Related papers: Polymer Translocation througha Pore in a Membrane
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
The transport of interacting Brownian particles in a periodic asymmetric (ratchet) substrate is studied numerically. In a zero-temperature regime, the system behaves as a reversible step motor, undergoing multiple sign reversals of the…
In this paper, we investigate the microscopic dynamics of a polymer of length $N$ translocating through a narrow pore. Characterization of its purportedly anomalous dynamics has so far remained incomplete. We show that the polymer dynamics…
In the paper a novel stochastic algorithm designed to study of chain-like bodies dynamics is introduced. This algorithm models chain movements induced by the tension propagation and its main idea relies on the sequentialization of each…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the…
We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
We study subdiffusive ratchet transport in periodically and randomly flashing potentials. Central Brownian particle is elastically coupled to surrounding auxiliary Brownian quasi-particles which account for the influence of viscoelastic…
We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each…
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…
The transport of a dimer, consisting of two Brownian particles bounded by a harmonic potential, moving on a periodic substrate is investigated both numerically and analytically. The mobility and diffusion of the dimer center of mass present…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
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…
Polymer translocation in three dimensions out of planar confinements is studied in this paper. Three membranes are located at $z=-h$, $z=0$ and $z=h_1$. These membranes are impenetrable, except for the middle one at $z=0$, which has a…
Polymers in confined spaces are compressed and have reduced conformational entropy, and will partially or fully escape from confinement if conditions are suitable. This is in particular the case for a polymer grafted in a pore. The escape…
We have used Langevin dynamics to simulate the forced translocation of linked polymer rings through a narrow pore. For fixed size (i.e. fixed number of monomers) the translocation time depends on the link type and on whether the rings are…
We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory…