相关论文: Heteropolymer translocation through nanopores
We consider single particle and polymer translocation where the frictional properties experienced from the environment are changing in time. This work is motivated by the interesting frequency responsive behaviour observed when a polymer is…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…
A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore and…
We study pore blockade times for a translocating polymer of length $N$, driven by a field $E$ across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical…
We show how dynamic heterogeneities (DH), a hallmark of glass-forming materials, depend on chain flexibility and chain length in polymers. For highly flexible polymers, a relatively large number of monomers ($N_c\sim500$) undergo correlated…
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…
We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. Using equilibrium…
We revisit the one-dimensional stochastic model of Lubensky and Nelson [Biophys. J 77, 1824 (1999)] for the electrically driven translocation of polynucleotides through alpha-hemolysin pores. We show that the model correctly describes two…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer…
Graphene-based nanostructured systems and van-der-Waals heterostructures comprise a material class of growing technological and scientific importance. Joining materials with vastly different properties, polymer-graphene heterosystems…
We show that the injection of polymer chains into nanochannels becomes easier as the channel becomes narrower. This counter intuitive result arises because of a decrease in the diffusive time scale of the chains with increasing confinement.…
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…
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…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…