arXiv subjects
Publications and source records attributed to Dorothy Buck.
We show that if a composite $θ$-curve has (proper rational) unknotting number one, then it is the order 2 sum of a (proper rational) unknotting number one knot and a trivial $θ$-curve. We also prove similar results for 2-strand tangles and knotoids.
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Here, we propose a new predictive modelling framework for the study of the integration patterns of TEs based on extensions of widely employed polymer models for genome organisation. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, we now show that it can also offer orthogonal and generic insights into the integration and distribution profiles (or "topography") of TEs across organisms. Here, we present polymer physics arguments and molecular dynamics simulations on TEs inserting into heterogeneously flexible polymers and show with a simple model that polymer folding and local flexibility affects TE integration patterns. The preliminary discussion presented herein lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.
By using double branched covers, we prove that there is a 1-1 correspondence between the set of knotoids in the 2-sphere, up to orientation reversion and rotation, and knots with a strong inversion, up to conjugacy. This correspondence allows us to study knotoids through tools and invariants coming from knot theory. In particular, concepts from geometrisation generalise to knotoids, allowing us to characterise invertibility and other properties in the hyperbolic case. Moreover, with our construction we are able to detect both the trivial knotoid in the 2-sphere and the trivial planar knotoid.
Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-mediated passages of double-stranded DNA segments through each other using the formalism of grid diagrams. We show that this grid diagram-based modelling approach captures the essence of the preferential unknotting mechanism, based on topoisomerase selectivity of hooked DNA juxtapositions as the sites of intersegmental passages. We show that grid diagram-based approach provide an important, new and computationally convenient framework for investigating entanglement in biopolymers.
We give explicit deformations of embeddings of abstractly planar graphs that lie on the standard torus $T^2 \subset \mathbb{R}^3$ and that contain neither a nontrivial knot nor a nonsplit link into the plane. It follows that ravels do not embed on the torus. Our results provide general insight into properties of molecules that are synthesized on a torus.
Determining unknotting numbers is a large and widely studied problem. We consider the more general question of the unknotting number of a spatial graph. We show the unknotting number of spatial graphs is subadditive. Let $g$ be an embedding of a planar graph $G$, then we show $u(g) \geq \max\{u(s) |$ $s$ is a non-overlapping set of constituents of $g\}$. Focusing on $θ$-curves, we determine the exact unknotting numbers of the $θ$-curves in the Litherland-Moriuchi Table. Additionally, we demonstrate unknotting crossing changes for all of the curves. In doing this we introduce new methods for obstructing unknotting number $1$ in $θ$-curves.
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small crossing number. We apply these results to place lower bounds on the minimum number of recombinant events separating DNA configurations, restrict the recombination pathways and determine chirality and/or orientation of the resulting recombinant DNA molecules.
We characterize cutting arcs on fiber surfaces that produce new fiber surfaces, and the changes in monodromy resulting from such cuts. As a corollary, we characterize band surgeries between fibered links and introduce an operation called Generalized Hopf banding. We further characterize generalized crossing changes between fibered links, and the resulting changes in monodromy.
A natural generalization of a crossing change is a rational subtangle replacement (RSR). We characterize the fundamental situation of the rational tangles obtained from a given rational tangle via RSR, building on work of Berge and Gabai, and determine the sites where these RSR may occur. In addition we also determine the sites for RSR distance at least two between 2-bridge links. These proofs depend on the geometry of the branched double cover. Furthermore, we classify all knots in lens spaces whose exteriors are generalized Seifert fibered spaces and their lens space surgeries, extending work of Darcy-Sumners. This work is in part motivated by the common biological situation of proteins cutting, rearranging and resealing DNA segments -- effectively performing RSR on DNA `tangles'.
We propose a classification of knots in S^1 x S^2 that admit a longitudinal surgery to a lens space. Any lens space obtainable by longitudinal surgery on some knots in S^1 x S^2 may be obtained from a Berge-Gabai knot in a Heegaard solid torus of S^1 x S^2, as observed by Rasmussen. We show that there are yet two other families of knots: those that lie on the fiber of a genus one fibered knot and the `sporadic' knots. All these knots in S^1 x S^2 are both doubly primitive and spherical braids. This classification arose from generalizing Berge's list of doubly primitive knots in S^3, though we also examine how one might develop it using Lisca's embeddings of the intersection lattices of rational homology balls bounded by lens spaces as a guide. We conjecture that our knots constitute a complete list of doubly primitive knots in S^1 x S^2 and reduce this conjecture to classifying the homology classes of knots in lens spaces admitting a longitudinal S^1 x S^2 surgery.
We provide a partial classification of the 3-strand pretzel knots $K = P(p,q,r)$ with unknotting number one. Following the classification by Kobayashi and Scharlemann-Thompson for all parameters odd, we treat the remaining families with $r$ even. We discover that there are only four possible subfamilies which may satisfy $u(K) = 1$. These families are determined by the sum $p+q$ and their signature, and we resolve the problem in two of these cases. Ingredients in our proofs include Donaldson's diagonalisation theorem (as applied by Greene), Nakanishi's unknotting bounds from the Alexander module, and the correction terms introduced by Ozsváth and Szabó. Based on our results and the fact that the 2-bridge knots with unknotting number one are already classified, we conjecture that the only 3-strand pretzel knots $P(p,q,r)$ with unknotting number one that are not 2-bridge knots are $P(3,-3,2)$ and its reflection.
We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used in modeling homologous DNA recombination. We show that the genus ranges are sets of consecutive integers. For any positive integer $n$, there are graphs with $2n $ vertices that have genus range ${m,m+1,...,m'}$ for all $0\le m<m'\le n$, and there are graphs with $2n-1$ vertices with genus range ${m,m+1,...,m'}$ for all $0\le m<m' <n$ or $0<m<m'\le n$. Further, we show that for every $n$ there is $k<n$ such that ${h}$ is a genus range for graphs with $2n-1$ and $2n$ vertices for all $h\le k$. It is also shown that for every $n$, there is a graph with $2n$ vertices with genus range ${0,1,...,n}$, but there is no such a graph with $2n-1$ vertices.
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and catenanes. Yet, our systematic understanding of their implication in DNA and important cellular processes like site-specific recombination is very limited. Here we present a topological model of site-specific recombination characterising all possible products of this reaction on twist knot substrates, extending previous work of Buck and Flapan. We illustrate how to use our model to examine previously uncharacterised experimental data. We also show how our model can help determine the sequence of products in multiple rounds of processive recombination and distinguish between products of processive and distributive recombination. This model studies generic site- specific recombination on arbitrary twist knot substrates, a subject for which there is limited global understanding. We also provide a systematic method of applying our model to a variety of different recombination systems.
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 well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly prescribed. Finally, we give two simple examples to illustrate how this model can help determine previously uncharacterized experimental data.
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 a connected sum of 4-plats. This is done by building on results on exceptional Dehn fillings at maximal distance. We then apply our results to the action of the Hin recombinase on mutated sites. In particular, after solving the tangle equations for processive recombination, we use our work to give a complete set of solutions to the tangle equations modelling distributive recombination.
Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We then characterize all possible knot or catenane products that arise from the most common substrates. We apply our model to tightly prescribe the knot or catenane type of previously uncharacterized data.
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 fall into a single family, and prove that the size of this family grows linearly with the cube of the minimum number of crossings. Additionally, we prove that the only possible products of an unknot substrate are either clasp knots and links or (2,m)-torus knots and links. Finally, in the (common) case of (2,m)-torus knot or link substrates whose products have minimal crossing number m+1, we prove that the types of products are tightly prescribed, and use this to examine previously uncharacterized experimental data.
Integrase proteins acting on circular double-stranded DNA often change its topology by transforming unknotted circles into torus knots and links. Two systems of tangle equations--corresponding to the two initial DNA sequences--arise when modelling this transformation: direct and inverted. With no a priori assumptions on the constituent tangles, we utilize Dehn surgery arguments to completely classify the tangle solutions for each of the two systems. A key step is to combine work of our previous paper with recent results of Kronheimer, Mrowka, Ozsvath and Szabo, and Ernst to show a certain prime tangle must in fact be a generalized Montesinos tangle. These tangle solutions are divided into three classes, common to both systems, plus a fourth class for the inverted system that contains the sole generalized Montesinos tangle. We discuss the possible biological implications of our classification, and of this novel solution.