Related papers: Knots in Macromolecules in Constraint Space
The random walk of a bonded monomer in a polymer melt is anisotropic due to local order and bond connectivity. We investigate both effects by molecular-dynamics simulations on melts of fully-flexible linear chains ranging from dimers…
In this paper we examine the relative knotting probabilities in a lattice model of ring polymers confined in a cavity. The model is of a lattice knot of size $n$ in the cubic lattice, confined to a cube of side-length $L$ and with volume…
We have analyzed the dependence of average ground state energy per monomer, $e$, of the complex of two random heteropolymers with quenched sequences, on chain length, $n$, in the ensemble of chains with uniform distribution of primary…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers $N$. The natural coordinate for translocation is the number of monomers on one side of…
We study the link between three seeming-disparate cases of self-avoiding polymers: strongly overlapping multiple chains in dilute solution, chains under spherical confinement, and the onset of semi-dilute solutions. Our main result is that…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
In last passage percolation models lying in the KPZ universality class, long maximizing paths have a typical deviation from the linear interpolation of their endpoints governed by the two-thirds power of the interpolating distance. This…
Let $p_n$ denote the number of self-avoiding polygons of length $n$ on a regular three-dimensional lattice, and let $p_n(K)$ be the number which have knot type $K$. The probability that a random polygon of length $n$ has knot type $K$ is…
We consider the problem of an inextensible but flexible fiber advected by a steady chaotic flow, and ask the simple question whether the fiber can spontaneously knot itself. Using a 1D Cosserat model, a simple local viscous drag model and…
Algorithm of construction of all knots, links with given number of crosses on diagram of knot, link is offered. This algorithm is based on simple proposition, that there is a representation of knot (link) as closure of braid with n threads…
Unconcatenated, unknotted polymer rings in the melt are subject to strong interactions with neighboring chains due to the presence of topological constraints. We study this by computer simulation using the bond-fluctuation algorithm for…
We study the statistics of branching polymers with excluded-volume interactions, by modeling them as single self-avoiding trees on a generic regular periodic lattice with coordination number $q$. Each lattice site can be occupied at most by…
We construct new knot polynomials. Let $V$ be the standard solid torus in 3-space and let $pr$ be its standard projection onto an annulus. Let $M$ be the space of all smooth oriented knots in $V$ such that the restriction of $pr$ is an…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
We investigate the asymptotics of the total number of simple $4a+1$-knots with Alexander polynomial of the form $mt^2 +(1-2m) t + m$ for some $m \in [-X, X]$. Using Kearton and Levine's classification of simple knots, we give equivalent…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate. Our model of the breakable polymer is related to the Rouse chain, with the only difference that the interaction between the monomers is…