Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

The study of biological characteristic and population dynamic of Caspian vimba (Vimba vimba persa), in coastal waters of Caspian Sea (Mazandaran Province)

This study was conducted to determine reproduction characteristics, diet regime, age structure and population dynamics parameters of the vimba vimba persa (Pallas, 1811) in Mazandaran waters of the Caspian Sea, from October 2008 to September 2009. A total of 994 specimens were monthly collected by beach seine and cast net from six fish landings of Ramsar, Tonekabon, Chaloos, Mahmood Abad, Sari and Behshahr. Biometric characters were measured for each specimen at the laboratory. Scales were used for age determination. Sex determination and fecundity were determined. Population dynamic parameters as well as stock assessment including cohort analysis were estimated using FISAT software. The finding showed that the mean of fork length and body weight of the Caspian Vimba were 168.4±2.6 mm and 71.94±32.24 g respectively. Strong correlation was found between these two variables (a= 0.012; b = 3.047; r2 = 0.955). 92 specimens were studied from the fecundity point of view. This species was found to have more abundance in spring (esp. Apr-May). The samples composed of 397(42.6%) male, 537(57.4%) female; Overall sex ratio (M: F =1: 1.35) was significantly different from the expected 1:1 ratio (p ≤0.05). The advanced stages of maturity (4th & 5th) were found in April and May. The highest Gonadosomatic Index in female was in May and the lowest one was in July. This fish is therefore a spring spawner. The maximum absolute and relative fecundities were 34640 and 260.9, respectively; the minimum absolute and relative fecundities were 5400 and 94.5 respectively. The averages of absolute and relative fecundities were 17198±7710 and 171.85±48.8, respectively. Coefficient vacuity index was 59.2% which indicates that this fish is mesophagous. Among of living creature consumes by Caspian Vimba mollusks, 76 arthropods, worms, plants, detritus and fishes were found 32.9% , 26.7% , 13.4% , 17% , 4.4% and 1.6% respectively. The infinite fork lengths were 261 mm for females, 25mm for males and 261 mm for both sexes respectively. For population growth and mortality parameters; K ( 0.28 per year for both sexes, 0.3 per year for males, 0.33 per year for females); t0 ( -0.65 year for both sexes, -0.23 year in females, -0.51 year in males ); Φ' ( 2.28 ); Z ( 0.98 per year ); M ( 0.59 per year); F ( 0.39 per year) and Exploitation coefficient was 0.4. The analysis showed that total biomass and MSY were 1336 and 528.8 tonnes respectively.

IUTAM Symposium on the Vibration Analysis of Structures with Uncertainties

The Symposium was aimed at the theoretical and numerical problems involved in modelling the dynamic response of structures which have uncertain properties due ...

Dynamic compressive response of composite square honeycombs

Carbon fibre-epoxy composite square honeycombs, and the parent composite material, were tested in quasi-static compression at a strain rate of 10 -3 s -1 and in dynamic compression at strain rates of 10 3-10 4 s -1 using an instrumented Kolsky bar arrangement. Taken together, these tests provide an assessment of the potential of this composite topology for use as a lightweight sandwich core. The honeycombs had two relative densities, 0.12 and 0.24, and two material orientations, ±45° and 0/90° with respect to the prismatic, loading direction of the honeycomb. Honeycomb manufacture was by slotting, assembling and bonding together carbon fibre/epoxy woven plies of composite sheets of 2 × 2 twill weave construction. The peak value of wall stress in the honeycombs was about one third that of the parent material, for all strain rates. An elastic finite element analysis was used to trace the source of this knock-down in strength: a stress concentration exists at the root of the slots and leads to premature failure by microbuckling. Shock-wave effects were evident at impact velocities exceeding 50 ms -1 for the honeycomb of relative density 0.12. This was traced to stubbing of the buckled cell walls against the face of the Kolsky bar. © 2011 Elsevier Ltd. All rights reserved.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

The effect of beam interruptions on the integrity of ADSR fuel pin cladding: A thermo-mechanical analysis

During its lifetime in the core, the cladding of an Accelerator Driven Subcritical Reactor (ADSR) fuel pin is expected to experience variable stresses due to frequent interruptions in the accelerator proton beam. This paper investigates the thermal fatigue damage in the cladding due to repetitive and unplanned beam interruptions under certain operational conditions. Beam trip data was obtained for four operating high power proton accelerators, among which the Spallation Neutron Source (SNS) superconducting accelerator was selected for further analysis. 9Cr-1Mo-Nb-V (T91) steel was selected as the cladding material because of its proven compatibility with proposed ADSR design concepts. The neutronic, thermal and stress analyses were performed using the PTS-ADS, a code that has been specifically developed for studying the dynamic response to beam-induced transients in accelerator driven subcritical systems. The lifetime of the fuel cladding in the core was estimated for three levels of allowed pin power and specific operating conditions. © 2012 Elsevier Ltd. All rights reserved.

Dynamic buckling of an inclined strut

The dynamic compressive response of a sandwich plate with a metallic corrugated core is predicted. The back face of the sandwich plate is held fixed whereas the front face is subjected to a uniform velocity, thereby compressing the core. Finite element analysis is performed to investigate the role of material inertia, strain hardening and strain rate hardening upon the dynamic collapse of the corrugated core. Three classes of collapse mode are identified as a function of impact velocity: (i) a three-hinge plastic buckling mode of wavelength equal to the strut length, similar to the quasi-static mode, (ii) a 'buckle-wave' regime involving inertia-mediated plastic buckling of wavelength less than that of the strut length, and (iii) a 'stubbing' regime, with shortening of the struts by local fattening at the front face. The presence of strain hardening reduces the regime of dominance of the stubbing mode. The influence of material strain rate sensitivity is evaluated by introducing strain rate dependent material properties representative of type 304 stainless steel. For this choice of material, strain rate sensitivity has a more minor influence than strain hardening, and consequently the dynamic collapse strength of a corrugated core is almost independent of structural dimension. © 2012 Elsevier Ltd. All rights reserved.

A probabilistic energy model for non-domestic building sectors applied to analysis of school buildings in greater London

The diversity of non-domestic buildings at urban scale poses a number of difficulties to develop models for large scale analysis of the stock. This research proposes a probabilistic, engineering-based, bottom-up model to address these issues. In a recent study we classified London's non-domestic buildings based on the service they provide, such as offices, retail premise, and schools, and proposed the creation of one probabilistic representational model per building type. This paper investigates techniques for the development of such models. The representational model is a statistical surrogate of a dynamic energy simulation (ES) model. We first identify the main parameters affecting energy consumption in a particular building sector/type by using sampling-based global sensitivity analysis methods, and then generate statistical surrogate models of the dynamic ES model within the dominant model parameters. Given a sample of actual energy consumption for that sector, we use the surrogate model to infer the distribution of model parameters by inverse analysis. The inferred distributions of input parameters are able to quantify the relative benefits of alternative energy saving measures on an entire building sector with requisite quantification of uncertainties. Secondary school buildings are used for illustrating the application of this probabilistic method. © 2012 Elsevier B.V. All rights reserved.

Dynamic behaviour of gas jets in laser cutting

The efficiency and overall quality of a laser cutting operation is highly dependent on the assist gas parameters. The desire to cut thicker material has led to the observation of small process operating windows for thicker sections. The gas jet delivery and subsequent dynamical behaviour have significant effects on the cutting operation as the sample thickness increases. To date, few workers have examined the dynamical behaviour of the gas jet. This paper examines the characteristics of oxygen gas jets during CO2 laser cutting of steel. Particular emphasis is placed on the mass transfer effects that are operating within the kerf. Oxygen concentration levels within a model kerf are measured for various laser cutting set-ups. The results show a substantial reduction in oxygen concentration within the kerf. A system for oxygen concentration maintenance is described and cutting results from this system are compared with conventional techniques for cutting steels in the range 10 to 20mm thick. A theoretical analysis of turbulent mass transfer within a kerf is presented and compared with experiment.

An efficient model for the dynamic behaviour of a single pile in viscoelastic soil

This paper presents a novel, three-dimensional, single-pile model, formulated in the wavenumber domain and adapted to account for boundary conditions using the superposition of loading cases. The pile is modelled as a column in axial vibration, and a Euler-Bernoulli beam in lateral vibration. The surrounding soil is treated as a viscoelastic continuum. The response of the pile is presented in terms of the stiffness and damping coefficients, and also the magnitude and phase of the pile-head frequency-response function. Comparison with existing models shows that excellent agreement is observed between this model, a boundary-element formulation, and an elastic-continuum-type formulation. This three-dimensional model has an accuracy equivalent to a 3D boundary-element model, and a runtime similar to a 2D plane-strain analytical model. Analysis of the response of the single pile illustrates a difference in axial and lateral vibration behaviour; the displacement along the pile is relatively invariant under axial loads, but in lateral vibration the pile exhibits localised deformations. This implies that a plane-strain assumption is valid for axial loadings and only at higher frequencies for lateral loadings. © 2013 Elsevier Ltd.

Static and dynamic errors in particle tracking microrheology.

Particle tracking techniques are often used to assess the local mechanical properties of cells and biological fluids. The extracted trajectories are exploited to compute the mean-squared displacement that characterizes the dynamics of the probe particles. Limited spatial resolution and statistical uncertainty are the limiting factors that alter the accuracy of the mean-squared displacement estimation. We precisely quantified the effect of localization errors in the determination of the mean-squared displacement by separating the sources of these errors into two separate contributions. A "static error" arises in the position measurements of immobilized particles. A "dynamic error" comes from the particle motion during the finite exposure time that is required for visualization. We calculated the propagation of these errors on the mean-squared displacement. We examined the impact of our error analysis on theoretical model fluids used in biorheology. These theoretical predictions were verified for purely viscous fluids using simulations and a multiple-particle tracking technique performed with video microscopy. We showed that the static contribution can be confidently corrected in dynamics studies by using static experiments performed at a similar noise-to-signal ratio. This groundwork allowed us to achieve higher resolution in the mean-squared displacement, and thus to increase the accuracy of microrheology studies.

Efficient numerical models for investigating the statistics of random dynamic systems

The study of random dynamic systems usually requires the definition of an ensemble of structures and the solution of the eigenproblem for each member of the ensemble. If the process is carried out using a conventional numerical approach, the computational cost becomes prohibitive for complex systems. In this work, an alternative numerical method is proposed. The results for the response statistics are compared with values obtained from a detailed stochastic FE analysis of plates. The proposed method seems to capture the statistical behaviour of the response with a reduced computational cost.

A coupled hydro-mechanical analysis for prediction of hydraulic fracture propagation in saturated porous media using EFG mesh-less method

The details of the Element Free Galerkin (EFG) method are presented with the method being applied to a study on hydraulic fracturing initiation and propagation process in a saturated porous medium using coupled hydro-mechanical numerical modelling. In this EFG method, interpolation (approximation) is based on nodes without using elements and hence an arbitrary discrete fracture path can be modelled.The numerical approach is based upon solving two governing partial differential equations of equilibrium and continuity of pore water simultaneously. Displacement increment and pore water pressure increment are discretized using the same EFG shape functions. An incremental constrained Galerkin weak form is used to create the discrete system of equations and a fully implicit scheme is used for discretization in the time domain. Implementation of essential boundary conditions is based on the penalty method. In order to model discrete fractures, the so-called diffraction method is used.Examples are presented and the results are compared to some closed-form solutions and FEM approximations in order to demonstrate the validity of the developed model and its capabilities. The model is able to take the anisotropy and inhomogeneity of the material into account. The applicability of the model is examined by simulating hydraulic fracture initiation and propagation process from a borehole by injection of fluid. The maximum tensile strength criterion and Mohr-Coulomb shear criterion are used for modelling tensile and shear fracture, respectively. The model successfully simulates the leak-off of fluid from the fracture into the surrounding material. The results indicate the importance of pore fluid pressure in the initiation and propagation pattern of fracture in saturated soils. © 2013 Elsevier Ltd.

Performance analysis and testing of a 250 kW medium-speed brushless doubly-fed induction generator

This study presents the performance analysis and testing of a 250 kW medium-speed brushless doubly-fed induction generator (DFIG), and its associated power electronics and control systems. The experimental tests confirm the design, and showthe system's steady-state and dynamic performance and grid low-voltage ride- through capability. The medium-speed brushless DFIG in combination with a simplified two-stage gearbox promises a low-cost low-maintenance and reliable drivetrain for wind turbine applications. © The Institution of Engineering and Technology 2013.

How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex.

BACKGROUND: Neuronal migration, the process by which neurons migrate from their place of origin to their final position in the brain, is a central process for normal brain development and function. Advances in experimental techniques have revealed much about many of the molecular components involved in this process. Notwithstanding these advances, how the molecular machinery works together to govern the migration process has yet to be fully understood. Here we present a computational model of neuronal migration, in which four key molecular entities, Lis1, DCX, Reelin and GABA, form a molecular program that mediates the migration process. RESULTS: The model simulated the dynamic migration process, consistent with in-vivo observations of morphological, cellular and population-level phenomena. Specifically, the model reproduced migration phases, cellular dynamics and population distributions that concur with experimental observations in normal neuronal development. We tested the model under reduced activity of Lis1 and DCX and found an aberrant development similar to observations in Lis1 and DCX silencing expression experiments. Analysis of the model gave rise to unforeseen insights that could guide future experimental study. Specifically: (1) the model revealed the possibility that under conditions of Lis1 reduced expression, neurons experience an oscillatory neuron-glial association prior to the multipolar stage; and (2) we hypothesized that observed morphology variations in rats and mice may be explained by a single difference in the way that Lis1 and DCX stimulate bipolar motility. From this we make the following predictions: (1) under reduced Lis1 and enhanced DCX expression, we predict a reduced bipolar migration in rats, and (2) under enhanced DCX expression in mice we predict a normal or a higher bipolar migration. CONCLUSIONS: We present here a system-wide computational model of neuronal migration that integrates theory and data within a precise, testable framework. Our model accounts for a range of observable behaviors and affords a computational framework to study aspects of neuronal migration as a complex process that is driven by a relatively simple molecular program. Analysis of the model generated new hypotheses and yet unobserved phenomena that may guide future experimental studies. This paper thus reports a first step toward a comprehensive in-silico model of neuronal migration.