Related papers: Efficient Convergent Boundary Integral Methods for…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet for fluid problems it only achieves first-order spatial accuracy near embedded boundaries for the velocity field and…
For scattering problems of time-harmonic waves, the boundary integral equation (BIE) methods are highly competitive, since they are formulated on lower-dimension boundaries or interfaces, and can automatically satisfy outgoing radiation…
The velocity and trajectory of particle moving along the corrugated (rough) surface under action of gravity is obtained by meshless Boundary Singularity Method (BSM). This physical situation is found often in biological systems and…
The immersed boundary (IB) method has been used as a means to simulate fluid-membrane interactions in a wide variety of biological and engineering applications. Although the numerical convergence of the method has been empirically verified,…
Fluid flows containing dilute or dense suspensions of thin fibers are widespread in biological and industrial processes. To describe the motion of a thin immersed fiber, or to describe the forces acting on it, it is convenient to work with…
The manuscript describes a quadrature rule that is designed for the high order discretization of boundary integral equations (BIEs) using the Nystr\"{o}m method. The technique is designed for surfaces that can naturally be parameterized…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…
Semiflexible slender filaments are ubiquitous in nature and cell biology, including in the cytoskeleton, where reorganization of actin filaments allows the cell to move and divide. Most methods for simulating semiflexible inextensible…
We present a fluctuating boundary integral method (FBIM) for overdamped Brownian Dynamics (BD) of two-dimensional periodic suspensions of rigid particles of complex shape immersed in a Stokes fluid. We develop a novel approach for…
We introduce a novel quadrature strategy for Isogeometric Analysis (IgA) boundary element discretizations, specifically tailored to collocation methods. Thanks to the dimensionality reduction and the natural handling of unbounded domains,…
The eigenvalues and eigenfunctions of the Stokes operator have been the subject of intense analytical investigation and have applications in the study and simulation of the Navier-Stokes equations. As the Stokes operator is a fourth-order…
A second-order accurate kernel-free boundary integral method is presented for Stokes and Navier boundary value problems on three-dimensional irregular domains. It solves equations in the framework of boundary integral equations, whose…
A fourth-order finite volume embedded boundary (EB) method is presented for the unsteady Stokes equations. The algorithm represents complex geometries on a Cartesian grid using EB, employing a technique to mitigate the "small cut-cell"…
In this work we consider how surface-adherent bacterial biofilm communities respond in flowing systems. We simulate the fluid-structure interaction and separation process using the immersed boundary method. In these simulations we model and…
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…
Slender fibers are ubiquitous in biology, physics, and engineering, with prominent examples including bacterial flagella and cytoskeletal fibers. In this setting, slender body theories (SBTs), which give the resistance on the fiber…
This paper introduces a new immersed boundary (IB) method for viscous incompressible flow, based on a Fourier spectral method for the fluid solver and on the nonuniform fast Fourier transform (NUFFT) algorithm for coupling the fluid with…
In this paper, we first develop a mathematical model for long-range, hydrophobic attraction between amphiphilic particles. The non-pairwise interactions follow from the first variation of a hydrophobic attraction domain functional. The…
The method of regularized stokeslets is a powerful numerical method to solve the Stokes flow equations for problems in biological fluid mechanics. A recent variation of this method incorporates a nearest-neighbor discretization to improve…