Related papers: Knot-controlled ejection of a polymer from a virus…
We study experimentally statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks…
We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at…
We find a power law for the number of knot-monomers with an exponent $0.39 \pm0.13$ in agreement with previous simulations. For the average size of a knot we also obtain a power law $N_m=2.56\cdot N^{0.20\pm0.04}$. We further present data…
We study how confinement affects topology and conformations in polymer films of varying thickness $h$. The knotting probability exhibits a maximum at intermediate thicknesses near the bulk radius of gyration $h \approx R_\mathrm{g,bulk}$,…
The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been…
It is often desirable to know the controlling mechanism of survival probability of nano - or microscale particles in small cavities such as, e.g., confined submicron particles in fiber beds of high-efficiency filter media or ions/small…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along…
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a…
When injected through a contraction, high molecular weight polymer solutions exhibit a sharp increase of apparent viscosity which originates from stretching polymer chains above a critical extension rate. This chain stretching can also…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
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…
Entangled knots form spontaneously in flexible filaments, yet the influence of the surrounding environment on this process is poorly understood. Here we demonstrate that free-moving particles act as kinetic catalysts for spontaneous…
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…
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…
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of…
A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or…
Flow in soft materials encompasses a wide range of viscous, plastic and elastic phenomena which provide challenges to modelling at the microscopic level. To create a controlled flow, we perform falling ball viscometry tests on packings of…