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Register a new userEnhancement of the Coloring Invariant for Folded Molecular Chains
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Folded linear molecular chains are ubiquitous in biology. Folding is mediated by intra-chain interactions that glue two or more regions of a chain. The resulting fold topology is widely believed to be a determinant of biomolecular properties and function. Recently, knot theory has been extended to describe the topology of folded linear chains such as proteins and nucleic acids. To classify and distinguish chain topologies, algebraic structure of quandles has been adapted and applied. However, the approach is limited as apparently distinct topologies may end up having the same number of colorings. Here, we enhance the resolving power of the quandle coloring approach by introducing Boltzmann weights. We demonstrate that the enhanced coloring invariants can distinguish fold topologies with an improved resolution.
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We study Kauffmans model of folded ribbon knots: knots made of a thin strip of paper folded flat in the plane. The folded ribbonlength is the length to width ratio of such a ribbon knot. We give upper bounds on the folded ribbonlength of 2-bridge, $(2,p)$ torus, twist, and pretzel knots, and these upper bounds turn out to be linear in crossing number. We give a new way to fold $(p,q)$ torus knots, and show that their folded ribbonlength is bounded above by $p+q$. This means, for example, that the trefoil knot can be constructed with a folded ribbonlength of 5. We then show that any $(p,q)$ torus knot $K$ has a constant $c>0$, such that the folded ribbonlength is bounded above by $ccdot Cr(K)^{1/2}$, providing an example of an upper bound on folded ribbonlength that is sub-linear in crossing number.
We enhance the psyquandle counting invariant for singular knots and pseudoknots using quivers analogously to quandle coloring quivers. This enables us to extend the in-degree polynomial invariants from quandle coloring quiver theory to the case of singular knots and pseudoknots. As a side effect we obtain biquandle coloring quivers and in-degree polynomial invariants for classical and virtual knots and links.
This survey article discusses three aspects of knot colorings. Fox colorings are assignments of labels to arcs, Dehn colorings are assignments of labels to regions, and Alexander-Briggs colorings assign labels to vertices. The labels are found among the integers modulo n. The choice of n depends upon the knot. Each type of coloring rules has an associated rule that must hold at each crossing. For the Alexander Briggs colorings, the rules hold around regions. The relationships among the colorings is explained.
Quandle coloring quivers are directed graph-valued invariants of oriented knots and links, defined using a choice of finite quandle $X$ and set $Ssubsetmathrm{Hom}(X,X)$ of endomorphisms. From a quandle coloring quiver, a polynomial knot invariant known as the textit{in-degree quiver polynomial} is defined. We consider quandle coloring quiver invariants for oriented surface-links, represented by marked graph diagrams. We provide example computations for all oriented surface-links with ch-index up to 10 for choices of quandles and endomorphisms.
We prove a splicing formula for the LMO invariant, which is the universal finite-type invariant of rational homology $3$-spheres. Specifically, if a rational homology $3$-sphere $M$ is obtained by gluing the exteriors of two framed knots $K_1 subset M_1$ and $K_2subset M_2$ in rational homology $3$-spheres, our formula expresses the LMO invariant of $M$ in terms of the Kontsevich-LMO invariants of $(M_1,K_1)$ and $(M_2,K_2)$. The proof uses the techniques that Bar-Natan and Lawrence developed to obtain a rational surgery formula for the LMO invariant. In low degrees, we recover Fujitas formula for the Casson-Walker invariant and we observe that the second term of the Ohtsuki series is not additive under standard splicing. The splicing formula also works when each $M_i$ comes with a link $L_i$ in addition to the knot $K_i$, hence we get a satellite formula for the Kontsevich-LMO invariant.
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