相关论文: Multiscale coupling of molecular dynamics and hydr…
We present a hybrid numerical method to introduce hydrodynamics in dynamic self-consistent field (SCF) studies of inhomogeneous polymer systems. It solves a set of coupled dynamical equations: The Navier-Stokes equations for the fluid flow,…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
An approach based on a lattice version of the Boltzmann kinetic equation for describing multi-phase flows in nano- and micro-corrugated devices is proposed. We specialize it to describe the wetting/dewetting transition of fluids in presence…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based upon dissipative coupling between…
Over the past few decades, tremendous progress has been made in the development of particle-based discrete simulation methods versus the conventional continuum-based methods. In particular, the lattice Boltzmann (LB) method has evolved from…
We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm…
Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
It is proposed a dimensional Lattice Boltzmann Method (LBM) of wide application for simulating fluid flow and heat transfer problems. The proposed LBM consists in the numerical solution of the discrete lattice Boltzmann equation (LBE) using…
This article presents a comprehensive review of the Hydrodynamic Scaling Model for the dynamics of polymers in dilute and nondilute solutions. The Hydrodynamic Scaling Model differs from some other treatments of non-dilute polymer solutions…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic…
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To…
Multicomponent multiphase reactive transport processes with dissolution-precipitation are widely encountered in energy and environment systems. A pore-scale two-phase multi-mixture model based on the lattice Boltzmann method (LBM) is…
A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and nanoparticles, we…
We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved…