Inertial Coupling Method for particles in an incompressible fluctuating fluid

We develop an inertial coupling method for modeling the dynamics of point-like 'blob' particles immersed in an incompressible fluid, generalizing previous work for compressible fluids. The coupling consistently includes excess (positive or negative) inertia of the particles relative to the displaced fluid, and accounts for thermal fluctuations in the fluid momentum equation. The coupling between the fluid and the blob is based on a no-slip constraint equating the particle velocity with the local average of the fluid velocity, and conserves momentum and energy. We demonstrate that the formulation obeys a fluctuation-dissipation balance, owing to the non-dissipative nature of the no-slip coupling. We develop a spatio-temporal discretization that preserves, as best as possible, these properties of the continuum formulation. In the spatial discretization, the local averaging and spreading operations are accomplished using compact kernels commonly used in immersed boundary methods. We find that the special properties of these kernels make the discrete blob a particle with surprisingly physically-consistent volume, mass, and hydrodynamic properties. We develop a second-order semi-implicit temporal integrator that maintains discrete fluctuation-dissipation balance, and is not limited in stability by viscosity. Furthermore, the temporal scheme requires only constant-coefficient Poisson and Helmholtz linear solvers, enabling a very efficient and simple FFT-based implementation on GPUs. We numerically investigate the performance of the method on several standard test problems...Comment: Contains a number of corrections and an additional Figure 7 (and associated discussion) relative to published versio

cuIBM -- A GPU-accelerated Immersed Boundary Method

A projection-based immersed boundary method is dominated by sparse linear algebra routines. Using the open-source Cusp library, we observe a speedup (with respect to a single CPU core) which reflects the constraints of a bandwidth-dominated problem on the GPU. Nevertheless, GPUs offer the capacity to solve large problems on commodity hardware. This work includes validation and a convergence study of the GPU-accelerated IBM, and various optimizations.Comment: Extended paper post-conference, presented at the 23rd International Conference on Parallel Computational Fluid Dynamics (http://www.parcfd.org), ParCFD 2011, Barcelona (unpublished

A Stochastic Immersed Boundary Method for Fluid-Structure Dynamics at Microscopic Length Scales

In this work it is shown how the immersed boundary method of (Peskin2002) for modeling flexible structures immersed in a fluid can be extended to include thermal fluctuations. A stochastic numerical method is proposed which deals with stiffness in the system of equations by handling systematically the statistical contributions of the fastest dynamics of the fluid and immersed structures over long time steps. An important feature of the numerical method is that time steps can be taken in which the degrees of freedom of the fluid are completely underresolved, partially resolved, or fully resolved while retaining a good level of accuracy. Error estimates in each of these regimes are given for the method. A number of theoretical and numerical checks are furthermore performed to assess its physical fidelity. For a conservative force, the method is found to simulate particles with the correct Boltzmann equilibrium statistics. It is shown in three dimensions that the diffusion of immersed particles simulated with the method has the correct scaling in the physical parameters. The method is also shown to reproduce a well-known hydrodynamic effect of a Brownian particle in which the velocity autocorrelation function exhibits an algebraic tau^(-3/2) decay for long times. A few preliminary results are presented for more complex systems which demonstrate some potential application areas of the method.Comment: 52 pages, 11 figures, published in journal of computational physic

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

We present a computational framework for the simulation of blood flow with fully resolved red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver for the blood plasma, a novel finite element based solver for the deformable bodies and an immersed boundary method for the fluid-solid interaction. For the RBCs, we propose a nodal projective FEM (npFEM) solver which has theoretical advantages over the more commonly used mass-spring systems (mesoscopic modeling), such as an unconditional stability, versatile material expressivity, and one set of parameters to fully describe the behavior of the body at any mesh resolution. At the same time, the method is substantially faster than other FEM solvers proposed in this field, and has an efficiency that is comparable to the one of mesoscopic models. At its core, the solver uses specially defined potential energies, and builds upon them a fast iterative procedure based on quasi-Newton techniques. For a known material, our solver has only one free parameter that demands tuning, related to the body viscoelasticity. In contrast, state-of-the-art solvers for deformable bodies have more free parameters, and the calibration of the models demands special assumptions regarding the mesh topology, which restrict their generality and mesh independence. We propose as well a modification to the potential energy proposed by Skalak et al. 1973 for the red blood cell membrane, which enhances the strain hardening behavior at higher deformations. Our viscoelastic model for the red blood cell, while simple enough and applicable to any kind of solver as a post-convergence step, can capture accurately the characteristic recovery time and tank-treading frequencies. The framework is validated using experimental data, and it proves to be scalable for multiple deformable bodies

A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting

An explicit moving boundary method for the numerical solution of time-dependent hyperbolic conservation laws on grids produced by the intersection of complex geometries with a regular Cartesian grid is presented. As it employs directional operator splitting, implementation of the scheme is rather straightforward. Extending the method for static walls from Klein et al., Phil. Trans. Roy. Soc., A367, no. 1907, 4559-4575 (2009), the scheme calculates fluxes needed for a conservative update of the near-wall cut-cells as linear combinations of standard fluxes from a one-dimensional extended stencil. Here the standard fluxes are those obtained without regard to the small sub-cell problem, and the linear combination weights involve detailed information regarding the cut-cell geometry. This linear combination of standard fluxes stabilizes the updates such that the time-step yielding marginal stability for arbitrarily small cut-cells is of the same order as that for regular cells. Moreover, it renders the approach compatible with a wide range of existing numerical flux-approximation methods. The scheme is extended here to time dependent rigid boundaries by reformulating the linear combination weights of the stabilizing flux stencil to account for the time dependence of cut-cell volume and interface area fractions. The two-dimensional tests discussed include advection in a channel oriented at an oblique angle to the Cartesian computational mesh, cylinders with circular and triangular cross-section passing through a stationary shock wave, a piston moving through an open-ended shock tube, and the flow around an oscillating NACA 0012 aerofoil profile.Comment: 30 pages, 27 figures, 3 table