Related papers: Driven polymer translocation through nanopores: sl…
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are…
We use Langevin dynamics (LD) simulations to investigate single-file diffusion (SFD) in a dilute solution of flexible linear polymers inside a narrow tube with periodic boundary conditions (a torus). The transition from SFD, where the time…
We theoretically investigate the time-dependent transport of a localized surface plasmon excitation through a linear array of identical and equidistantly spaced metal nanoparticles. Two different signals propagating through the array are…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
We consider the statics and dynamics of a flexible polymer confined between parallel plates both in the presence and absence of hydrodynamic interactions. The hydrodynamic interactions are described at the level of the fluctuating,…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes…
We study unbiased translocation of a flexible polymer chain through a membrane pore under the influence of active noise and steric exclusion using Langevin dynamics simulations. The active noise is incorporated by introducing nonchiral and…
We develop a scaling theory to describe dynamic fluctuations of a semiflexible polymer and find several distinct regimes. We performed simulations to characterize the longitudinal and transverse dynamics; using ensemble averaging for a…
The dynamics of polymers in a random smooth flow is investigated in the framework of the Hookean dumbbell model. The analytical expression of the time-dependent probability density function of polymer elongation is derived explicitly for a…
In an earlier preprint (V. V. Ginzburg, O. V. Gendelman, R. Casalini, and A. Zaccone, arxiv:2409.17291), we demonstrated that the dynamic (relaxation time) and volume equations of state for many amorphous polymers are near-universal -- each…
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…
We study properties of dilute polymer solutions which are known to depend strongly on polymer elongation. The probability density function (PDF) of polymer end-to-end extensions $R$ in turbulent flows is examined. We demonstrate that if the…
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…
The temporal evolution of step-edge fluctuations under electromigration conditions is analysed using a continuum Langevin model. If the electromigration driving force acts in the step up/down direction, and step-edge diffusion is the…
Thin polymer films have striking dynamical properties that differ from their bulk counterparts. With the simple geometry of a stepped polymer film on a substrate, we probe mobility above and below the glass transition temperature…
Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore…
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…