相关论文: Rational tangle surgery and Xer recombination on c…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We develop a topological model of site-specific recombination that applies to substrates which are the connected sum of two torus links of the form $T(2,n)\#T(2,m)$. Then we use our model to prove that all knots and links that can be…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
We show that if the branched double cover of an alternating link arises as $p/q \in \mathbb{Q} \setminus \mathbb{Z}$ surgery on a knot in $S^3$, then this is exhibited by a rational tangle replacement in an alternating diagram.
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
We extend the tangle model, originally developed by Ernst and Sumners, to include composite knots. We show that, for any prime tangle, there are no rational tangle attachments of distance greater than one that first yield a 4-plat and then…
We show that the $X$-torsion order of a knot, which is defined in terms of a generalised Lee complex, can be calculated using the reduced Bar-Natan--Lee--Turner spectral sequence. We use this for extensive calculations, including an example…
We classify which positive integral surgeries on positive torus knots bound rational homology balls. Additionally, for a given knot K we consider which cables K(p,q) admit integral surgeries that bound rational homology balls. For such…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
The large size limit of matrix integrals with quartic potential may be used to count alternating links and tangles. The removal of redundancies amounts to renormalizations of the potential. This extends into two directions: higher genus and…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
We present three large families of new examples of plumbed 3-manifolds that bound rational homology 4-balls. These are constructed using two operations, also defined here, that preserve the lack of a lattice embedding obstruction to…
We apply results from both contact topology and exceptional surgery theory to study when Legendrian surgery on a knot yields a reducible manifold. As an application, we show that a reducible surgery on a non-cabled positive knot of genus g…
We develop a calculus of surgery data, called bridged links, which involves besides links also pairs of balls that describe one-handle attachements. As opposed to the usual link calculi of Kirby and others this description uses only…
We present an end-to-end Convolutional Neural Network (CNN) approach for 3D reconstruction of knee bones directly from two bi-planar X-ray images. Clinically, capturing the 3D models of the bones is crucial for surgical planning, implant…
Knitted and woven textile structures are examples of doubly periodic structures in a thickened plane made out of intertwining strands of yarn. Factoring out the group of translation symmetries of such a structure gives rise to a link…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
We develop a topological model of knots and links arising from a single (or multiple processive) round(s) of recombination starting with an unknot, unlink, or (2,m)-torus knot or link substrate. We show that all knotted or linked products…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…