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Degree distribution of nodes, especially a power law degree distribution, has been regarded as one of the most significant structural characteristics of social and information networks. Node degree, however, only discloses the first-order…
The set of visited sites and the number of visited sites are two basic properties of the random walk trajectory. We consider two independent random walks on a hyper-cubic lattice and study ordering probabilities associated with these…
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 random-cluster model, a correlated bond percolation model, unifies a range of important models of statistical mechanics in one description, including independent bond percolation, the Potts model and uniform spanning trees. By…
While the problem of computing the genus of a knot is now fairly well understood, no algorithm is known for its four-dimensional variants, both in the smooth and in the topological locally flat category. In this article, we investigate a…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Networks are widely used to model the interaction between individual dynamical systems. In many instances, the total number of units as well as the interaction coupling are not fixed in time, but rather constantly evolve. In terms of…
Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long…
The $N$ vertices of a quantum random graph are each a circle independently punctured at Poisson points of arrivals, with parallel connections derived through for each pair of these punctured circles by yet another independent Poisson…
The existence of stable links and knots is demonstrated in three-dimensional, bistable, chemical media. The reaction-diffusion medium segregates into regions of high and low concentration separated by sharp interfaces. The interfaces repel…
By twisting a given link $L$ along an unknotted circle $c$, we obtain an infinite family of links $\{ L_n \}$. We introduce the ``stable unknotting number'' which describes the asymptotic behavior of unknotting numbers of links in the twist…
Data describing the three-dimensional structure of physical networks is increasingly available, leading to a surge of interest in network science to explore the relationship between the shape and connectivity of physical networks. We…
In this study, we use a correspondence between two-periodic weft-knitted textiles and links in the thickened torus to study the former using link invariants. We establish a criterion to identify the set of links whose elements are realized…
We partially determine grid homology (combinatorial knot Floer homology) of diagonal knots, which are conjectured to be equivalent to positive braid knots, by exploiting nice grid diagrams. Its next-to-top term detects the number of prime…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
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…
The altenating knots, links and twists projected on the S_2 sphere are identified with the phase Space of a Hamiltonian dynamic system of one degree of freedom. The saddles of the system correspond to the crossing points, the edges, to the…
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…
In 2000, Habiro introduced the notion of $C_k$-equivalence of knots and links. This geometric filtration is closely connected to finite type invariants, a class of invariants including Milnor's invariants. Shortly thereafter, Ohyama,…
This paper focuses on the graphs in the Petersen family, the set of minor minimal intrinsically linked graphs. We prove there is a relationship between algebraic linking of an embedding and knotting in an embedding. We also present a more…