'BioNessie(G) - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

SamACO: variable sampling ant colony optimization algorithm for continuous optimization

An ant colony optimization (ACO) algorithm offers algorithmic techniques for optimization by simulating the foraging behavior of a group of ants to perform incremental solution constructions and to realize a pheromone laying-and-following mechanism. Although ACO is first designed for solving discrete (combinatorial) optimization problems, the ACO procedure is also applicable to continuous optimization. This paper presents a new way of extending ACO to solving continuous optimization problems by focusing on continuous variable sampling as a key to transforming ACO from discrete optimization to continuous optimization. The proposed SamACO algorithm consists of three major steps, i.e., the generation of candidate variable values for selection, the ants’ solution construction, and the pheromone update process. The distinct characteristics of SamACO are the cooperation of a novel sampling method for discretizing the continuous search space and an efficient incremental solution construction method based on the sampled values. The performance of SamACO is tested using continuous numerical functions with unimodal and multimodal features. Compared with some state-of-the-art algorithms, including traditional ant-based algorithms and representative computational intelligence algorithms for continuous optimization, the performance of SamACO is seen competitive and promising

A node-based smoothed conforming point interpolation method (NS-CPIM) for elasticity problems

This paper formulates a node-based smoothed conforming point interpolation method (NS-CPIM) for solid mechanics. In the proposed NS-CPIM, the higher order conforming PIM shape functions (CPIM) have been constructed to produce a continuous and piecewise quadratic displacement field over the whole problem domain, whereby the smoothed strain field was obtained through smoothing operation over each smoothing domain associated with domain nodes. The smoothed Galerkin weak form was then developed to create the discretized system equations. Numerical studies have demonstrated the following good properties: NS-CPIM (1) can pass both standard and quadratic patch test; (2) provides an upper bound of strain energy; (3) avoid the volumetric locking; (4) provides the higher accuracy than those in the node-based smoothed schemes of the original PIMs

Self-optimization of optical confinement in ultraviolet photonic crystal slab laser

We studied numerically and experimentally the effects of structural disorder on the performance of ultraviolet photonic crystal slab lasers. Optical gain selectively amplifies the high-quality modes of the passive system. For these modes, the in-plane and out-of-plane leakage rates may be automatically balanced in the presence of disorder. The spontaneous optimization of in-plane and out-of-plane confinement of light in a photonic crystal slab may lead to a reduction of the lasing threshold.Comment: 5 pages, 5 figure

Fermion localization on degenerate and critical branes

In this work we analyze the localization of fermions on degenerate and critical Bloch branes. This is done directly on physical coordinates, in constrast to some works that has been using conformal coordinates. We find the range of coupling constants of the interaction of fermions with the scalar fields that allow us to have normalizable fermion zero-mode localized on the brane on both, critical and degenerate Bloch branes. In the case of critical branes our results agree with those found in [Class. Quantum Grav. \textbf{27} (2010) 185001]. The results on fermion localization on degenerate Bloch branes are new. We also propose a coupling of fermions to the scalar fields which leads to localization of massless fermion on both sides of a double-brane.Comment: 16 pages, 6 figure