The topological structure of 2D disordered cellular systems

We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged concentrically around a germ cell. We single out the most significant parameters that characterize statistically the organization of these patterns. Universality and specificity in disordered cellular structures are discussed.Comment: 18 Pages LaTeX, 16 Postscript figure

Gauge theory approach to glass transitions

This theory combines a thermodynamic approach with a dynamic one in order to describe glass transition. Glass transition is regarded as an inaccessible second order phase transition, which is interrupted because of premature critical slowing down, caused by the system's frustration. The frustration-induced vortices are present in the structure besides thermoactivated vortices, and prevent the development of the order parameter fluctuations, that leads to the critical slowing down the system kinetics at some temperature above the phase transition point

Conotoxins

Journal ArticleMany successful animal and plant families have developed distinctive biochemical strategies; one of the more unusual examples is found in a group of marine gastropods, the cone snails (Conus) (1). These animals have evolved a specialized biochemistry of small constrained peptides, the conotoxins. These peptides are the direct translation products of genes (2). However, because they are small enough for direct chemical synthesis and sufficiently constrained for three-dimensional conformation determination, conotoxins bridge protein chemistry and molecular genetics. Furthermore, the strategy that the cone snails have evolved over millions of years for the generation and design of an enormous array of small peptide ligands, each with high affinity and specificity for a particular receptor protein target, may be adaptable for use in vitro

Neuronal calcium channel inhibitors: synthesis of ω-conotoxin GVIA and effects on 45Ca-uptake by synaptosomes

Journal ArticleWe previously described a 27-amino acid peptide neurotoxin from the venom of Conus geographus, wconotoxin GVIA, which inhibits neuronal voltage-activated calcium channels. In this paper we describe the total synthesis of ω-conotoxin GVIA and demonstrate that it efficiently blocks voltage-activated uptake of 46Ca by standard synaptosomal preparations from chick brain. Dihydropyridines do not block 46Ca uptake under these conditions

Conotoxin MI: disulfide bonding and conformational states

Journal ArticleThe toxic peptide from Conus magus venom (conotoxin MI) is a 14-amino acid peptide (McIntosh, M., Cruz, L. J., Hunkapiller, M. W., Gray, W. R., and Olivera, B. M. (1982) Arch. Biochem. Biophys. 218, 329-334) which inhibits the acetylcholine ceptor. In this work we have confirmed the primary structure and established the disulfide bonding configuration (Cys 3-Cys 8; Cys 4-Cys 14) by direct chemical synthesis of the toxin with specific disulfide bridges

An Efficient Spectral Dynamical Core for Distributed Memory Computers

The practical question of whether the classical spectral transform method, widely used in atmospheric modeling, can be efficiently implemented on inexpensive commodity clusters is addressed. Typically, such clusters have limited cache and memory sizes. To demonstrate that these limitations can be overcome, the authors have built a spherical general circulation model dynamical core, called BOB (“Built on Beowulf”), which can solve either the shallow water equations or the atmospheric primitive equations in pressure coordinates. That BOB is targeted for computing at high resolution on modestly sized and priced commodity clusters is reflected in four areas of its design. First, the associated Legendre polynomials (ALPs) are computed “on the fly” using a stable and accurate recursion relation. Second, an identity is employed that eliminates the storage of the derivatives of the ALPs. Both of these algorithmic choices reduce the memory footprint and memory bandwidth requirements of the spectral transform. Third, a cache-blocked and unrolled Legendre transform achieves a high performance level that resists deterioration as resolution is increased. Finally, the parallel implementation of BOB is transposition-based, employing load-balanced, one-dimensional decompositions in both latitude and wavenumber. A number of standard tests is used to compare BOB's performance to two well-known codes—the Parallel Spectral Transform Shallow Water Model (PSTSWM) and the dynamical core of NCAR's Community Climate Model CCM3. Compared to PSTSWM, BOB shows better timing results, particularly at the higher resolutions where cache effects become important. BOB also shows better performance in its comparison with CCM3's dynamical core. With 16 processors, at a triangular spectral truncation of T85, it is roughly five times faster when computing the solution to the standard Held–Suarez test case, which involves 18 levels in the vertical. BOB also shows a significantly smaller memory footprint in these comparison tests