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  • Open Access


    A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids

    Magdalini Ntetsika, Panayiotis Papadopoulos*

    CMES-Computer Modeling in Engineering & Sciences, Vol.129, No.3, pp. 1243-1258, 2021, DOI:10.32604/cmes.2021.017404

    Abstract A new and computationally efficient version of the immersed boundary method, which is combined with the coarse-graining method, is introduced for modeling inextensible filaments immersed in low-Reynolds number flows. This is used to represent actin biopolymers, which are constituent elements of the cytoskeleton, a complex network-like structure that plays a fundamental role in shape morphology. An extension of the traditional immersed boundary method to include a stochastic stress tensor is also proposed in order to model the thermal fluctuations in the fluid at smaller scales. By way of validation, the response of a single, massless, inextensible semiflexible filament immersed in… More >

  • Open Access


    Improvement of Coarse-Grained Particle Method for Materials: Finite-Temperature and Inhomogeneity Effects

    T. Nakamura1, R. Kobyashi1, S. Ogata1

    CMES-Computer Modeling in Engineering & Sciences, Vol.73, No.4, pp. 357-386, 2011, DOI:10.3970/cmes.2011.073.357

    Abstract The coarse-grained particle (CGP) method has been proposed to coarse-grain a crystalline system of atoms to meso-scale. In the method, virtual particles are distributed in the system, and the inter-particle interaction is calculated through the constrained statistical ensemble average of the atomic Hamiltonian at a given temperature. For simplicity, however, the harmonic approximation has been used for the inter-atomic interaction and hence anharmonicity at finite temperatures has been ignored. We improve the former CGP method to incorporate the anharmonicity of atomic system at finite temperatures into the inter-particle interaction. Also the divide-and-conquer strategy is applied to calculate the inter-particle interaction… More >

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