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.

Algorithm for simulating fracture processes in concrete by lattice modeling

To simulate fracture behaviors in concrete more realistically, a theoretical analysis on the potential question in the quasi-static method is presented, then a novel algorithm is proposed which takes into account the inertia effect due to unstable crack propagation and meanwhile requests much lower computational efforts than purely dynamic method. The inertia effect due to load increasing becomes less important and can be ignored with the loading rate decreasing, but the inertia effect due to unstable crack propagation remains considerable no matter how low the loading rate is. Therefore, results may become questionable if a fracture process including unstable cracking is simulated by the quasi-static procedure excluding completely inertia effects. However, it requires much higher computational effort to simulate experiments with not very high loading rates by the dynamic method. In this investigation which can be taken as a natural continuation, the potential question of quasi-static method is analyzed based on the dynamic equations of motion. One solution to this question is the new algorithm mentioned above. Numerical examples are provided by the generalized beam (GB) lattice model to show both fracture processes under different loading rates and capability of the new algorithm.

Numerical investigation of crack growth in concrete subjected to compression by the generalized beam lattice model

The beam lattice-type models, such as the Euler-Bernoulli (or Timoshenko) beam lattice and the generalized beam (GB) lattice, have been proved very effective in simulating failure processes in concrete and rock due to its simplicity and easy implementation. However, these existing lattice models only take into account tensile failures, so it may be not applicable to simulation of failure behaviors under compressive states. The main aim in this paper is to incorporate Mohr-Coulomb failure criterion, which is widely used in many kinds of materials, into the GB lattice procedure. The improved GB lattice procedure has the capability of modeling both element failures and contact/separation of cracked elements. The numerical examples show its effectiveness in simulating compressive failures. Furthermore, the influences of lateral confinement, friction angle, stiffness of loading platen, inclusion of aggregates on failure processes are respectively analyzed in detail.

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

Small-scale commercial production of tilapia fry and fingerlings in concrete raceways

This paper discusses the investment prospects in Tilapia fry and fingerling production in raceways created from the concrete drainage channel of a reservoir or pond of an existing fish farm in Nigeria. With an initial capital of 1,300 and an annual operating cost of 310 spent on procurement of fish feed and brood stock for a 10 m super(2) raceway per se, a net profit of 4,100 and 5,090 would be realized from Sarotherodon galilaeus in the first year and subsequent years of production respectively, assuming that the fingerling production rate has been maintained through the production period. It is concluded that the application of this approach of optimizing the use of available resources in the fish farm for the productive breeding of Tilapia fry and fingerlings will apart from alleviating the problem of scarcity of stocking materials in the country, increase the profit margin accruing to the fish farmer

Commercial production of Clarias fry and fingerlings in indoor and outdoor concrete tank systems

Induced breeding technique by hypophysation is being applied at the Kainji Lake Research Institute Fisheries Division Hatchery complex in New Bussa, Nigeria, for the production of Clarias fry and fingerlings in indoor and outdoor concrete tank systems. The hatchlings are fed on livefood (zooplankton) and artificial feed. Source of zooplankton is from cultured stock which is maintained throughout the breeding season by fertilization. Production values show that an average of over 4,000 hatchlings (larvae) can be produced by a female breeder (over-700g wt) and percentage survival after two months ranges between 70 to 75%. With the proposed modification and expansion project, an estimated production of over 0.5 million fingerlings per breeding season is projected

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.

The variation of water quality in the outdoor concrete tank and earthen pond

The paper reports on the study carried out at the Federal College of Freshwater Fisheries and Technology (Nigeria) and the Hatchery Complex in 1997. The physico-chemical parameters of an earthen fish pond and concrete tank were analysed. The abundance and distribution of phytoplankton and zooplankton were recorded. A total of eight species of phytoplankton were observed. These species can be classified as Chlorophyceae (green algae), Bacillariophyceae (diatom algae) and Cyanophyta (blue-green algae). Eight zooplankton species were observed in the pond and 6 in the tank. Moina was observed and recorded as the most abundant cladoceran species in the tank

Effect of different feeding levels on the production of Heterobranchus bidorsalis in outdoor concrete tanks

Fry of Heterobranchus bidorsalis (mean weight, 0.03g) were fed at 10, 20, 30, 40 or 50% of their body weight (bw)/day in outdoor concrete tanks in New Bussa, Nigeria. The fry attained the highest average weight of 6.66g in 10 weeks when fed at 40% bw/day. Feed conversion ratio ranged from 2.13 to 9.65, the protein efficiency ratio from 1.33 to 5.93. Results indicated that H. bidorsalis are efficient feed converters. Feed intake was significantly different (p<0.05) between the treatments, specific growth rate (SGR), daily growth rate (DGR), production and average weight gain indicated that 40% of fish biomass was the optimum feeding level

Compressible flows at small Reynolds numbers

The problem of the slow viscous flow of a gas past a sphere is considered. The fluid cannot be treated incompressible in the limit when the Reynolds number Re, and the Mach number M, tend to zero in such a way that Re ~ o(M^2 ). In this case, the lowest order approximation to the steady Navier-Stokes equations of motion leads to a paradox discovered by Lagerstrom and Chester. This paradox is resolved within the framework of continuum mechanics using the classical slip condition and an iteration scheme that takes into account certain terms in the full Navier-Stokes equations that drop out in the approximation used by the above authors. It is found however that the drag predicted by the theory does not agree with R. A. Millikan's classic experiments on sphere drag.

The whole question of the applicability of the Navier-Stokes theory when the Knudsen number M/Re is not small is examined. A new slip condition is proposed. The idea that the Navier-Stokes equations coupled with this condition may adequately describe small Reynolds number flows when the Knudsen number is not too large is looked at in some detail. First, a general discussion of asymptotic solutions of the equations for all such flows is given. The theory is then applied to several concrete problems of fluid motion. The deductions from this theory appear to interpret and summarize the results of Millikan over a much wider range of Knudsen numbers (almost up to the free molecular or kinetic limit) than hitherto Believed possible by a purely continuum theory. Further experimental tests are suggested and certain interesting applications to the theory of dilute suspensions in gases are noted. Some of the questions raised in the main body of the work are explored further in the appendices.