Browsing by Subject "Fluid-structure interaction"

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    Modeling and Simulation of Osteocyte-Fluid Interaction in a Lacuno-Canalicular Network in Three Dimensions
    (2024-12) Karimli, Nigar; Barber, Jared; Zhu, Luoding; Arciero, Julia; Na, Sungsoo
    Bone health relies on its cells' ability to sense and respond to mechanical forces, a process primarily managed by osteocytes embedded within the bone matrix. The cells reside in the lacuno-canalicular network (LCN), a complex structure, comprised of lacunae (small cavities) and canaliculi (microscopic channels), through which they communicate and receive nutrients. The mechanotransduction (MT) process, by which osteocytes convert mechanical signals from mechanical loading into biochemical responses, is essential for bone remodeling but remains poorly understood. Both in-vitro and in-vivo studies present challenges in directly measuring the cellular stresses and strains involved, making computational modeling a valuable tool for studying osteocyte mechanics. In this dissertation, we present a coarse-grained, integrative model designed to simulate stress and strain distributions within an osteocyte and its microenvironment. Our model features the osteocyte membrane represented as a network of viscoelastic springs, with six slender, arm-like osteocytic processes extending from the membrane. The osteocyte is immersed in interstitial fluid and encompassed by the rigid extracellular matrix (ECM). The cytosol and interstitial fluid are both modeled as water-like, viscous incompressible fluids, allowing us to capture the fluid-structure interactions crucial to understanding the MT. To simulate these interactions, we employ the Lattice Boltzmann - Immersed Boundary (LB-IB) method. This approach couples the Lattice Boltzmann method, which numerically solves fluid equations, with the immersed boundary method, which handles the interactions between the osteocyte structures and the surrounding fluids. This framework consists of a system of integro-partial differential equations describing both fluid and solid dynamics, enabling a detailed examination of force, strain, and stress distribution within the osteocyte. Major results include 1) increased incoming flow routes results in increased stress and strain, 2) regions of higher stress and strain are concentrated near the junctions where the osteocytic processes meet the main body.
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    Towards a high performance parallel library to compute fluid flexible structures interactions
    (2015-04-08) Nagar, Prateek; Song, Fengguang; Zhu, Luoding; Mukhopadhyay, Snehasis
    LBM-IB method is useful and popular simulation technique that is adopted ubiquitously to solve Fluid-Structure interaction problems in computational fluid dynamics. These problems are known for utilizing computing resources intensively while solving mathematical equations involved in simulations. Problems involving such interactions are omnipresent, therefore, it is eminent that a faster and accurate algorithm exists for solving these equations, to reproduce a real-life model of such complex analytical problems in a shorter time period. LBM-IB being inherently parallel, proves to be an ideal candidate for developing a parallel software. This research focuses on developing a parallel software library, LBM-IB based on the algorithm proposed by [1] which is first of its kind that utilizes the high performance computing abilities of supercomputers procurable today. An initial sequential version of LBM-IB is developed that is used as a benchmark for correctness and performance evaluation of shared memory parallel versions. Two shared memory parallel versions of LBM-IB have been developed using OpenMP and Pthread library respectively. The OpenMP version is able to scale well enough, as good as 83% speedup on multicore machines for <=8 cores. Based on the profiling and instrumentation done on this version, to improve the data-locality and increase the degree of parallelism, Pthread based data centric version is developed which is able to outperform the OpenMP version by 53% on manycore machines. A distributed version using the MPI interfaces on top of the cube based Pthread version has also been designed to be used by extreme scale distributed memory manycore systems.