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Finite State Automata Generator for DNA Motif Template as Preparation Step for Motif Mining

There are many tools and S/W systems to generate finite state automata, FSA, due to its importance in modeling and simulation and its wide variety of applications. However, no appropriate tool that can generate finite state automata, FSA, for DNA motif template due to the huge size of the motif template. In addition to the optional paths in the motif structure which are represented by the gap. These reasons lead to the unavailability of the specifications of the automata to be generated. This absence of specifications makes the generating process very difficult. This paper presents a novel algorithm to construct FSAs for DNA motif templates. This research is the first research presents the problem of generating FSAs for DNA motif templates and offers novel algorithm to accomplish this. It is tested using many simple and compound motif templates of different sizes and various numbers of gaps that have unlimited ranges of intervals. The motifs sizes are up to 2M Bases. The motif templates include up to 2000 gaps and the interval of a gap is [1,100] up to [1, 1000000]. All of these cases were processed successfully.

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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Evaluation of Seepage Force and Overall Stability Factor Along Proposed Baghdad Metro Tunnel Across Tigris River

Baghdad Metro is a vital project to fulfill the rapidly increased traffic volume requirements. The proposed metro will connect both sides of Baghdad City, passing under the Tigris River. This study is employed finite elements software (PLAXIS 3D) to evaluate the seepage force developed around the sub-river segment during different construction stages and for other water levels of Tigris. The study found that when the water level changes from maximum to minimum, the developed seepage force decreases by (8 to 13%) and (22 to 27%) respectively. The seepage forces were found to be maximum during the excavation stage. The concrete lining process led to a noticeable reduction in seepage forces at all locations. The study also

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Publication Date
Sat Jul 28 2018
Journal Name
Journal Of Engineering
Effectiveness of Meso-Scale Approach in Modeling of Plain Concrete Beam

The main aim of this research paper is investigating the effectiveness and validity of Meso-Scale Approach (MSA) as a modern technique for the modeling of plain concrete beams. Simply supported plain concrete beam was subjected to two-point loading to detect the response in flexural. Experimentally, a concrete mix was designed and prepared to produce three similar standard concrete prisms for flexural testing. The coarse aggregate used in this mix was crushed aggregate. Numerical Finite Element Analysis (FEA) was conducted on the same concrete beam using the meso-scale modeling. The numerical model was constructed to be a bi-phasic material consisting of cement mortar and coarse aggregate. The interface between the two c

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Mixed Convection in a Square Cavity Filled with Porous Medium with Bottom Wall Periodic Boundary Condition

Transient mixed convection heat transfer in a confined porous medium heated at periodic sinusoidal heat flux is investigated numerically in the present paper. The Poisson-type pressure equation, resulted from the substituting of the momentum Darcy equation in the continuity equation, was discretized by using finite volume technique. The energy equation was solved by a fully implicit control volume-based finite difference formulation for the diffusion terms with the use of the quadratic upstream interpolation for convective kinetics scheme to discretize the convective terms and the temperature values at the control volume faces. The numerical study covers a range of the hydrostatic  pressure sinusoidal  amplitude  range and

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Publication Date
Mon Mar 23 2020
Journal Name
Journal Of Engineering
Experimental and Numerical Study on CFRP-Confined Square Concrete Compression Members Subjected to Compressive Loading

    

Strengthening of the existing structures is an important task that civil engineers continuously face. Compression members, especially columns, being the most important members of any structure, are the most important members to strengthen if the need ever arise. The method of strengthening compression members by direct wrapping by Carbon Fiber Reinforced Polymer (CFRP) was adopted in this research. Since the concrete material is a heterogeneous and complex in behavior, thus, the behavior of the confined compression members subjected to uniaxial stress is investigated by finite element (FE) models created using Abaqus CAE 2017 software.

The aim of this research is to study experime

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Publication Date
Thu Feb 01 2024
Journal Name
Journal Of Engineering
Numerical Study of Composite Concrete Castellated Double Channel Beams with Strengthening Techniques

Current numerical research was devoted to investigating the effect of castellated steel beams without and with strengthening. The composite concrete asymmetrical double hot rolled steel channels bolted back to back to obtain a built-up I-shape form are used in this study. The top half part of the steel is smaller than the bottom half part, and the two parts were connected by bolting and welding. The ABAQUS/2019 program employed the same length and conditions of loading for four models: The first model is the reference without castellated and strengthening; the second model was castellated without strengthened; the third model was castellated and strengthened with reactive powder concrete encased in the

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Heave Behavior of Granular Pile Anchor-Foundation System (GPA-Foundation System) in Expansive Soil

Granular  Pile  Anchor  (GPA)  is  one  of  the  innovative  foundation  techniques,  devised  for mitigating heave of footing resulting from the expansive soils. This research attempts to study the heave behavior of (GPA-Foundation System) in expansive soil. Laboratory tests have been conducted on an experimental model in addition to a series of numerical modeling and analysis using the finite element package PLAXIS software. The effects of different parameters, such as (GPA) length (L) and diameter (D), footing diameter (B), expansive clay layer thickness (H) and presence of non-expansive clay are studied. The results proved the efficiency of (GPA) in reducing the heave of exp

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Publication Date
Sat Oct 30 2021
Journal Name
Iraqi Journal Of Science
Synthesis and Characterisation of Zinc-doped Antimony Selenide

         Antimony selenide substituted with Sb0.4Se0.6 and doped with zinc at three doping ratios (x=0, 0.01 and 0.03) was prepared via the solid state reaction method. The three prepared compositions were reacted thermally at 400 °C for 3 h. The structure of specimens was characterised via X-ray powder diffractometer to obtain the type of crystalline structure and lattice parameters of the prepared specimens, which showed a polycrystalline, orthorhombic structure. Optical characterisation was then achieved via UV-visible spectroscopy to exhibit the transmittance and reflectance spectra and estimate the band gap values of the prepared compositions. The samples showed high abs

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Publication Date
Fri Aug 10 2018
Journal Name
Ceramics International
Application of zirconia surface coating to improve fracture resistance and stress distribution of zirconia ceramic restorations

Zirconia ceramic restoration (ZCR) has a higher fracture incidence rate than metal ceramic restoration. Different surface treatments were used to improve fracture performance of ZCR such as grit blasting (GB) by aluminium oxide powder. This type of surface treatment generate residual stresses on veneering ceramic causing crack initiation and ending with a fracture. In order to overcome the stress generated by GB, zirconia surface coating is used as a surface treatment to improve fracture resistance and to accommodate stresses along the ZCR layers. Fifty zirconia ceramic crowns were fabricated and divided according to the type of surface treatment into three groups; the first group is (ZG), involving 20 cores were coated with a mixture of pa

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Publication Date
Wed Aug 30 2023
Journal Name
Iraqi Journal Of Science
Computational Study of the Flow of Newtonian Fluid Through A Straight Channel and Lid-Driven Cavity

     This article aims to introducenumerical study of two different incompressible Newtonian fluid flows. The first type of flow is through the straight channel, while the second flow is enclosed within a square cavity and the fluid is moved by the upper plate at a specific velocity. Numerically, a Taylor-Galerkin\ pressure-correction finite element method (TGPCFEM) is chosen to address the relevant governing equations. The Naiver-Stoke partial differential equations are usually used to describe the activity of fluids. These equations consist of the continuity equation (conservation of mass) and the time-dependent conservation of momentum, which are preserved in Cartesian coordinates. In this study, the effect of Reynolds number (

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Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
Buckling Analysis Of Damaged Composite Plates Under Uniform Or Non-Uniform Compressive Load

The present study focused mainly on the buckling behavior of composite laminated plates subjected to mechanical loads. Mechanical loads are analyzed by experimental analysis, analytical analysis (for laminates without cutouts) and numerical analysis by finite element method (for laminates with and without cutouts) for different type of loads which could be uniform or non-uniform, uniaxial or biaxial. In addition to many design parameters of the laminates such as aspect ratio, thickness ratio, and lamination angle or the parameters of the cutout such as shape, size, position, direction, and radii rounding) which are changed to studytheir effects on the buckling characteristics with various boundary conditions. Levy method of classical lam

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