Related papers: Translational Mobilities of Proteins in Nanochanne…
Tunable nanopores in elastomeric membranes have been used to study the dependence of ionic current blockade rate on the concentration and electrophoretic mobility of particles in aqueous suspensions. A range of nanoparticle sizes, materials…
A practical, biologically motivated case of protein complexes (immunoglobulin G and FcRII receptors) moving on the surface of mastcells, that are common parts of an immunological system, is investigated. Proteins are considered as…
We perform molecular dynamics simulations to understand the translational and rotational diffusion of Janus nanoparticles at the interface between two immiscible fluids. Considering spherical particles with different affinity to fluid…
Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of…
Algorithm is constructed which models single-file motion of particles interacting with each other and with the surroundings. As an example, we present the results of Brownian Dynamics simulations of the motion of cations moving through a…
The diffusive transport of biased Brownian particles in a two-dimensional symmetric channel is investigated numerically considering both the no-flow and the reflection boundary conditions at the channel boundaries. Here, the geometrical…
We study the motion of dispersed nanoprobes in entangled active-passive polymer mixtures. By comparing the two architectures of linear vs. unconcatenated and unknotted circular polymers, we demonstrate that novel, rich physics emerge. For…
We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
Hierarchically nanostructured materials, where disorder is introduced in various length scales (at the atomic scale, the nanoscale, and the mesoscale) is one of the most promising directions to achieve extremely low thermal conductivities…
First-principles molecular dynamics simulations of heat transport in systems with large-scale structural features are challenging due to their high computational cost. Here, using polycrystalline graphene as a case study, we demonstrate the…
The engineering problems involving clay under non-isothermal conditions (e.g., geothermal energy harvest, landfill cover system, and nuclear waste disposal) are multiscale and multiphysics by nature. The nanoscale hydrodynamics of clay at…
We use Molecular Dynamics simulations to study how the nanopore and the fluid structures affects the dynamic, thermodynamic and structural properties of a confined anomalous fluid. The fluid is modeled using an effective pair potential…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
Polymer solutions subject to pressure driven flow and in nanoscale slit pores are systematically investigated using the dissipative particle dynamics approach. We investigated the effect of molecular weight, polymer concentration and flow…
Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the…
We use molecular dynamics simulations to investigate the displacement of a simple butterfly-like molecular motor inside nanopores of various radii filled with a viscous medium. The medium is modeled with a versatile potential that may be…
Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding.…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
Control of transport processes in composite microstructures is critical to the development of high performance functional materials for a variety of energy storage applications. The fundamental process of conduction and its control through…