Related papers: A Discrete Ion Stochastic Continuum Overdamped Sol…
The immersed boundary (IB) method is an approach to fluid-structure interaction that uses Lagrangian variables to describe the structure and Eulerian variables to describe the fluid. Explicit time stepping schemes for the IB method require…
The immersed boundary method (IBM) of Peskin (J. Comput. Phys., 1977), and derived forms such as the projection method of Taira and Colonius (J. Comput. Phys., 2007), have been useful for simulating flow physics in problems with moving…
We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within Density Functional Theory (DFT), with particular emphasis on linear-scaling (LS)…
We develop a numerical method for simulating the dynamics of a droplet immersed in a generic time-dependent velocity gradient field. This approach is grounded on the hybrid coupling between the lattice Boltzmann (LB) method, employed for…
We present an efficient and accurate immersed boundary (IB) finite element (FE) method for internal flow problems with complex geometries (e.g., blood flow in the vascular system). In this study, we use a voxelized flow domain (discretized…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
A subsystem approach for obtaining electron binding energies in the valence region and apply it to the case of halide ions (X$^-$, X = F-At) in water. This approach is based on electronic structure calculations combining the relativistic…
We introduce a Rigid-Body Fluctuating Immersed Boundary (RB-FIB) method to perform large-scale Brownian dynamics simulations of suspensions of rigid particles in fully confined domains, without any need to explicitly construct Green's…
In this paper, we solve the linearized Poisson-Boltzmann equation, used to model the electric potential of macromolecules in a solvent. We derive a corrected trapezoidal rule with improved accuracy for a boundary integral formulation of the…
This work develops advanced numerical methods for free-surface simulations of polymer mixing processes, integrating a Volume of Fluid (VOF) interface-capturing approach with a non-conforming Immersed Boundary (IB) method to model two-phase…
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…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
We present a new mesoscale model for ionic liquids based on a low Mach number fluctuating hydrodynamics formulation for multicomponent charged species. The low Mach number approach eliminates sound waves from the fully compressible…
Immersed boundary methods are extensively used for simulations of dynamic solid objects interacting with fluids due to their computational efficiency and modelling flexibility compared to body-fitted grid methods. However, thin geometries,…
A new parallel, computationally efficient immersed boundary method for solving three-dimensional, viscous, incompressible flows on unbounded domains is presented. Immersed surfaces with prescribed motions are generated using the…
We present a novel formulation based on an immersed coupling of Isogeometric Analysis (IGA) and Peridynamics (PD) for the simulation of fluid-structure interaction (FSI) phenomena for air blast. We aim to develop a practical computational…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
We describe a method to simulate the dynamics of charged colloidal particles suspended in a liquid containing dissociated ions and salt ions. Regimes of prime current interest are those of large volume fraction of colloids, highly charged…