Related papers: Knots in Macromolecules in Constraint Space
It is nontrivial whether the average size of a ring polymer should become smaller or larger under a topological constraint. Making use of some knot invariants, we evaluate numerically the mean square radius of gyration for ring polymers…
Spontaneous formation of knots in long polymers at equilibrium is inevitable but becomes rare in sufficiently short chains. Here, we show that knotting and knot complexity increase by orders of magnitude in diblock polymers with a fraction…
The ropelength of a knot is the minimum contour length of a tube of unit radius that traces out the knot in three dimensional space without self-overlap, colloquially the minimum amount of rope needed to tie a given knot. Theoretical upper…
We model the typical behavior of knots and links using grid diagrams. Links are ubiquitous in the sciences, and their "normal" or "typical" behavior is of significant importance in understanding situations such as the topological state of…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
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…
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 develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…
Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
We present simulation data for the motion of a polymer chain through a regular lattice of impenetrable obstacles (Evans-Edwards model). Chain lengths range from N=20 to N=640, and time up to $10^{7}$ Monte Carlo steps. For $N \geq 160$ we…
We present a computer simulation study of the compact self-avoiding loops as regards their length and topological state. We use a Hamiltonian closed path on the cubic-shaped segment of a 3D cubic lattice as a model of a compact polymer. The…
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 have developed a reinforcement learning agent that often finds a minimal sequence of unknotting crossing changes for a knot diagram with up to 200 crossings, hence giving an upper bound on the unknotting number. We have used this to…
We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two…
We have evaluated by numerical simulation the average size $R_K$ of random polygons of fixed knot topology $K = \emptyset, 3_1, 3_1\sharp4_1$, and we have confirmed the scaling law $R^2_K \sim N^{2\nu_K}$ for the number $N$ of polygonal…
We give statistical definitions of the length, l, of a loose prime knot tied into a long, fluctuating ring macromolecule. Monte Carlo results for the equilibrium, good solvent regime show that < l > ~ N^t, where N is the ring length and t ~…
Based on the data of 12-17-crossing knots, we establish three new conjectures about the hyperbolic volume and knot cohomology: (1) There exists a constant $a \in R_{>0}$ such that the percentage of knots for which the following inequality…
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…
A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, $\theta$-chains, i.e., chains at the transition from a swollen…