相关论文: Packing and ejection dynamics of polymers: Role of…
We use a mesoscale simulation approach to explore the impact of different capsid geometries on the packaging and ejection dynamics of polymers of different flexibility. We find that both packing and ejection times are faster for flexible…
Living organisms employ diverse strategies to navigate confined environments. Inspired by translocation observations on California blackworms (\textit{Lumbriculus variegatus}), we combine biological experiments and active-polymer…
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 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…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational…
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…
Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules…
We study translocation of semiflexible polymers driven by force $f_d$ inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time $\tau$ increases with increasing bending rigidity…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
We consider the dynamics of a translocation process of a flexible linear polymer through a nanopore into an environment of active rods in the {\it trans} side. Using Langevin dynamics simulations we find that the rods facilitate…
We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial…
We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore…
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…
Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better…