The cyclotide family of circular miniproteins: Nature's combinatorial peptide template

The cyclotides are a recently discovered family of miniproteins that contain a head-to-tail cyclized backbone and a knotted arrangement of disulfide bonds. They are approximately 30 amino acids in size and are present in high abundance in plants from the Violaceae, Rubiaceae, and Cucurbitaceae families, with individual plants containing a suite of up to 100 cyclotides. They have a diverse range of biological activities, including uterotonic, anti-HIV, antitumor, and antimicrobial activities, although their natural function is likely that of defending their host plants from pathogens and pests. This review focuses on the structural aspects of cyclotides, which may be thought of as a natural combinatorial peptide template in which a wide range of amino acids is displayed on a compact molecular core made up of the cyclic cystine knot structural motif. Cyclotides are exceptionally stable and are resistant to denaturation via thermal, chemical, or enzymatic treatments. The struclural features that contribute to their remarkable stability are described ill this review. (c) 2006 Wiley Periodicals, Inc.

Erratum: Two-Dimensional Failure Modeling with Minimal Repair which appeared in this journal of April 2004, Volume 51:3 on pages 345–362

In this Erratum, we point out the reason for an error in the derivation of a result in our earlier paper, “Two-Dimensional Failure Modeling with Minimal Repair” [1], which appeared in the April 2004 issue of this journal, 51:3, on pages 345–362, and give the correct derivation.

A flaw in the use of minimal defining sets for secret sharing schemes

It is shown that in some cases it is possible to reconstruct a block design D uniquely from incomplete knowledge of a minimal defining set for D. This surprising result has implications for the use of minimal defining sets in secret sharing schemes.

Minimal Homogeneous Latin Trades

A latin trade is a subset of a latin square which may be replaced with a disjoint mate to obtain a new latin square. A d-homogeneous latin trade is one which intersects each row, each column and each entry of the latin square either 0 or d times. In this paper we give a construction for minimal d-homogeneous latin trades of size dm, for every integer d >= 3, and m >= 1.75d(2) + 3. We also improve this bound for small values of d. Our proof relies on the construction of cyclic sequences whose adjacent sums are distinct. (c) 2006 Elsevier B.V. All rights reserved.

Partitioning of deformation within a subduction channel during exhumation of high-pressure rocks: a case study from the Western Alps

The metamorphic belt of the Western Alps was subjected to widespread extensional tectonism at the end of the Eocene (ca. 45-35 Ma). Extension was accommodated by hinterland-directed movements along gently inclined extensional shear zones, which facilitated rapid exhumation of high-pressure and ultra-high-pressure rocks. This deformation resulted in a normal metamorphic sequence. Extension in the inner parts of the Western Alps was coeval with shortening at the front of the belt (foreland-directed thrusts), which took place during decompression, and emplaced higher grade metamorphic units over lower grade metamorphic rocks, thus forming an inverse metamorphic sequence. Two mechanisms for this extensional episode are discussed: (1) collapse of an overthickened lithosphere, and (2) internal readjustments within the orogenic wedge due to subduction channel dynamics. We favour the latter mechanism because it can account for the development of the observed inverse and normal metamorphic sequences along foreland-directed thrusts and hinterland-directed detachments, respectively. This hypothesis is supported by published structural, metamorphic and geochronological data from four geological transects through the Western Alps. This study also emphasizes the importance of post-shearing deformation (e.g. horizontal buckling versus vertical flattening), which can modify the distribution of hinterland- and foreland-directed shear zones in orogenic belts. (c) 2006 Elsevier Ltd. All rights reserved.

Anisotropic viscous models of large-deformation Mohr-Coulomb failure

We have developed a way to represent Mohr-Coulomb failure within a mantle-convection fluid dynamics code. We use a viscous model of deformation with an orthotropic viscoplasticity (a different viscosity is used for pure shear to that used for simple shear) to define a prefered plane for slip to occur given the local stress field. The simple-shear viscosity and the deformation can then be iterated to ensure that the yield criterion is always satisfied. We again assume the Boussinesq approximation, neglecting any effect of dilatancy on the stress field. An additional criterion is required to ensure that deformation occurs along the plane aligned with maximum shear strain-rate rather than the perpendicular plane, which is formally equivalent in any symmetric formulation. We also allow for strain-weakening of the material. The material can remember both the accumulated failure history and the direction of failure. We have included this capacity in a Lagrangian-integration-point finite element code and show a number of examples of extension and compression of a crustal block with a Mohr-Coulomb failure criterion. The formulation itself is general and applies to 2- and 3-dimensional problems.

Finite deformation model of simple shear of fault with microrotations: apparent strain localisation and en-echelon fracture pattern

Strain localisation is a widespread phenomenon often observed in shear and compressive loading of geomaterials, for example, the fault gouge. It is believed that the main mechanisms of strain localisation are strain softening and mismatch between dilatancy and pressure sensitivity. Observations show that gouge deformation is accompanied by considerable rotations of grains. In our previous work as a model for gouge material, we proposed a continuum description for an assembly of particles of equal radius in which the particle rotation is treated as an independent degree of freedom. We showed that there exist critical values of the model parameters for which the displacement gradient exhibits a pronounced localisation at the mid-surface layers of the fault, even in the absence of inelasticity. Here, we generalise the model to the case of finite deformations characteristic for the gouge deformation. We derive objective constitutive relationships relating the Jaumann rates of stress and moment stress to the relative strain and curvature rates, respectively. The model suggests that the pattern of localisation remains the same as in the linear case. However, the presence of the Jaumann terms leads to the emergence of non-zero normal stresses acting along and perpendicular to the shear layer (with zero hydrostatic pressure), and localised along the mid-line of the gouge; these stress components are absent in the linear model of simple shear. These additional normal stresses, albeit small, cause a change in the direction in which the maximal normal stresses act and in which en-echelon fracturing is formed.