Magdalini Ntetsika, Panayiotis Papadopoulos^*

CMES-Computer Modeling in Engineering & Sciences, Vol.129, No.3, pp. 1243-1258, 2021, DOI:10.32604/cmes.2021.017404 - 25 November 2021

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, More >

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 More >