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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…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
A graph spanner is a fundamental graph structure that faithfully preserves the pairwise distances in the input graph up to a small multiplicative stretch. The common objective in the computation of spanners is to achieve the best-known…
It is known that any open necklace with beads of $t$ types in which the number of beads of each type is divisible by $k$, can be partitioned by at most $(k-1)t$ cuts into intervals that can be distributed into $k$ collections, each…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
A spanner of a graph is a subgraph that preserves lengths of shortest paths up to a multiplicative distortion. For every $k$, a spanner with size $O(n^{1+1/k})$ and stretch $(2k+1)$ can be constructed by a simple centralized greedy…
Kauffman and Lomonaco explored the idea of understanding quantum entanglement (the non-local correlation of certain properties of particles) topologically by viewing unitary entangling operators as braiding operators. In the work of G.…
Uniform random intersection graphs have received much interest and been used in diverse applications. A uniform random intersection graph with $n$ nodes is constructed as follows: each node selects a set of $K_n$ different items uniformly…
We investigate the concept of molecular-sized outward-swinging gate, which allows for entropy decrease in an isolated system. The theoretical analysis, the Monte Carlo simulation, and the direct solution of governing equations all suggest…
We consider the Constrained-degree percolation model in random environment on the square lattice. In this model, each vertex $v$ has an independent random constraint ${\kappa}_v$ which takes the value $j\in \{0,1,2,3\}$ with probability…
A classical knot is described by a one-stroke trajectory with entanglements of a string. The replica method appears as a powerful tool in statistical mechanics for a polymer or self-avoiding walk. We consider this replica N to 0 limit in…
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…
We introduce an alternative stratification of knots: by the size of lattice on which a knot can be first met. Using this classification, we find ratio of unknots and knots with more than 10 minimal crossings inside different lattices and…
Fix $p>1$, not necessarily integer, with $p(d-2)<d$. We study the $p$-fold self-intersection local time of a simple random walk on the lattice $\Z^d$ up to time $t$. This is the $p$-norm of the vector of the walker's local times, $\ell_t$.…
A growing self-avoiding walk (GSAW) is a stochastic process that starts from the origin on a lattice and grows by occupying an unoccupied adjacent lattice site at random. A sufficiently long GSAW will reach a state in which all adjacent…
We present efficient counting and sampling algorithms for random $k$-SAT when the clause density satisfies $\alpha \le \frac{2^k}{\mathrm{poly}(k)}.$ In particular, the exponential term $2^k$ matches the satisfiability threshold…
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…
We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three…
We construct a tractable model to describe the rate at which a knotted polymer is ejected from a spherical capsid via a small pore. Knots are too large to fit through the pore and must reptate to the end of the polymer for ejection to…
In this paper we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing…