Related papers: Numerical Methods for a Poisson-Nernst-Planck-Ferm…
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed…
First-order energy dissipative schemes in time are available in literature for the Poisson-Nernst-Planck (PNP) equations, but second-order ones are still in lack. This work proposes novel second-order discretization in time and finite…
Water-borne diseases are still a major public health concern, as there are circumstances under which water could act as a carrier of the pathogen, extending their modeling beyond direct contact between hosts. In the present work, we…
The Position Based Fluids (PBF) method is a state-of-the-art approach for fluid simulations in the context of real-time applications like games. It uses an iterative solver concept that tries to maintain a constant fluid density…
In ionic solutions, there are multi-species charged particles (ions) with different properties like mass, charge etc. Macroscopic continuum models like the Poisson-Nernst-Planck (PNP) systems have been extensively used to describe the…
In this paper we present a computer simulation study of ionic conductivity in solid polymeric electrolytes. The multiphase nature of the material is taken into account. The polymer is represented by a regular lattice whose sites represent…
In this research, we explore how permanent charges affect the movement of ionic currents through ion channels. We use a quasi-one-dimensional classical Poisson-Nernst-Planck (PNP) model to study two types of ions, one positively charged and…
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles…
Modelling interfacial dynamics with soluble surfactants in a multiphase system is a challenging task. Here, we consider the numerical approximation of a phase-field surfactant model with fluid flow. The nonlinearly coupled model consists of…
The flow of charge carriers in materials can, under some circumstances, mimic the flow of viscous fluids. In order to visualize the consequences of such effects, new methodologies must be developed that can probe the quasiparticle flow…
We formulate theoretical modeling approaches and develop practical computational simulation methods for investigating the non-equilibrium statistical mechanics of fluid interfaces with passive and active immersed particles. Our approaches…
This is an early but comprehensive review of the PNP Poisson Nernst Planck theory of ion channels. Extensive reference is made to the earlier literature. The starting place for this theory of open channels is a theory of electrodiffusion…
As the characteristic lengths of advanced electronic devices are approaching the atomic scale, ab initio simulation method, with fully consideration of quantum mechanical effects, becomes essential to study the quantum transport phenomenon…
Recent advance in nanotechnology has led to rapid advances in nanofluidics, which has been established as a reliable means for a wide variety of applications, including molecular separation, detection, crystallization and biosynthesis.…
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore on two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
We present a method for performing path integral molecular dynamics (PIMD) simulations for fermions and address its sign problem. PIMD simulations are widely used for studying many-body quantum systems at thermal equilibrium. However, they…
In order to describe the dynamics of crowded ions (charged particles), we use an energetic variation approach to derive a modified Poisson-Nernst-Planck (PNP) system which includes an extra dissipation due to the effective velocity…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
Severe accident analysis using system-level codes such as MELCOR is indispensable for nuclear safety assessment, yet the computational cost of repeated simulations poses a significant bottleneck for parametric studies and uncertainty…