Related papers: Polymer translocation into a fluidic channel throu…
We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the {\it cis} side subchain. We present theoretical and…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any…
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We study the propulsion of a one-dimensional (1D) polymer chain under sinusoidal external forces in the overdamped (low Reynolds number) regime. We show that, when hydrodynamical interactions are included, the polymer presents directional…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
Processes on different length scales affect the dynamics of chain molecules. In this work, we focus on structures on the scale of a monomer and investigate polyolefins, i.e. hydrocarbon chains with different small scale architectures. We…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded…
Using continuous time Monte-Carlo method we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have…
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 use molecular dynamics simulations to investigate the tracer diffusion in a sea of polymers with specific binding zones for the tracer. These binding zones act as traps. Our simulations show that the tracer can undergo normal yet…
Recent studies have suggested that the Nuclear Pore Complex (NPC) plays a significant role in mechanotransduction. When a force is exerted, the NPC's diameter widens, leading to an increased molecular flux into the nucleus. In this study,…
Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
In this paper we study the tunneling using a background independent (polymer) quantization scheme. We show that at low energies, for the tunneling through a single potential barrier, the polymer transmission coefficient and the polymer…
We analyze the free energy for translocation of a polymer from the outside of a spherical vesicle to the inside. The process is assumed to be driven by the adsorption of the polymer on the inner surface of the vesicle. We argue that in the…
In this work a stochastic model of gaseous transfer in polymer/CNT nanocomposites is presented. The model takes into account interfacial areas, i.e. polymer depletion regions. The local regime of transport is controlled by the density of…