Journals / ICCES / Vol.13, No.3
Table of Content

  • ABSTRACT

    A Lattice Boltzmann Method for modeling the oscillation of Min proteins: Oscillation pattern due to the initial copy of MinD and MinE

    Somchai Sriyab1, Wannapong Triampo2
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 51-52, 2009, DOI:10.3970/icces.2009.013.051
    Abstract Understanding of Bacteria cell division is essential for an understanding of microorganism as well as the origin of the life. Particularly, in cell division process of \emph {E. coli}, Min proteins (MinD and MinE) play crucial roles to regulate the dividing dynamics physically via their oscillatory dynamics from pole to pole. In this work, we have developed a numerical scheme based on the mesoscopic Lattice Boltzmann Method (LBM) to simulate the coarse-grained coupled reaction-diffusion equations model used to describe the MinD/MinE interaction in two dimensions. Biologically, we have focused on investigating how the protein copies affect the oscillation patterns as… More >

  • ABSTRACT

    Fractional diffusion-advection and pattern formations of MinE Protein dynamics in Escherichia coli: experiments and theories

    Sitta Aroonnual Paisan Kanthang, Wannapong Triampo1
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 53-54, 2009, DOI:10.3970/icces.2009.013.053
    Abstract How does a cell successfully divide is one of very fundamental questions in biological and medical science especially concerning mechanism. With this regards, MinE proteins are very important for Escherichia coli cell division process because it supports FtsZ proteins to form at mid-cell which lead to cell division at that region. In this work, we quantitatively studied the physical properties of MinE protein clusters including pattern formations and dynamic motions using both theoretical and experimental approach. Experimentally, through the spot tracking technique (STT) and diffusion analysis, it was found that MinE globally performed oscillatory motion from middle cell to the… More >

  • ABSTRACT

    A Framework for Parallel Adaptive FEM Computations with Dynamic Load Balancing

    Z. Bittnar1, B. Patzák1, D. Rypl1
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 55-56, 2009, DOI:10.3970/icces.2009.013.055
    Abstract This paper deals with the design of framework for adaptive FEM analysis with dynamic load balancing in nondedicated parallel cluster computing environments. It describes in detail the structure and design of individual components of the framework.
    The application of adaptivity paradigm to engineering problems results in computationally very demanding analysis in terms of both computational time and computer resources (memory, disk space, etc.). These demands can be alleviated by performing the analysis in a parallel computing environment. Typical parallel application decreases the demands on memory and other resources by spreading the task over several mutually interconnected computers and speeds… More >

  • ABSTRACT

    A Numerical Solution of 2D Buckley-Leverett Equation via Gradient Reproducing Kernel Particle Method

    Hossein M. Shodja1, 2, 3, Alireza Hashemian2, 4
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 57-58, 2009, DOI:10.3970/icces.2009.013.057
    Abstract Gradient reproducing kernel particle method (GRKPM) is a meshless technique which incorporates the first gradients of the function into the reproducing equation of RKPM. Therefore, in two-dimensional space GRKPM introduces three types of shape functions rather than one. The robustness of GRKPM's shape functions is established by reconstruction of a third-order polynomial. To enforce the essential boundary conditions (EBCs), GRKPM's shape functions are modified by transformation technique. By utilizing the modified shape functions, the weak form of the nonlinear evolutionary Buckley-Leverett (BL) equation is discretized in space, rendering a system of nonlinear ordinary differential equations (ODEs). Subsequently, Gear's method is… More >

  • ABSTRACT

    Modeling Intergranular Stress Corrosion Cracking A Voronoi-Markovian-Monte Carlo Approach

    M.A. Arafin, J.A. Szpunar
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 59-60, 2009, DOI:10.3970/icces.2009.013.059
    Abstract This paper introduce a novel approach for face image segmentation base on Voronoi Diagram (VD) technique. We used intensity value and region pixels value for enhance preprocessing step on gray-scale image. The method for locating and extraction face/head boundary are applied feature point of the original image which are useful dual tessellation of the VD is know as Delaunay Triangulation (DT). A target of experiment is reported face image segmentation that uses still face image from BioID database. The result of this method clearly demonstrates the segmentation which performs in comparison with another method in quality of gray value and… More >

  • ABSTRACT

    Fragment Molecular Orbital Method for Large-Scale Biomolecular Systems

    Shigenori Tanaka1
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 61-62, 2009, DOI:10.3970/icces.2009.013.061
    Abstract Recent developments in ab initio calculations for biomolecular systems such as proteins and nucleic acids are illustrated on the basis of the fragment molecular orbital (FMO) method. Examples of the calculated systems include nuclear receptors with small ligands, cAMP receptor protein complexed with DNA, influenza virus hemagglutinin complexes, and bioluminescent oxyluciferin-luciferase complex. Quantitative calculations with the inclusion of relevant electron correlation effects have well reproduced those experimental results concerning the binding affinity, the mutation effects, the emission spectra, and so on. Feasibility of massively parallel computations with the FMO method is also discussed. More >

  • ABSTRACT

    Hybrid Quantum/Classical Approaches of Nano- and Meta-Materials

    Kenji Tsuruta1
    The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.3, pp. 63-64, 2009, DOI:10.3970/icces.2009.013.063
    Abstract Unique properties in artificially designed new materials are demonstrated via multiple-scale computational techniques. A density-functional/classical molecular-dynamics method is employed to investigate segregation dynamics of dopants in nanostructured ceramics/semiconductors. We also develop a classical electromagnetic simulation algorithm combining with an electronic-structure calculation for analysis on optical properties of meta-materials. We demonstrate that these novel algorithms are highly optimized for ultra-scale parallel computers. More >

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