A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

An Improved Ce/Se Scheme For Multi-Material Elastic-Plastic Flows And Its Applications

In this paper, a new definition of SE and CE, which is based on the hexahedron mesh and simpler than Chang's original CE/SE method (the space-time Conservation Element and Solution Element method), is proposed and an improved CE/SE scheme is constructed. Furthermore, the improved CE/SE scheme is extended in order to solve the elastic-plastic flow problems. The hybrid particle level set method is used for tracing the interfaces of materials. Proper boundary conditions are presented in interface tracking. Two high-velocity impact problems are simulated numerically and the computational results are carefully compared with the experimental data, as well as the results from other literature and LS-DYNA software. The comparisons show that the computational scheme developed currently is clear in physical concept, easy to be implemented and high accurate and efficient for the problems considered. (C) 2008 Elsevier Ltd. All rights reserved.

A Hybrid Scheme Based on Finite Element/Volume Methods for Two Immiscible Fluid Flows

We have successfully extended our implicit hybrid finite element/volume (FE/FV) solver to flows involving two immiscible fluids. The solver is based on the segregated pressure correction or projection method on staggered unstructured hybrid meshes. An intermediate velocity field is first obtained by solving the momentum equations with the matrix-free implicit cell-centered FV method. The pressure Poisson equation is solved by the node-based Galerkin FE method for an auxiliary variable. The auxiliary variable is used to update the velocity field and the pressure field. The pressure field is carefully updated by taking into account the velocity divergence field. This updating strategy can be rigorously proven to be able to eliminate the unphysical pressure boundary layer and is crucial for the correct temporal convergence rate. Our current staggered-mesh scheme is distinct from other conventional ones in that we store the velocity components at cell centers and the auxiliary variable at vertices. The fluid interface is captured by solving an advection equation for the volume fraction of one of the fluids. The same matrix-free FV method, as the one used for momentum equations, is used to solve the advection equation. We will focus on the interface sharpening strategy to minimize the smearing of the interface over time. We have developed and implemented a global mass conservation algorithm that enforces the conservation of the mass for each fluid.

Investment prospects in inland capture fisheries -- revolving loan scheme to artisanal fishermen

Fishing inputs in the form of the netting materials, boats and outboard engines were issued to 20 fishermen on revolving loan basis at 2 centres - Shagunu. and Monai along the western bank of Kainji Lake, Nigeria. The agreement was that the recipients should sell all their catches to the Institute and surrender 20% as part payment of the loan, until they offset the loan after which the inputs would become theirs'. The scheme was monitored for 5 years during which time most recipients had completed payment. It was observed that adequate revenue could be made from the scheme provided there was effective supervision. A proposal has been made for large scale supply of fishing inputs to one hundred fishermen. The scheme is laudable as a means of improving the lot of the fishermen and implementing management proposals in water bodies through the recipients

An Improved CE/SE Scheme for Numerical Simulation of Gaseous and Two-Phase Detonations

A new structure of solution elements and conservation elements based on rectangular mesh was pro- posed and an improved space-time conservation element and solution element (CE/SE) scheme with sec- ond-order accuracy was constructed. Furthermore, the application of improved CE/SE scheme was extended to detonation simulation. Three models were used for chemical reaction in gaseous detonation. And a two-fluid model was used for two-phase (gas–droplet) detonation. Shock reflections were simu- lated by the improved CE/SE scheme and the numerical results were compared with those obtained by other different numerical schemes. Gaseous and gas–droplet planar detonations were simulated and the numerical results were carefully compared with the experimental data and theoretical results based on C–J theory. Mach reflection of a cellular detonation was also simulated, and the numerical cellular pat- terns were compared with experimental ones. Comparisons show that the improved CE/SE scheme is clear in physical concept, easy to be implemented and high accurate for above-mentioned problems.

A CE/SE Scheme for Flows in Porous Media and Its Applications

In this paper, a new computational scheme for solving flows in porous media was proposed. The scheme was based on an improved CE/SE method (the space-time Conservation Element and Solution Element method). We described porous flows by adopting DFB (Brinkman-Forchheimer extended Darcy) equation. The comparison between our computational results and Ghia's confirmed the high accuracy, resolution, and efficiency of our CE/SE scheme. The proposed first-order CE/SE scheme is a new reliable way for numerical simulations of flows in porous media. After investigation of effects of Darcy number on porous flow, it shows that Darcy number has dominant influence on porous flow for the Reynolds number and porosity considered.