electric field, E-0*, beyond which the lamellar stack becomes unstable with respect to undulations. This E-0* rapidly decreases towards zero as the number of lamellae in the stack diverges. Our quantitative predictions for E-0* are consistent with previous experimental measurements by Xu and co-workers.

A block in virus-like particle maturation following assembly of murine leukaemia virus in insect cells

Expression of the murine leukaemia virus (MLV) major Gag antigen p65(Gag) using the baculovirus expression system leads to efficient assembly and release of virus-like particles (VLP) representative of immature MLV. Expression of P180(Gag-Pol), facilitated normally in mammalian cells by readthrough of the p65(Gag) termination codon, also occurs efficiently in insect cells to provide a source of the MLV protease and a pattern of p65(Gag) processing similar to that observed in mammalian cells. VLP release from P180(Gag-Pol) expressing cells however remains essentially immature with disproportionate levels of the uncleaved p65(Gag) precursor when compared to the intracellular Gag profile. Changing the p65(Gag) termination codon altered the level of p65(Gag) and p180(Gag-Pol) within expressing cells but did not alter the pattern of released VLP, which remained immature. Coexpression of p65(Gag) with a fixed readthrough p180(Gag-Pol) also led to only immature VLP release despite high intracellular protease levels. Our data suggest a mechanism that preferentially selects uncleaved p65(Gag) for the assembly of MLV in this heterologous expression system and implies that, in addition to their relative levels, active sorting of the correct p65(Gag) and p180(Gag-Pol) ratios may occur in producer cells. (C) 2003 Elsevier Inc. All rights reserved.

Self assembly of a model amphiphilic phenylalanine peptide/polyethylene glycol block copolymer in aqueous solution

There has been great interest recently in peptide amphiphiles and block copolymers containing biomimetic peptide sequences due to applications in bionanotechnology. We investigate the self-assembly of the peptide-PEG amphiphile FFFF-PEG5000 containing the hydrophobic sequence of four phenylalanine residues conjugated to PEG of molar mass 5000. This serves as a simple model peptide amphiphile. At very low concentration, association of hydrophobic aromatic phenylalanine residues occurs, as revealed by circular dichroism and UV/vis fluorescence experiments. A critical aggregation concentration associated with the formation of hydrophobic domains is determined through pyrene fluorescence assays. At higher concentration, defined beta-sheets develop as revealed by FTIR spectroscopy and X-ray diffraction. Transmission electron microscopy reveals self-assembled straight fibril structures. These are much shorter than those observed for amyloid peptides, the finite length may be set by the end cap energy due to the hydrophobicity of phenylalanine. The combination of these techniques points to different aggregation processes depending on concentration. Hydrophobic association into irregular aggregates occurs at low concentration, well-developed beta-sheets only developing at higher concentration. Drying of FFFF-PEG5000 solutions leads to crystallization of PEG, as confirmed by polarized optical microscopy (POM), FTIR and X-ray diffraction (XRD). PEG crystallization does not disrupt local beta-sheet structure (as indicated by FTIR and XRD). However on longer lengthscales the beta-sheet fibrillar structure is perturbed because spheruilites from PEG crystallization are observed by POM. (C) 2009 Elsevier B.V. All rights reserved.