Related papers: Numerical calculation of protein-ligand binding ra…
This work presents a comprehensive framework for enhanced diffusion modeling in fluid-structure interactions by combining the Immersed Boundary Method (IBM) with stochastic trajectories and high-order spectral boundary conditions. Using…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
This paper proposes the first free-stream boundary condition in a purely Lagrangian framework for weakly-compressible smoothed particle hydrodynamics (WCSPH). The boundary condition is implemented based on several numerical techniques,…
The Smoluchowski approach to diffusion-controlled reactions is generalized to interacting substrate particles by including the osmotic pressure and hydrodynamic interactions of the nonideal particles in the Smoluchoswki equation within a…
The Smoluchowski diffusion equation describes diffusion in the presence of external forces. Studying the mechanical response of soft materials to linear forces, such as shear, results in a boundary value problem involving an…
A novel numerical formulation for solving fluid-structure interaction (FSI) problems is proposed where the fluid field is spatially discretized using smoothed particle hydrodynamics (SPH) and the structural field using the finite element…
The Smoluchowski equation is a system of partial differential equations modelling the diffusion and binary coagulation of a large collection of tiny particles. The mass parameter may be indexed either by positive integers, or by positive…
In this study, a smoothed particle hydrodynamics (SPH) model that applies a segment-based boundary treatment is used to simulate natural convection. In a natural convection simulated using an SPH model, the wall boundary treatment is a…
Although the Smoothed Particle Hydrodynamics (SPH) method has been demonstrated as a promising numerical solver for multiphase flow problems due to its Lagrangian nature, its application to complex channel flow may encounter additional…
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…
We present a fully analytic approach for evaluating boundary integrals in two dimensions for Smoothed Particle Hydrodynamics (SPH). Conventional methods often rely on boundary particles or wall re-normalization approaches derived from…
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…
Since its inception, the full Lagrangian meshless smoothed particle hydrodynamics (SPH) method has experienced a tremendous enhancement in methodology and impacted a range of multi-physics applications in science and engineering. The paper…
In this paper, breakup of liquid jet is simulated using smoothed particle hydrodynamics (SPH) which is a meshless Lagrangian numerical method. For this aim, flow governing equations are discretized based on SPH method. In this paper,…
The Smoothed Particle Hydrodynamics (SPH) is a particle-based, Lagrangian method for fluid-flow simulations. In this work, fundamental concepts of this method are first briefly recalled. Then, the ability to accurately model granular…
A popular approach to modeling bimolecular reactions between diffusing molecules is through the use of reactive boundary conditions. One common model is the Smoluchowski partial absorption condition, which uses a Robin boundary condition in…
In this paper we test a special-relativistic formulation of Smoothed Particle Hydrodynamics (SPH) that has been derived from the Lagrangian of an ideal fluid. Apart from its symmetry in the particle indices, the new formulation differs from…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Resolvent analysis is used to study the low-frequency behaviour of the laminar oblique shock wave / boundary layer interaction (SWBLI). It is shown that the computed optimal gain, which can be seen as a transfer function of the system,…