相关论文: The ICC* Algorithm: A fast way to include dielectr…
We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The direct-forcing immersed boundary method (DF-IBM) algorithm previously developed by the authors is extended by coupling the Navier-Stokes equations with the Newton-Euler equations for rigid body dynamics within the DF-IBM framework. This…
The Immersed Boundary Method (IBM) is one of the popular one-fluid mixed Eulerian-Lagrangian methods to simulate motion of droplets. While the treatment of a moving complex boundary is an extremely time consuming and formidable task in a…
In this article we develop an algorithm for the efficient simulation of electrolytes in the presence of physical boundaries. In previous work the Discrete Ion Stochastic Continuum Overdamped Solvent (DISCOS) algorithm was derived for triply…
A novel smooth immersed boundary method (IBM) based on a direct-forcing formulation is proposed to simulate incompressible dense particle-laden flows. This IBM relies on a regularization of the transfer function between the Eulerian grid…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
We extend the recently introduced divergence-conforming immersed boundary (DCIB) method [1] to fluid-structure interaction (FSI) problems involving closed co-dimension one solids. We focus on capsules and vesicles, whose discretization is…
The immersed boundary method (IB) is an elegant way to fully couple the motion of a fluid and deformations of an immersed elastic structure. In that vein, the IB2d software allows for expedited explorations of fluid-structure interaction…
The coarse-grained molecular dynamics (MD) 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…
We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a…
In this work, we explore various relevant aspects of the Smoothed Particle Hydrodynamics regarding Burger's equation. The stability, precision, and efficiency of the algorithm are investigated in terms of different implementations. In…
The immersed boundary-finite element method (IBFE) is an approach to describing the dynamics of an elastic structure immersed in an incompressible viscous fluid. In this formulation, there are discontinuities in the pressure and viscous…
Tasker type III polar terminations of ionic crystals carry a net surface charge as well as a dipole moment and are fundamentally unstable. In contact with electrolytes, such polar surfaces can be stabilized by adsorption of counter ions…
The aim of this paper is to provide a survey of the state of the art in the finite element approach to the Immersed Boundary Method (FE-IBM) which has been investigated by the authors during the last decade. In a unified setting, we present…
Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
We present a novel framework to deal with static and moving immersed boundaries (IB). In this strategy, called Volume-Filtering Immersed Boundary (VFIB) method, transport equations are derived by filtering the Navier-Stokes equations and…
A boundary thickening-based direct forcing (BTDF) immersed boundary (IB) method is proposed for fully resolved simulation of incompressible viscous flows laden with finite size particles. By slightly thickening the boundary thickness, the…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…