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 DNA or the statistical mechanics of ring polymers. We examine three invariants: the expected size of a random knot; the expected number of components of a random link; and the expected writhe of a random knot. We investigate the first two numerically and produce generating functions which codify the observed patterns: knot size is uniformly distributed and linearly dependent upon grid size, and the number of components follows a distribution whose mean and variance grow with log_2 of grid size; in particular, for any fixed k, the k-component links grow vanishingly rare as grid size increases. Finally, we observe that the odd moments of writhe vanish, and we perform an exploratory data analysis to discover that variance grows with the square of grid size and kurtosis is constant at approximately 3.5. We continue this project in a future work, where we investigate genus and the effects of crossing change on it.
We introduce and study the writhe of a permutation, a circular variant of the well-known inversion number. This simple permutation statistics has several interpretations, which lead to some interesting properties. For a permutation sampled uniformly at random, we study the asymptotics of the writhe, and obtain a non-Gaussian limit distribution. This work is motivated by the study of random knots. A model for random framed knots is described, which refines the Petaluma model. The distribution of the framing in this model is equivalent to the writhe of random permutations.
We give a new interpretation of the Alexander polynomial $Δ_0$ for virtual knots due to Sawollek and Silver and Williams, and use it to show that, for any virtual knot, $Δ_0$ determines the writhe polynomial of Cheng and Gao (equivalently, Kauffman's affine index polynomial). We also use it to define a second-order writhe polynomial, and give some applications.
We study the variation of the Tait number of a closed space curve according to its different projections. The results are used to compute the writhe of a knot, leading to a closed formula in case of polygonal curves.
The writhe polynomial is a fundamental invariant of an oriented virtual knot. We introduce a kind of local moves for oriented virtual knots called shell moves. The first aim of this paper is to prove that two oriented virtual knots have the same writhe polynomial if and only if they are related by a finite sequence of shell moves. The second aim of this paper is to classify oriented $2$-component virtual links up to shell moves by using several invariants of virtual links.
A weak chord index $Ind'$ is constructed for self crossing points of virtual links. Then a new writhe polynomial $W$ of virtual links is defined by using $Ind'$. $W$ is a generalization of writhe polynomial defined in [6]. Based on $W$, three invariants of virtual links are constructed. These invariants can be used to detect the non-trivialities of Kishino knot and flat Kishino knot.
In this paper we study rational real algebraic knots in $\R P^3$. We show that two real algebraic knots of degree $\leq5$ are rigidly isotopic if and only if their degrees and encomplexed writhes are equal. We also show that any irreducible smooth knot which admits a plane projection with less than or equal to four crossings has a rational parametrization of degree $\leq 6$. Furthermore an explicit construction of rational knots of a given degree with arbitrary encomplexed writhe (subject to natural restrictions) is presented.
The inclusion of the space of all knots of a prescribed writhe in a particular isotopy class into the space of all knots in that isotopy class is a weak homotopy equivalence.
A detailed version of preprint "Self-linking number of a real algebraic link" by the same author, alg-geom/9410030. For a nonsingular real algebraic curve in 3-dimensional projective space or 3-sphere, a new integer-valued characteristic is introduced. It is invariant under rigid isotopy and multiplied by -1 under mirror reflections. In a sense, it is a Vassiliev invariant of degree 1 and a counterpart of a link diagram writhe. For a regular complete intersection this invariant vanishes, while for rational knots of degree d it takes all the values between -(d-1)(d-2)/2 and (d-1)(d-2)/2.
It is known that the writhe calculated from any reduced alternating link diagram of the same (alternating) link has the same value. That is, it is a link invariant if we restrict ourselves to reduced alternating link diagrams. This is due to the fact that reduced alternating link diagrams of the same link are obtainable from each other via flypes and flypes do not change writhe. In this paper, we introduce several quantities that are derived from Seifert graphs of reduced alternating link diagrams. We prove that they are "writhe-like" invariants in the sense that they are also link invariants …
We define a homology theory of virtual links built out of the direct sum of the standard Khovanov complex with itself, motivating the name doubled Khovanov homology. We demonstrate that it can be used to show that some virtual links are non-classical, and that it yields a condition on a virtual knot being the connect sum of two unknots. Further, we show that doubled Khovanov homology possesses a perturbation analogous to that defined by Lee in the classical case and define a doubled Rasmussen invariant. This invariant is used to obtain various cobordism obstructions; in particular it is an obs…
In this paper we give two new criteria of detecting the checkerboard colorability of virtual links by using odd writhe and arrow polynomial of virtual links, respectively. By applying new criteria, we prove that 6 virtual knots are not checkerboard colorable, leaving only one virtual knot whose checkerboard colorability is unknown among all virtual knots up to four classical crossings.
Both classical and virtual knots arise as formal Gauss diagrams modulo some abstract moves corresponding to Reidemeister moves. If we forget about both over/under crossings structure and writhe numbers of knots modulo the same Reidemeister moves, we get a dramatic simplification of virtual knots, which kills all classical knots. However, many virtual knots survive after this simplification. We construct invariants of these objects and present their applications to minimality problems of virtual knots as well as some questions related to graph-links. One can easily generalize these results for …
Writhe-Based Polymer Link Classification Using Machine Learning
School of Physics and Astronomy, The University of Edinburgh（物理与天文学学院，爱丁堡大学）；School of Mathematics, The University of Edinburgh（数学学院，爱丁堡大学）；MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh（人类遗传学单位，遗传与癌症研究所，爱丁堡大学）
Given any oriented link diagram, one can construct knot invariants using skein relations. Usually such a skein relation contains three or four terms. In this paper, the author introduces several new ways to smooth a crossings, and uses a system of skein equations to construct link invariant. This invariant can also be modified by writhe to get a more powerful invariant. The modified invariant is a generalization of both the HOMFLYPT polynomial and the two-variable Kauffman polynomial. Using the diamond lemma, a simplified version of the modified invariant is given. It is easy to compute and is…
In this paper, we define some polynomial invariants for virtual knots and links. In the first part we use Manturov's parity axioms to obtain a new polynomial invariant of virtual knots. This invariant can be regarded as a generalization of the odd writhe polynomial defined by the first author. The relation between this new polynomial invariant and the affine index polynomial is discussed. In the second part we introduce a polynomial invariant for long flat virtual knots. In the third part we define a polynomial invariant for 2-component virtual links. This polynomial invariant can be regarded …
Milnor's $\barμ$-invariants of links in the $3$-sphere $S^3$ vanish on any link concordant to a boundary link. In particular, they are trivial on any knot in $S^3$. Here we consider knots in thickened surfaces $Σ\times [0,1]$, where $Σ$ is closed and oriented. We construct new concordance invariants by adapting the Chen-Milnor theory of links in $S^3$ to an extension of the group of a virtual knot. A key ingredient is the Bar-Natan $\textit{Zh}$ map, which allows for a geometric interpretation of the group extension. The group extension itself was originally defined by Silver-Williams. Our ext…
We investigate the minimal number of links and knots in complete partite graphs. We provide exact values or bounds on the minimal number of links for all complete partite graphs with all but 4 vertices in one partition, or with 9 vertices in total. In particular, we find that the minimal number of links for $K_{4,4,1}$ is 74. We also provide exact values or bounds on the minimal number of knots for all complete partite graphs with 8 vertices.
If there are any 2-component counterexamples to the Generalized Property R Conjecture, a least genus component of all such counterexamples cannot be a fibered knot. Furthermore, the monodromy of a fibered component of any such counterexample has unexpected restrictions. The simplest plausible counterexample to the Generalized Property R Conjecture could be a 2-component link containing the square knot. We characterize all two-component links that contain the square knot and which surger to (S^1 x S^2) # (S^1 x S^2). We exhibit a family of such links that are probably counterexamples to General…
Experimental data from Dunfield et al using random grid diagrams suggests that the genus of a knot grows linearly with respect to the crossing number. Using billiard table diagrams of Chebyshev knots developed by Koseleff and Pecker and a random model of 2-bridge knots via these diagrams developed by the author with Krishnan and then with Even-Zohar and Krishnan, we introduce a further-truncated model of all 2-bridge knots of a given crossing number, almost all counted twice. We present a convenient way to count Seifert circles in this model and use this to compute a lower bound for the averag…
It is shown, using sutured manifold theory, that if there are any 2-component counterexamples to the Generalized Property R Conjecture, then any knot of least genus among components of such counterexamples is not a fibered knot. The general question of what fibered knots might appear as a component of such a counterexample is further considered; much can be said about the monodromy of the fiber, particularly in the case in which the fiber is of genus two.
Given a knot $K$ inside an integer homology sphere $Y$, the Casson-Lin-Herald invariant can be interpreted as a signed count of conjugacy classes of irreducible representations of the knot complement into $SU(2)$ which map the meridian of the knot to a fixed conjugacy class. It has the interesting feature that it determines the Tristram-Levine signature of the knot associated to the conjugacy class chosen. Turning things around, given a 4-manifold $X$ with the integral homology of $S^{1}\times S^{3}$, and an embedded torus $T$ inside $X$ such that $H_{1}(T;\mathbb{Z})$ surjects onto $H_{1}(X;\…
We present various examples of cosmetic bandings on knots and links, that is, bandings on knots and links leaving their types unchanged. As a byproduct, we give a hyperbolic knot which admits exotic chirally cosmetic surgeries yielding hyperbolic manifolds. This gives a counterexample to a conjecture raised by Bleiler, Hodgson and Weeks.
Many invariants of knots rely upon smoothing the knot at its crossings. To compute them, it is necessary to know how to count the number of connected components the knot diagram is broken into after the smoothing. In this paper, it is shown how to use a modification of a theorem of Zulli together with a modification of the spectral theory of graphs to approach such problems systematically. We give an application to counting subdiagrams of pretzel knots which have one component after oriented and unoriented smoothings.
We generalize the notion of the quandle polynomial to the case of singquandles. We show that the singquandle polynomial is an invariant of finite singquandles. We also construct a singular link invariant from the singquandle polynomial and show that this new singular link invariant generalizes the singquandle counting invariant. In particular, using the new polynomial invariant, we can distinguish singular links with the same singquandle counting invariant.
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's entanglement while ignoring their intrachain interactions. We remedy this by using stuck knots and links, which provide a way to emphasize both their entanglement and intrachain interactions. We first give a generating set of the oriented stuck Reidemeister moves for oriented stuck links. We then introduce an algebraic structure to axiomatize the oriented stuck Reide…
A model of random walk on knot diagrams is used to study the Alexander polynomial and the colored Jones polynomial of knots. In this context, the inverse of the Alexander polynomial of a knot plays the role of an Ihara-Selberg zeta function of a directed weighted graph, counting with weights cycles of random walk on a 1-string link whose closure is the knot in question. The colored Jones polynomial then counts with weights families of ``self-avoiding'' cycles of random walk on the cabling of the 1-string link. As a consequence of such interpretations of the Alexander and colored Jones polynomi…
We introduce an algebraic structure we call semiquandles whose axioms are derived from flat Reidemeister moves. Finite semiquandles have associated counting invariants and enhanced invariants defined for flat virtual knots and links. We also introduce singular semiquandles and virtual singular semiquandles which define invariants of flat singular virtual knots and links. As an application, we use semiquandle invariants to compare two Vassiliev invariants.
Let $G$ be a nonabelian, simple group with a nontrivial conjugacy class $C \subseteq G$. Let $K$ be a diagram of an oriented knot in $S^3$, thought of as computational input. We show that for each such $G$ and $C$, the problem of counting homomorphisms $π_1(S^3\setminus K) \to G$ that send meridians of $K$ to $C$ is almost parsimoniously $\mathsf{\#P}$-complete. This work is a sequel to a previous result by the authors that counting homomorphisms from fundamental groups of integer homology 3-spheres to $G$ is almost parsimoniously $\mathsf{\#P}$-complete. Where we previously used mapping class…
We study the 4-move invariant \crl\ for links in the 3-sphere developed by Dabkowski and Sahi, which is defined as a quotient of the fundamental group of the link complement. We develop techniques for computing this invariant and show that for several classes of knots it is equal to the invariant for the unknot; therefore, in these cases the invariant cannot detect a counterexample to the 4-move conjecture.
We define and study a family of link invariants $\mathit{HFK}_{n}(L)$. Although these homology theories are defined using holomorphic disc counts, they share many properties with $sl_{n}$ homology. Using these theories, we give a framework that generalizes the conjectured spectral sequence from Khovanov homology to $δ$-graded knot Floer homology. In particular, we conjecture that for all links $L$ in $S^3$ and all $n\ge 1$, there is a spectral sequence from the $sl_{n}$ homology of $L$ to $\mathit{HFK}_{n}(L)$.
Biracks are algebraic structures related to knots and links. We define a new enhancement of the birack counting invariant for oriented classical and virtual knots and links via algebraic structures called birack dynamical cocycles. The new invariants can also be understood in terms of partitions of the set of birack labelings of a link diagram determined by a homomorphism $p:X\to Y$ between finite labeling biracks. We provide examples to show that the new invariant is stronger than the unenhanced birack counting invariant and examine connections with other knot and link invariants.
We construct a new invariant of transverse links in the standard contact structure on R^3. This invariant is a doubly filtered version of the knot contact homology differential graded algebra (DGA) of the link. Here the knot contact homology of a link in R^3 is the Legendrian contact homology DGA of its conormal lift into the unit cotangent bundle S^*R^3 of R^3, and the filtrations are constructed by counting intersections of the holomorphic disks of the DGA differential with two conormal lifts of the contact structure. We also present a combinatorial formula for the filtered DGA in terms of b…
Reducing a 6d fivebrane theory on a 3-manifold $Y$ gives a $q$-series 3-manifold invariant $\widehat{Z}(Y)$. We analyse the large-$N$ behaviour of $F_K=\widehat{Z}(M_K)$, where $M_K$ is the complement of a knot $K$ in the 3-sphere, and explore the relationship between an $a$-deformed ($a=q^N$) version of $F_{K}$ and HOMFLY-PT polynomials. On the one hand, in combination with counts of holomorphic annuli on knot complements, this gives an enumerative interpretation of $F_K$ in terms of counts of open holomorphic curves. On the other, it leads to closed form expressions for $a$-deformed $F_K$ fo…
