Browsing by Author "Zhu, Luoding"
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Item 3D simulation of a viscous flow past a compliant model of arteriovenous-graft annastomosis(Elsevier, 2019-03) Bai, Zengding; Zhu, Luoding; Mathematical Sciences, School of ScienceHemodialysis is a common treatment for end-stage renal-disease patients to manage their renal failure while awaiting kidney transplant. Arteriovenous graft (AVG) is a major vascular access for hemodialysis but often fails due to the thrombosis near the vein-graft anastomosis. Almost all of the existing computational studies involving AVG assume that the vein and graft are rigid. As a first step to include vein/graft flexibility, we consider an ideal vein-AVG anastomosis model and apply the lattice Boltzmann-immersed boundary (LB-IB) framework for fluid-structure-interaction. The framework is extended to the case of non-uniform Lagrangian mesh for complex structure. After verification and validation of the numerical method and its implementation, many simulations are performed to simulate a viscous incompressible flow past the anastomosis model under pulsatile flow condition using various levels of vein elasticity. Our simulation results indicate that vein compliance may lessen flow disturbance and a more compliant vein experiences less wall shear stress (WSS).Item Accuracy improvement of the immersed boundary–lattice Boltzmann coupling scheme by iterative force correction(Elsevier, 2016-01) Zhang, Chunze; Cheng, Yongguang; Zhu, Luoding; Wu, Jiayang; Department of Mathematical Sciences, School of ScienceThe non-slip boundary condition at solid walls cannot be accurately achieved by the conventional immersed boundary–lattice Boltzmann (IB–LB) coupling schemes due to insufficient interpolation accuracy. To solve this problem, an iterative force correction procedure for the IB–LB coupling scheme is proposed. Cheng’s external forcing term in the LB equation is selected to properly incorporate the present and the next time step effects. The unknown IB force and the corresponding force on fluid at the next time step are calculated by iterative correction, based on the known immersed boundary speed, flow velocity, and the relationship between the IB speed and the IB force. Instead of the Dirac delta function, the Lagrange interpolation polynomial is used to obtain the IB speed from nearby fluid velocity. Typical cases, including the flow around a circular cylinder, shearing flow near a non-slip wall, and circular Couette flow between two inversely rotating cylinders, are simulated to verify and validate the method. It is shown that the present method guarantees the non-slip boundary condition and maintain the overall first-order spatial convergence rate of the conventional immersed boundary method (IBM). The accuracy improvement is obvious for both stationary and moving solid boundaries in both viscous flows and strong shearing flows. To demonstrate application possibility, a mechanical heart valve flow is also simulated, and better agreements with experimental data are achieved compared to those by commercial software.Item Computational Methods and Models in Circulatory and Reproductive Systems(Hindawi, 2016) Tian, Fang-Bao; Sui, Yi; Zhu, Luoding; Shu, Chang; Sung, Hyung J.; Department of Mathematical Sciences, School of ScienceItem A deformable plate interacting with a non-Newtonian fluid in three dimensions(AIP, 2017-08) Zhu, Luoding; Yu, Xijun; Liu, Nansheng; Cheng, Yongguang; Lu, Xiyun; Mathematical Sciences, School of ScienceWe consider a deformable plate interacting with a non-Newtonian fluid flow in three dimensions as a simple model problem for fluid-structure-interaction phenomena in life sciences (e.g., red blood cell interacting with blood flow). A power-law function is used for the constitutive equation of the non-Newtonian fluid. The lattice Boltzmann equation (the D3Q19 model) is used for modeling the fluid flow. The immersed boundary (IB) method is used for modeling the flexible plate and handling the fluid-plate interaction. The plate drag and its scaling are studied; the influences of three dimensionless parameters (power-law exponent, bending modulus, and generalized Reynolds number) are investigated.Item Designing a Parallel Memory-Aware Lattice Boltzmann Algorithm on Manycore Systems(IEEE, 2018-09) Fu, Yuankun; Li, Feng; Song, Fengguang; Zhu, Luoding; Computer and Information Science, School of ScienceLattice Boltzmann method (LBM) is an important computational fluid dynamics (CFD) approach to solving the Naiver-Stokes equations and simulating complex fluid flows. LBM is also well known as a memory bound problem and its performance is limited by the memory access time on modern computer systems. In this paper, we design and develop both sequential and parallel memory-aware algorithms to optimize the performance of LBM. The new memory-aware algorithms can enhance data reuses across multiple time steps to further improve the performance of the original and fused LBM. We theoretically analyze the algorithms to provide an insight into how data reuses occur in each algorithm. Finally, we conduct experiments and detailed performance analysis on two different manycore systems. Based on the experimental results, the parallel memory-aware LBM algorithm can outperform the fused LBM by up to 292% on the Intel Haswell system when using 28 cores, and by 302 % on the Intel Skylake system when using 48 cores.Item An IB Method for Non-Newtonian-Fluid Flexible-Structure Interactions in Three-Dimensions(Tech Science Press, 2019) Zhu, Luoding; Mathematical Sciences, School of ScienceProblems involving fluid flexible-structure interactions (FFSI) are ubiquitous in engineering and sciences. Peskin’s immersed boundary (IB) method is the first framework for modeling and simulation of such problems. This paper addresses a three-dimensional extension of the IB framework for non-Newtonian fluids which include power-law fluid, Oldroyd-B fluid, and FENE-P fluid. The motion of the non-Newtonian fluids are modelled by the lattice Boltzmann equations (D3Q19 model). The differential constitutive equations of Oldroyd-B and FENE-P fluids are solved by the D3Q7 model. Numerical results indicate that the new method is first-order accurate and conditionally stable. To show the capability of the new method, it is tested on three FFSI toy problems: a power-law fluid past a flexible sheet fixed at its midline, a flexible sheet being flapped periodically at its midline in an Oldroyd-B fluid, and a flexible sheet being rotated at one edge in a FENE-P fluid.Item Interactive 3D simulation for fluid–structure interactions using dual coupled GPUs(Springer, 2018-01) Zigon, Bob; Zhu, Luoding; Song, Fengguang; Mathematical Sciences, School of ScienceThe scope of this work involves the integration of high-speed parallel computation with interactive, 3D visualization of the lattice-Boltzmann-based immersed boundary method for fluid–structure interaction. An NVIDIA Tesla K40c is used for the computations, while an NVIDIA Quadro K5000 is used for 3D vector field visualization. The simulation can be paused at any time step so that the vector field can be explored. The density and placement of streamlines and glyphs are adjustable by the user, while panning and zooming is controlled by the mouse. The simulation can then be resumed. Unlike most scientific applications in computational fluid dynamics where visualization is performed after the computations, our software allows for real-time visualizations of the flow fields while the computations take place. To the best of our knowledge, such a tool on GPUs for FSI does not exist. Our software can facilitate debugging, enable observation of detailed local fields of flow and deformation while computing, and expedite identification of ‘correct’ parameter combinations in parametric studies for new phenomenon. Therefore, our software is expected to shorten the ‘time to solution’ process and expedite the scientific discoveries via scientific computing.Item IUPUI Center for Mathematical Biosciences(Office of the Vice Chancellor for Research, 2010-04-09) Boukai, Benzion; Chin, Ray; Dziubek, Andrea; Fokin, Vladimir; Ghosh, Samiran; Kuznetsov, Alexey; Li, Fang; Li, Jiliang; Rader, Andrew; Rubchinsky, Leonid; Sarkar, Jyotirmoy; Guidoboni, Giovanna; Worth, Robert; Zhu, LuodingAt-Large Mission: “to serve as an umbrella center for spearheading research and programmatic activities in the general bio-mathematics area” • promote and facilitate faculty excellence in mathematical and Computational research in the biosciences; • provide a mechanism and an environment that fosters collaborative research activities across the mathematical sciences and the life and health sciences schools at IUPUI— specifically with the IUSOM; • provide foundations and resources for further strategic development in targeted areas of mathematical and computational biosciences research; and • create greater opportunities and increase competitiveness in seeking and procuring extramural funding.Item Modeling and Implementation of an Asynchronous Approach to Integrating HPC and Big Data Analysis(Elsevier, 2016-06) Fu, Yuankun; Song, Fengguang; Zhu, Luoding; Department of Computer & Information Science, School of ScienceWith the emergence of exascale computing and big data analytics, many important scientific applications require the integration of computationally intensive modeling and simulation with data-intensive analysis to accelerate scientific discovery. In this paper, we create an analytical model to steer the optimization of the end-to-end time-to-solution for the integrated computation and data analysis. We also design and develop an intelligent data broker to efficiently intertwine the computation stage and the analysis stage to practically achieve the optimal time-to-solution predicted by the analytical model. We perform experiments on both synthetic applications and real-world computational fluid dynamics (CFD) applications. The experiments show that the analytic model exhibits an average relative error of less than 10%, and the application performance can be improved by up to 131% for the synthetic programs and by up to 78% for the real-world CFD application.Item Modeling and simulation of flow–osteocyte interaction in a lacuno-canalicular network(AIP, 2023-09) Barber, Jared; Manring, Isaac; Boileau, Sophie; Zhu, Luoding; Mathematical Sciences, School of ScienceOsteocytes are bone cells that can sense mechanical cues (stress and strain) and respond by releasing biochemical signals that direct bone remodeling. This process is called mechanotransduction which, in osteocytes, is not well understood yet because in vivo studies have proven difficult due to the complexity and inaccessibility of the flow–osteocyte lacuna-canaliculi system. While in silico studies (modeling and simulation) have become powerful, currently computational studies for the system often omit the fluid–structure interaction (FSI) between the cell and the surrounding fluids. To investigate the role of FSI in osteocyte mechanotransduction, we introduce a two-dimensional coarse-grained yet integrative model for flow–osteocyte interaction in a lacuno-canalicular network. The model uses the lattice Boltzmann immersed boundary framework to incorporate the flexible osteocyte (membrane, cytoskeleton, and cytosol), its processes, the interstitial fluid, and the rigid extracellular matrix that encases the system. One major result of our model is that the stress and strain tend to attain their local maxima near the regions where the processes meet the membrane of the main body.