Related papers: The ICC* Algorithm: A fast way to include dielectr…
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is…
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…
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid…
Computational fluid dynamics (CFD) studies have been increasingly used for blood flow simulations in intracranial aneurysms (ICAs). However, despite the continuous progress of body-fitted CFD solvers, generating a high quality mesh is still…
We have studied by Molecular Dynamics computer simulations the dynamics of water confined in ionic surfactants phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed…
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)…
In transient simulations of particulate Stokes flow, to accurately capture the interaction between the constituent particles and the confining wall, the discretization of the wall often needs to be locally refined in the region approached…
Precise prediction of phase diagrams in molecular dynamics (MD) simulations is challenging due to the simultaneous need for long time scales, large length scales and accurate interatomic potentials. We show that thermodynamic integration…
We explore a new way to handle flux boundary conditions imposed on level sets. The proposed approach is a diffuse interface version of the shifted boundary method (SBM) for continuous Galerkin discretizations of conservation laws in…
We present an efficient and accurate immersed boundary (IB) finite element (FE) solver for numerically solving incompressible Navier--Stokes equations. Particular emphasis is given to internal flows with complex geometries (blood flow in…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…
In this paper we develop a stochastic boundary conditions (SBC) for event-driven molecular dynamics simulations of a finite volume embedded within an infinite environment. In this method, we first collect the statistics of…
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…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
The immersed boundary (IB) method is a non-body conforming approach to fluid-structure interaction (FSI) that uses an Eulerian description of the momentum, viscosity, and incompressibility of a coupled fluid-structure system and a…
Like many other biological processes, calcium dynamics in neurons containing an endoplasmic reticulum are governed by diffusion-reaction equations on interface-separated domains. Interface conditions are typically described by systems of…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The wetting dynamics of liquid particles, from coated droplets to soft capsules, holds significant technological interest. Motivated by the need to simulate liquid metal droplet with an oxidize surface layer, in this work we introduce a…