A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints. We illustrate, with several examples, to which extent the proposed formulation offers a flexible and versatile framework for the quantitative modeling of flexible fibers deformation and rotation in shear flow, the dynamics of actuated filaments and the propulsion of active swimmers. Furthermore, a new contact model called Gears Model is proposed and successfully tested. It avoids the use of numerical artifices such as repulsive forces between adjacent beads, a source of numerical difficulties in the temporal integration of previous Bead Models.Comment: 41 pages, 15 figure

Parallel algorithms for direct blood flow simulations

Fluid mechanics of blood can be well approximated by a mixture model of a Newtonian fluid and deformable particles representing the red blood cells. Experimental and theoretical evidence suggests that the deformation and rheology of red blood cells is similar to that of phospholipid vesicles. Vesicles and red blood cells are both area preserving closed membranes that resist bending. Beyond red blood cells, vesicles can be used to investigate the behavior of cell membranes, intracellular organelles, and viral particles. Given the importance of vesicle flows, in this thesis we focus in efficient numerical methods for such problems: we present computationally scalable algorithms for the simulation of dilute suspension of deformable vesicles in two and three dimensions. Our method is based on the boundary integral formulation of Stokes flow. We present new schemes for simulating the three-dimensional hydrodynamic interactions of large number of vesicles with viscosity contrast. The algorithms incorporate a stable time-stepping scheme, high-order spatiotemporal discretizations, spectral preconditioners, and a reparametrization scheme capable of resolving extreme mesh distortions in dynamic simulations. The associated linear systems are solved in optimal time using spectral preconditioners. The highlights of our numerical scheme are that (i) the physics of vesicles is faithfully represented by using nonlinear solid mechanics to capture the deformations of each cell, (ii) the long-range, N-body, hydrodynamic interactions between vesicles are accurately resolved using the fast multipole method (FMM), and (iii) our time stepping scheme is unconditionally stable for the flow of single and multiple vesicles with viscosity contrast and its computational cost-per-simulation-unit-time is comparable to or less than that of an explicit scheme. We report scaling of our algorithms to simulations with millions of vesicles on thousands of computational cores.PhDCommittee Chair: Biros, George; Committee Member: Alben, Silas; Committee Member: Fernandez-Nieves, Alberto; Committee Member: Hu, David; Committee Member: Vuduc, Richar

Numerical Methods for Fluid-Structure Interaction - A Review

The interactions between incompressible fluid flows and immersed structures are nonlinear multi-physics phenomena that have applications to a wide range of scientific and engineering disciplines. In this article, we review representative numerical-methods based on conforming and non-conforming meshes that are currently available for computing fluid-structure interaction problems, with an emphasis on some of the recent developments in the field. A goal is to categorize the selected methods and assess their accuracy and efficiency. We discuss challenges faced by researchers in this field, and we emphasize the importance of interdisciplinary effort for advancing the study in fluid-structure interaction

A numerical method for fluid-structure interactions of slender rods in turbulent flow

This thesis presents a numerical method for the simulation of fluid-structure interaction (FSI) problems on high-performance computers. The proposed method is specifically tailored to interactions between Newtonian fluids and a large number of slender viscoelastic structures, the latter being modeled as Cosserat rods. From a numerical point of view, such kind of FSI requires special techniques to reach numerical stability. When using a partitioned fluid-structure coupling approach this is usually achieved by an iterative procedure, which drastically increases the computational effort. In the present work, an alternative coupling approach is developed based on an immersed boundary method (IBM). It is unconditionally stable and exempt from any global iteration between the fluid part and the structure part. The proposed FSI solver is employed to simulate the flow over a dense layer of vegetation elements, usually designated as canopy flow. The abstracted canopy model used in the simulation consists of 800 strip-shaped blades, which is the largest canopy-resolving simulation of this type done so far. To gain a deeper understanding of the physics of aquatic canopy flows the simulation data obtained are analyzed, e.g., concerning the existence and shape of coherent structures

Efficient coarse-grained brownian dynamics simulations for dna and lipid bilayer membrane with hydrodynamic interactions

The coarse-grained molecular dynamics (CGMD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the so-called hydrodynamic interactions (HIs). From simple biological systems such as a single DNA macromolecule to large and complicated systems, for instances, vesicles and red blood cells (RBCs), the numerical results have shown outstanding agreements with experiments and continuum modeling by adopting Stokesian dynamics and explicit solvent model. Finally, when combined with fast algorithms such as the fast multipole method (FMM) which has nearly optimal complexity in the total number of CG particles, the resulting method is parallelizable, scalable to large systems, and stable for large time step size, thus making the long-time large-scale BD simulation within practical reach. This will be useful for the study of a large collection of molecules or cells immersed in the fluids. This dissertation can be divided into three main subjects: (1) An efficient algorithm is proposed to simulate the motion of a single DNA molecule in linear flows. The algorithm utilizes the integrating factor method to cope with the effect of the linear flow of the surrounding fluid and applies the Metropolis method (MM) in [N. Bou-Rabee, A. Donev, and E. Vanden-Eijnden, Multiscale Model. Simul. 12, 781 (2014)] to achieve more efficient BD simulation. More importantly, this proposed method permits much larger time step size than methods in previous literature while still maintaining the stability of the BD simulation, which is advantageous for long-time BD simulation. The numerical results on λ-DNA agree very well with both experimental data and previous simulation results. (2) Lipid bilayer membranes have been extensively studied by CGMD simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 ~ 6 nm so that there is only one particle in the thickness direction. In [H. Yuan et al., Phys. Rev. E, 82, 011905 (2010)], Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity. This dissertation provides a detailed implementation of this interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamellar vesicle (GUV) and RBCs. Moreover, this work also considers the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporates coarse-grained water molecules to account for hydrodynamic interactions. (3) An action field method for lipid bilayer membrane model is introduced where several lipid molecules are represented by a Janus particle with corresponding orientation pointing from lipid head to lipid tail. With this level of coarse-grained modeling, as the preliminary setup, the lipid tails occupy a half sphere and the lipid heads take the other half. An action field is induced from lipid-lipid interactions and exists everywhere in the computational domain. Therefore, a hydrophobic attraction energy can be described from utilizing the variational approach and its minimizer with respect to the action field is the so-called screened Laplace equation. For the numerical method, the well-known integral equation method (IEM) has great capability to solve exterior screened Laplace equation with Dirichlet boundary conditions. Finally, one then can obtain the lipid dynamics to validate the self-assembly property and other physical properties of lipid bilayer membrane. This approach combines continuum modeling with CGMD and gives a different perspective to the membrane energy model from the traditional Helfrich membrane free energy

A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints. We illustrate, with several examples, to which extent the proposed formulation offers a flexible and versatile framework for the quantitative modeling of flexible fibers deformation and rotation in shear flow, the dynamics of actuated filaments and the propulsion of active swimmers. Furthermore, a new contact model called Gears Model is proposed and successfully tested. It avoids the use of numerical artifices such as repulsive forces between adjacent beads, a source of numerical difficulties in the temporal integration of previous Bead Models

Novel Paradigms in Physics-Based Animation: Pointwise Divergence-Free Fluid Advection and Mixed-Dimensional Elastic Object Simulation

This thesis explores important but so far less studied aspects of physics-based animation: a simulation method for mixed-dimensional and/or non-manifold elastic objects, and a pointwise divergence-free velocity interpolation method applied to fluid simulation. Considering the popularity of single-type models e.g., hair, cloths, soft bodies, etc., in deformable body simulations, more complicated coupled models have gained less attention in graphics research, despite their relative ubiquity in daily life. This thesis presents a unified method to simulate such models: elastic bodies consisting of mixed-dimensional components represented with potentially non-manifold simplicial meshes. Building on well-known simplicial rod, shell, and solid models, this thesis categorizes and defines a comprehensive palette expressing all possible constraints and elastic energies for stiff and flexible connections between the 1D, 2D, and 3D components of a single conforming simplicial mesh. For fluid animation, this thesis proposes a novel methodology to enhance grid-based fluid animation with pointwise divergence-free velocity interpolation. Unlike previous methods which interpolate discrete velocity values directly for advection, this thesis proposes using intermediate steps involving vector potentials: first build a discrete vector potential field, interpolate these values to form a pointwise potential, and apply the continuous curl to recover a pointwise divergence-free flow field. Particles under these pointwise divergence-free flows exhibit significantly better particle distributions than divergent flows over time. To accelerate the use of vector potentials, this thesis proposes an efficient method that provides boundary-satisfying and smooth discrete potential fields on uniform and cut-cell grids. This thesis also introduces an improved ramping strategy for the “Curl-Noise” method of Bridson et al. (2007), which enforces exact no-normal-flow on the exterior domain boundaries and solid surfaces. The ramping method in the thesis effectively reduces the incidence of particles colliding with obstacles or creating erroneous gaps around the obstacles, while significantly alleviating the artifacts the original ramping strategy produces