Related papers: Rational tangle surgery and Xer recombination on c…
The motivation for this work was to construct a nontrivial knot with trivial Jones polynomial. Although that open problem has not yielded, the methods are useful for other problems in the theory of knot polynomials. The subject of the…
Layers of two-dimensional materials arranged at a twist angle with respect to each other lead to enlarged unit cells with potentially strongly altered band structures, offering a new arena for novel and engineered many-body ground states.…
In the wood industry, logs are commonly quality screened by discrete X-ray scans on a moving conveyor belt from a few source positions. Typically, the measurements are obtained in a single two-dimensional (2D) plane (a "slice") by a…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable worm-like chain model. Here we show, by means of analytical results and computer…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
Suppose $K$ is a hyperbolic knot in a solid torus $V$ intersecting a meridian disk $D$ twice. We will show that if $K$ is not the Whitehead knot and the frontier of a regular neighborhood of $K \cup D$ is incompressible in the knot…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
Given a simply-connected closed 4-manifold $X$ and a smoothly embedded oriented surface $\Sigma$, various constructions based on Fintushel-Stern knot surgery have produced new surfaces in $X$ that are pairwise homeomorphic to $\Sigma$, but…
Knotted ribbons form an important topic in knot theory. They have applications in natural sciences, such as cyclic duplex DNA modeling. A flat knotted ribbon can be obtained by gently pulling a knotted ribbon tight so that it becomes flat…
A ribbon is, intuitively, a smooth mapping of an annulus $S^1 \times I$ in 3-space having constant width $\varepsilon$. This can be formalized as a triple $(x,\varepsilon, \mathbf{u})$ where $x$ is smooth curve in 3-space and $\mathbf{u}$…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
X-ray computed tomography (CT) reconstructs cross-sectional images from projection data. However, ionizing X-ray radiation associated with CT scanning might induce cancer and genetic damage. Therefore, the reduction of radiation dose has…
A torti-rational knot, denoted by K(2a,b|r), is a knot obtained from the 2-bridge link B(2a,b) by applying Dehn twists an arbitrary number of times, r, along one component of B(2a,b). We determine the genus of K(2a,b|r) and solve a question…
Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot…
We show that if $p/q$-surgery on a nontrivial knot $K$ yields the branched double cover of an alternating knot or link, then $|p/q|\leq 4g(K)+3$. This generalises a bound for lens space surgeries first established by Rasmussen. We also show…
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from…