相关论文: Polymer packaging and ejection in viral capsids: s…

The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…

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…

Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials…

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 present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, virus-like capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the…

The shape of biological shells, such as cell nuclei, membranes, and vesicles, often deviates from a perfect sphere due to an interplay of complex interactions with a myriad of molecular structures. In particular, semiflexible biopolymers…

Translocation of a polymer out of curved surface or membrane is studied via mean first passage time approach. Membrane curvature gives rise to a constraint on polymer conformation, which effectively drives the polymer to the outside of…

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 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…

From understanding the sand on the beach to the foam on your beer, soft sphere simulations have been crucial to the study of the amorphous world around us. However, many of the materials we interact with on a daily basis aren't comprised of…

Polymer ejection from nano-confinement has been of interest due to its relation to various fundamental sciences and applications. However, the ejection dynamics of a polymer with different persistence lengths from confinement through a…

Space-saving design is a requirement that is encountered in biological systems and the development of modern technological devices alike. Many living organisms dynamically pack their polymer chains, filaments or membranes inside of…

We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…

The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…

Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…

The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of…

We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…

Molecular dynamics simulations are performed to investigate the plastic response of a model glass to a local shear transformation in a quiescent system. The deformation of the material is induced by a spherical inclusion that is gradually…