相关论文: Multiscale modeling of a rectifying bipolar nanopo…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
We present an adaptive reduced-order model for the efficient time-resolved simulation of fluid-structure interaction problems with complex and non-linear deformations. The model is based on repeated linearizations of the structural balance…
We present a flexible discretization technique for computational models of thin tubular networks embedded in a bulk domain, for example a porous medium. These systems occur in the simulation of fluid flow in vascularized biological tissue,…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
This paper presents a novel methodology for the direct numerical modeling and simulation of turbulent flows. The kinetic model equation is firstly extended to turbulent flow with the account of coupled evolution of kinetic, thermal, and…
The association of ions in electrolyte solutions at very low concentration and low temperature is studied using computer simulations and quasi-chemical ion-pairing theory. The specific case of the restricted primitive model (charged hard…
The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon,…
This work demonstrates algorithms to accurately compute solutions to thermal radiation transport problems using a reduced floating-point precision implementation of the Implicit Monte Carlo method. Several techniques falling into the…
We investigate the mobility of nanometer-size solutes in water in a uniform external electric field. General arguments are presented to show that a closed surface cutting a volume from a polar liquid will carry an effective non-zero surface…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
We present porous electrode theory for capacitive deionization (CDI) with electrodes containing nanoparticles that consist of a redox-active intercalation material. A geometry of a desalination cell is considered which consists of two…
Bipolar nanopores, with asymmetric charge distributions, can induce significant ionic current rectification (ICR) at ultra-short lengths, finding potential applications in nanofluidic devices, energy conversion, and other related fields.…
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…
In this paper, we put forth an evolve-then-correct reduced order modeling approach that combines intrusive and nonintrusive models to take hidden physical processes into account. Specifically, we split the underlying dynamics into known and…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and other properties of a model solution consisting of NaCl salt dissolved in water-methanol mixture. The SPC/E water model and the united atom…
Kinetic equations are crucial for modeling non-equilibrium phenomena, but their computational complexity is a challenge. This paper presents a data-driven approach using reduced order models (ROM) to efficiently model non-equilibrium flows…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…