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We show that the standard boundary integral operators, defined on the unit sphere, for the Stokes equations diagonalize on a specific set of vector spherical harmonics and provide formulas for their spectra. We also derive analytical expressions for evaluating the operators away from the boundary. When two particle are located close to each other, we use a truncated series expansion to compute the hydrodynamic interaction. On the other hand, we use the standard spectrally accurate quadrature scheme to evaluate smooth integrals on the far-field, and accelerate the resulting discrete sums using the fast multipole method (FMM). We employ this discretization scheme to analyze several boundary integral formulations of interest including those arising in porous media flow, active matter and magneto-hydrodynamics of rigid particles. We provide numerical results verifying the accuracy and scaling of their evaluation. [ABSTRACT FROM AUTHOR]

In this paper, we develop a new boundary integral equation formulation that describes the coupled electro- and hydro-dynamics of a vesicle suspended in a viscous fluid and subjected to external flow and electric fields. The dynamics of the vesicle are characterized by a competition between the elastic, electric and viscous forces on its membrane. The classical Taylor–Melcher leaky-dielectric model is employed for the electric response of the vesicle and the Helfrich energy model combined with local inextensibility is employed for its elastic response. The coupled governing equations for the vesicle position and its transmembrane electric potential are solved using a numerical method that is spectrally accurate in space and first-order in time. The method uses a semi-implicit time-stepping scheme to overcome the numerical stiffness associated with the governing equations. [ABSTRACT FROM AUTHOR]

We propose numerical algorithms for the simulation of the dynamics of three-dimensional vesicles suspended in viscous Stokesian fluid. Our method is an extension of our previous work (S.K. Veerapaneni et al., 2011) [37] to flows with viscosity contrast. This generalization requires a change in the boundary integral formulation of the solution, in which a double-layer Stokes integral is introduced, and leads to changes in the fluid dynamics due to the viscosity contrast of the vesicles, which can no longer be efficiently resolved with existing algorithms. In this paper we describe the algorithms needed to handle flows with viscosity contrast accurately and efficiently. We show that a globally semi-implicit method does not have any time-step stability constraint for flows with single and multiple vesicles with moderate viscosity contrast and the computational cost per simulation unit time is comparable to or less than that of an explicit scheme. Automatic oversampling adaptation enables us to achieve high accuracy with very low spectral resolution. We conduct numerical experiments to investigate the stability, accuracy, and the computational cost of the algorithms. Overall, our method achieves several orders of magnitude speed-up compared to the standard explicit schemes. [ABSTRACT FROM AUTHOR]

Abstract: Vesicles are locally-inextensible fluid membranes that can sustain bending. In this paper, we extend the study of Veerapaneni et al. [S.K. Veerapaneni, D. Gueyffier, G. Biros, D. Zorin, A numerical method for simulating the dynamics of 3D axisymmetric vesicles suspended in viscous flows, Journal of Computational Physics 228 (19) (2009) 7233–7249] to general non-axisymmetric vesicle flows in three dimensions. Although the main components of the algorithm are similar in spirit to the axisymmetric case (spectral approximation in space, semi-implicit time-stepping scheme), important new elements need to be introduced for a full 3D method. In particular, spatial quantities are discretized using spherical harmonics, and quadrature rules for singular surface integrals need to be adapted to this case; an algorithm for surface reparameterization is needed to ensure stability of the time-stepping scheme, and spectral filtering is introduced to maintain reasonable accuracy while minimizing computational costs. To characterize the stability of the scheme and to construct preconditioners for the iterative linear system solvers used in the semi-implicit time-stepping scheme, we perform a spectral analysis of the evolution operator on the unit sphere. By introducing these algorithmic components, we obtain a time-stepping scheme that circumvents the stability constraint on the time-step and achieves spectral accuracy in space. We present results to analyze the cost and convergence rates of the overall scheme. To illustrate the applicability of the new method, we consider a few vesicle-flow interaction problems: a single vesicle in relaxation, sedimentation, shear flows, and many-vesicle flows. [Copyright &y& Elsevier]

Abstract: We consider numerical algorithms for the simulation of hydrodynamics of two-dimensional vesicles suspended in a viscous Stokesian fluid. The motion of vesicles is governed by the interplay between hydrodynamic and elastic forces. Continuum models of vesicles use a two-phase fluid system with interfacial forces that include tension (to maintain local “surface” inextensibility) and bending. Vesicle flows are challenging to simulate. On the one hand, explicit time-stepping schemes suffer from a severe stability constraint due to the stiffness related to high-order spatial derivatives in the bending term. On the other hand, implicit time-stepping schemes can be expensive because they require the solution of a set of nonlinear equations at each time step. Our method is an extension of the work of Veerapaneni et al. [S.K. Veerapaneni, D. Gueyffier, D. Zorin, G. Biros, A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D, Journal of Computational Physics 228(7) (2009) 2334–2353], in which a semi-implicit time-marching scheme based on a boundary integral formulation of the Stokes problem for vesicles in an unbounded medium was proposed. In this paper, we consider two important generalizations: (i) confined flows within arbitrary-shaped stationary/moving geometries; and (ii) flows in which the interior (to the vesicle) and exterior fluids have different viscosity. In the rest of the paper, we will refer to this as the “viscosity contrast”. These two problems require solving additional integral equations and cause nontrivial modifications to the previous numerical scheme. Our method does not have severe time-step stability constraints and its computational cost-per-time-step is comparable to that of an explicit scheme. The discretization is pseudo-spectral in space, and multistep BDF in time. We conduct numerical experiments to investigate the stability, accuracy and the computational cost of the algorithm. Overall, our method achieves several orders of magnitude speed-up compared to standard explicit schemes. As a preliminary validation of our scheme, we study the dependence of the inclination angle of a single vesicle in shear flow on the viscosity contrast and the reduced area of the vesicle, the lateral migration of vesicles in shear flow, the dispersion of two vesicles, and the effective viscosity of a dilute suspension of vesicles. [Copyright &y& Elsevier]

Abstract: We extend [Shravan K. Veerapaneni, Denis Gueyffier, Denis Zorin, George Biros, A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D, Journal of Computational Physics 228(7) (2009) 2334–2353] to the case of three-dimensional axisymmetric vesicles of spherical or toroidal topology immersed in viscous flows. Although the main components of the algorithm are similar in spirit to the 2D case—spectral approximation in space, semi-implicit time-stepping scheme—the main differences are that the bending and viscous force require new analysis, the linearization for the semi-implicit schemes must be rederived, a fully implicit scheme must be used for the toroidal topology to eliminate a CFL-type restriction and a novel numerical scheme for the evaluation of the 3D Stokes single layer potential on an axisymmetric surface is necessary to speed up the calculations. By introducing these novel components, we obtain a time-scheme that experimentally is unconditionally stable, has low cost per time step, and is third-order accurate in time. We present numerical results to analyze the cost and convergence rates of the scheme. To verify the solver, we compare it to a constrained variational approach to compute equilibrium shapes that does not involve interactions with a viscous fluid. To illustrate the applicability of method, we consider a few vesicle-flow interaction problems: the sedimentation of a vesicle, interactions of one and three vesicles with a background Poiseuille flow. [Copyright &y& Elsevier]

Abstract: We present a new method for the evolution of inextensible vesicles immersed in a Stokesian fluid. We use a boundary integral formulation for the fluid that results in a set of nonlinear integro-differential equations for the vesicle dynamics. The motion of the vesicles is determined by balancing the non-local hydrodynamic forces with the elastic forces due to bending and tension. Numerical simulations of such vesicle motions are quite challenging. On one hand, explicit time-stepping schemes suffer from a severe stability constraint due to the stiffness related to high-order spatial derivatives and a milder constraint due to a transport-like stability condition. On the other hand, an implicit scheme can be expensive because it requires the solution of a set of nonlinear equations at each time step. We present two semi-implicit schemes that circumvent the severe stability constraints on the time step and whose computational cost per time step is comparable to that of an explicit scheme. We discretize the equations by using a spectral method in space, and a multistep third-order accurate scheme in time. We use the fast multipole method (FMM) to efficiently compute vesicle–vesicle interaction forces in a suspension with a large number of vesicles. We report results from numerical experiments that demonstrate the convergence and algorithmic complexity properties of our scheme. [Copyright &y& Elsevier]

Abstract: We present a method for the fast and accurate computation of distributed heat potentials in two dimensions. The distributed source is assumed to be given in terms of piecewise space–time Chebyshev polynomials. We discretize uniformly in time, whereas in space the polynomials are defined on the leaf nodes of a quadtree. The quadtree can vary at each time step. We combine a product integration rule with fast algorithms (fast heat potentials, nonuniform FFT, fast Gauss transform) to obtain a high-order accurate method with optimal complexity. If N is the number of time steps, M is the maximum number of leaf nodes over all the time steps and the input contains a qth-order polynomial representation of f, then, our method requires work to evaluate the heat potential at arbitrary space–time target locations. The overall convergence rate of the method is of order q. We present numerical experiments for q =4, 8, and 16, and we verify the theoretical convergence rate of the method. When the solution is sufficiently smooth, the 16th-order variant results in significant computational savings, even in the case in which we require only a few digits of accuracy. [Copyright &y& Elsevier]

While potential theoretic techniques have received significant interest and found broad success in the solution of linear partial differential equations (PDEs) in mathematical physics, limited adoption is reported in the case of nonlinear and/or inhomogeneous problems (i.e. with distributed volumetric sources) owing to outstanding challenges in producing a particular solution on complex domains while simultaneously respecting the competing ideals of allowing complete geometric flexibility, enabling source adaptivity, and achieving optimal computational complexity. This article presents a new high-order accurate algorithm for finding a particular solution to the PDE by means of a convolution of the volumetric source function with the Green's function in complex geometries. Utilizing volumetric domain decomposition, the integral is computed over a union of regular boxes (lending the scheme compatibility with adaptive box codes) and triangular regions (which may be potentially curved near boundaries). Singular and near-singular quadrature is handled by converting integrals on volumetric regions to line integrals bounding a reference volume cell using cell mappings and elements of the Poincaré lemma, followed by leveraging existing one-dimensional near-singular and singular quadratures appropriate to the singular nature of the kernel. The scheme achieves compatibility with fast multipole methods (FMMs) and thereby optimal asymptotic complexity by coupling global rules for target-independent quadrature of smooth functions to local target-dependent singular quadrature corrections, and it relies on orthogonal polynomial systems on each cell for well-conditioned, high-order and efficient (with respect to number of required volume function evaluations) approximation of arbitrary volumetric sources. Our domain discretization scheme is naturally compatible with standard meshing software such as Gmsh, which are employed to discretize a narrow region surrounding the domain boundaries. We present 8th-order accurate results, demonstrate the success of the method with examples showing up to 12-digit accuracy on complex geometries, and, for static geometries, our numerical examples show well over 99% of evaluation time of the particular solution is spent in the FMM step. • High-order accurate evaluation of Newton potential in complex geometry. • High-order accurate solution of inhomogeneous PDEs using potential theory. • Optimal complexity, adaptivity-compatible algorithms. • Novel methods for singular and near-singular multi-dimensional quadrature. [ABSTRACT FROM AUTHOR]

We present a new derivation of a boundary integral equation (BIE) for simulating the three-dimensional dynamics of arbitrarily-shaped rigid particles of genus zero immersed in a Stokes fluid, on which are prescribed forces and torques. Our method is based on a single-layer representation and leads to a simple second-kind integral equation. It avoids the use of auxiliary sources within each particle that play a role in some classical formulations. We use a spectrally accurate quadrature scheme to evaluate the corresponding layer potentials, so that only a small number of spatial discretization points per particle are required. The resulting discrete sums are computed in O ( n ) time, where n denotes the number of particles, using the fast multipole method (FMM). The particle positions and orientations are updated by a high-order time-stepping scheme. We illustrate the accuracy, conditioning and scaling of our solvers with several numerical examples. [ABSTRACT FROM AUTHOR]

• Collision resolution by convex quadratic programming. • Scalable and efficient parallel algorithm and implementation. • Accurate second-kind boundary integral formulation. We describe a computational framework for simulating suspensions of rigid particles in Newtonian Stokes flow. One central building block is a collision-resolution algorithm that overcomes the numerical constraints arising from particle collisions. This algorithm extends the well-known complementarity method for non-smooth multi-body dynamics to resolve collisions in dense rigid body suspensions. This approach formulates the collision resolution problem as a linear complementarity problem with geometric 'non-overlapping' constraints imposed at each time-step. It is then reformulated as a constrained quadratic programming problem and the Barzilai-Borwein projected gradient descent method is applied for its solution. This framework is designed to be applicable for any convex particle shape, e.g., spheres and spherocylinders, and applicable to any Stokes mobility solver, including the Rotne-Prager-Yamakawa approximation, Stokesian Dynamics, and PDE solvers (e.g., boundary integral and immersed boundary methods). In particular, this method imposes Newton's Third Law and records the entire contact network. Further, we describe a fast, parallel, and spectrally-accurate boundary integral method tailored for spherical particles, capable of resolving lubrication effects. We show weak and strong parallel scalings up to 8 × 10 4 particles with approximately 4 × 10 7 degrees of freedom on 1792 cores. We demonstrate the versatility of this framework with several examples, including sedimentation of particle clusters, and active matter systems composed of ensembles of particles driven to rotate. [ABSTRACT FROM AUTHOR]

• A spectrally-accurate close evaluation scheme for Stokes boundary integral operators. • Adaptive panel refinement for arbitrarily shaped boundaries. • Graded meshes to treat corners. • Example problems from microfluidic chip design and vascular network flows. We present a fast, high-order accurate and adaptive boundary integral scheme for solving the Stokes equations in complex—possibly nonsmooth—geometries in two dimensions. We apply the panel-based quadratures of Helsing and coworkers to evaluate to high accuracy the weakly-singular, hyper-singular, and super-singular integrals arising in the Nyström discretization, and also the near-singular integrals needed for flow and traction evaluation close to boundaries. The resulting linear system is solved iteratively via calls to a Stokes fast multipole method. We include an automatic algorithm to "panelize" a given geometry, and choose a panel order, which will efficiently approximate the density (and hence solution) to a user-prescribed tolerance. We show that this adaptive panel refinement procedure works well in practice even in the case of complex geometries with large number of corners, or close-to-touching smooth curves. In one example, for instance, a model 2D vascular network with 378 corners required less than 200K discretization points to obtain a 9-digit solution accuracy. [ABSTRACT FROM AUTHOR]