Related papers: Knotted globular ring polymers: how topology affec…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Using canonical Monte Carlo simulations, we introduce a new numerical procedure for comparing the entropic exponents of polymers with different constraints and/or topologies. Setting up competitions between polymer segments which can…
We present a molecular dynamics study of the influence of knot complexity and molecular mass on glass formation upon cooling in knotted ring polymer melts. We find that cooperative motion, rigidity, and glassy dynamics can be tuned over a…
A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
We consider the probability of knotting in equilateral random polygons in Euclidean 3-dimensional space, which model, for instance, random polymers. Results from an extensive Monte Carlo dataset of random polygons indicate a universal…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
In this review we provide an organized summary of the theoretical and computational results which are available for polymers subject to spatial or topological constraints. Because of the interdisciplinary character of the topic, we provide…
The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for…
Using molecular dynamics simulation, we investigate the effect of confinement on a system that comprises several stiff segmented polymer chains where each chain has similar segments, but length and stiffness of the segments vary among the…
The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in Polymer Physics. At the same time, the nature of the glass transition in polymeric systems is also not well…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
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…
In this work a new strategy is proposed in order to build analytic and microscopic models of fluctuating polymer rings subjected to topological constraints. The topological invariants used to fix these constraints belong to a wide class of…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
The size of a zero thickness (no excluded volume) polymer ring is shown to scale with chain length $N$ in the same way as the size of the excluded volume (self-avoiding) linear polymer, as $N^{\nu}$, where $\nu \approx 0.588$. The…