Simulation of cell movement through evolving environment: a fictitious domain approach

A numerical method for simulating the movement of unicellular organisms which respond to chemical signals is presented. Cells are modelled as objects of finite size while the extracellular space is described by reaction-diffusion partial differential equations. This modular simulation allows the implementation of different models at the different scales encountered in cell biology and couples them in one single framework. The global computational cost is contained thanks to the use of the fictitious domain method for finite elements, allowing the efficient solve of partial differential equations in moving domains. Finally, a mixed formulation is adopted in order to better monitor the flux of chemicals, specifically at the interface between the cells and the extracellular domain

Simulating water-entry/exit problems using Eulerian-Lagrangian and fully-Eulerian fictitious domain methods within the open-source IBAMR library

In this paper we employ two implementations of the fictitious domain (FD) method to simulate water-entry and water-exit problems and demonstrate their ability to simulate practical marine engineering problems. In FD methods, the fluid momentum equation is extended within the solid domain using an additional body force that constrains the structure velocity to be that of a rigid body. Using this formulation, a single set of equations is solved over the entire computational domain. The constraint force is calculated in two distinct ways: one using an Eulerian-Lagrangian framework of the immersed boundary (IB) method and another using a fully-Eulerian approach of the Brinkman penalization (BP) method. Both FSI strategies use the same multiphase flow algorithm that solves the discrete incompressible Navier-Stokes system in conservative form. A consistent transport scheme is employed to advect mass and momentum in the domain, which ensures numerical stability of high density ratio multiphase flows involved in practical marine engineering applications. Example cases of a free falling wedge (straight and inclined) and cylinder are simulated, and the numerical results are compared against benchmark cases in literature.Comment: The current paper builds on arXiv:1901.07892 and re-explains some parts of it for the reader's convenienc

Modelling mitral valvular dynamics–current trend and future directions

Dysfunction of mitral valve causes morbidity and premature mortality and remains a leading medical problem worldwide. Computational modelling aims to understand the biomechanics of human mitral valve and could lead to the development of new treatment, prevention and diagnosis of mitral valve diseases. Compared with the aortic valve, the mitral valve has been much less studied owing to its highly complex structure and strong interaction with the blood flow and the ventricles. However, the interest in mitral valve modelling is growing, and the sophistication level is increasing with the advanced development of computational technology and imaging tools. This review summarises the state-of-the-art modelling of the mitral valve, including static and dynamics models, models with fluid-structure interaction, and models with the left ventricle interaction. Challenges and future directions are also discussed

A Review on Contact and Collision Methods for Multi-body Hydrodynamic problems in Complex Flows

Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the combustion process, to aerosol deposition in spray medication, along with many others. Due to their strongly nonlinear and multiscale nature, the above complex phenomena still raise a very steep challenge to the most computational methods. In this review, we provide comprehensive coverage of multibody hydrodynamic (MBH) problems focusing on particulate suspensions in complex fluidic systems that have been simulated using hybrid Eulerian-Lagrangian particulate flow models. Among these hybrid models, the Immersed Boundary-Lattice Boltzmann Method (IB-LBM) provides mathematically simple and computationally-efficient algorithms for solid-fluid hydrodynamic interactions in MBH simulations. This paper elaborates on the mathematical framework, applicability, and limitations of various 'simple to complex' representations of close-contact interparticle interactions and collision methods, including short-range inter-particle and particle-wall steric interactions, spring and lubrication forces, normal and oblique collisions, and mesoscale molecular models for deformable particle collisions based on hard-sphere and soft-sphere models in MBH models to simulate settling or flow of nonuniform particles of different geometric shapes and sizes in diverse fluidic systems.Comment: 37 pages, 12 Figure

Pore-scale direct numerical simulation of particle transport in porous media

A computational platform for direct numerical simulation of fluid-particle two-phase flow in porous media is presented in this study. In the proposed platform, the Navier-Stokes equations are used to describe the motion of the continuous phase, while the discrete element method (DEM) is employed to evaluate particle-particle and particle-wall interactions, with a fictitious domain method being adopted to evaluate particle-fluid interactions. Particle-wall contact states are detected by the ERIGID scheme. Moreover, a new scheme, namely, base point-increment method is developed to improve the accuracy of particle tracking in porous media. In order to improve computationally efficiency, a time splitting strategy is applied to couple the fluid and DEM solvers, allowing different time steps to be used which are adaptively determined according to the stability conditions of each solver. The proposed platform is applied to particle transport in a porous medium with its pore structure being reconstructed from micro-CT scans from a real rock. By incorporating the effect of pore structure which has a comparable size to the particles, numerical results reveal a number of distinct microscopic flow mechanisms and the corresponding macroscopic characteristics. The time evolution of the inlet to outlet pressure-difference consists of large-scale spikes and small-scale fluctuations. Apart from the influence through direct contacts between particles, the motion of a particle can also be affected by particles without contact through blocking a nearby passage for fluid flow. Particle size has a profound influence on the macroscopic motion behavior of particles. Small particles are easier to move along the main stream and less dispersive in the direction perpendicular to the flow than large particles

Development and application of a three dimensional numerical model for predicting pollutant and sediment transport using an Eulerian-Lagrangian marker particle technique

A computer coded Lagrangian marker particle in Eulerian finite difference cell solution to the three dimensional incompressible mass transport equation, Water Advective Particle in Cell Technique, WAPIC, was developed, verified against analytic solutions, and subsequently applied in the prediction of long term transport of a suspended sediment cloud resulting from an instantaneous dredge spoil release. Numerical results from WAPIC were verified against analytic solutions to the three dimensional incompressible mass transport equation for turbulent diffusion and advection of Gaussian dye releases in unbounded uniform and uniformly sheared uni-directional flow, and for steady-uniform plug channel flow. WAPIC was utilized to simulate an analytic solution for non-equilibrium sediment dropout from an initially vertically uniform particle distribution in one dimensional turbulent channel flow

A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies

We present a moving control volume (CV) approach to computing hydrodynamic forces and torques on complex geometries. The method requires surface and volumetric integrals over a simple and regular Cartesian box that moves with an arbitrary velocity to enclose the body at all times. The moving box is aligned with Cartesian grid faces, which makes the integral evaluation straightforward in an immersed boundary (IB) framework. Discontinuous and noisy derivatives of velocity and pressure at the fluid-structure interface are avoided and far-field (smooth) velocity and pressure information is used. We re-visit the approach to compute hydrodynamic forces and torques through force/torque balance equation in a Lagrangian frame that some of us took in a prior work (Bhalla et al., J Comp Phys, 2013). We prove the equivalence of the two approaches for IB methods, thanks to the use of Peskin's delta functions. Both approaches are able to suppress spurious force oscillations and are in excellent agreement, as expected theoretically. Test cases ranging from Stokes to high Reynolds number regimes are considered. We discuss regridding issues for the moving CV method in an adaptive mesh refinement (AMR) context. The proposed moving CV method is not limited to a specific IB method and can also be used, for example, with embedded boundary methods