Related papers: Parallel multiscale modeling of biopolymer dynamic…
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 polymer model given in terms of beads, interacting through Hookean springs and hydrodynamic forces, is studied. Brownian dynamics description of this bead-spring polymer model is extended to multiple resolutions. Using this multiscale…
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
In this paper we establish a new efficient method for simulating polymer-solvent systems which combines a lattice Boltzmann approach for the fluid with a continuum molecular dynamics (MD) model for the polymer chain. The two parts are…
By analyzing the real space nonequilibrium dynamics of polymers, we elucidate the physics of driven translocation and propose its dynamical scaling scenario analogous to that in the surface growth phenomena. We provide a detailed account of…
By means of the multicomponent Shan-Chen lattice Boltzmann method (LBM), we investigate the multiphase flow through porous media. Despite the excellent accuracy of the LBM, large domains result in unaffordable computational expenses. The…
Methane adsorption and its effect on fluid flow in shale matrix are investigated through multi-scale simulation scheme by using molecular dynamics (MD) and lattice Boltzmann (LB) methods. Equilibrium MD simulations are conducted to study…
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
We investigate several scaling properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulation in three dimension (3D). Specifically motivated by…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
The crossover region in the phase diagram of polymer solutions, in the regime above the overlap concentration, is explored by Brownian Dynamics simulations, to map out the universal crossover scaling functions for the gyration radius and…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
In this work, we investigate the interaction of free and porous media flow by large scale lattice Boltzmann simulations. We study the transport phenomena at the porous interface on multiple scales, i.e., we consider both, computationally…
We investigate nanoflows through dilute disordered media by means of joint lattice Boltzmann (LB) and molecular dynamics (MD) simulations -- when the size of the obstacles is comparable to the size of the flowing particles -- for randomly…