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Allison H. Moore

Publications and source records attributed to Allison H. Moore.

At least 19 recordsLinked to original sources
arXiv2025

Methods for Analyzing RNA Pseudoknots via Chord Diagrams and Intersection Graphs

RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of the molecular configurations of RNA. Chord diagrams are mathematical objects widely used to represent RNA secondary structures and to analyze structural motifs, however a mathematically rigorous enumeration of pseudoknots remains a challenge. We introduce a method that incorporates a distance-based metric $\tau$ to analyze the intersection graph of a chord diagram associated with a pseudoknotted structure. In particular, our method formally defines a pseudoknot in terms of a weighted vertex cover of a certain intersection graph constructed from a partition of the chord diagram representing the nucleotide sequence of the RNA molecule. In this graph-theoretic context, we introduce a rigorous algorithm that enumerates pseudoknots, classifies secondary structures, and is sensitive to three-dimensional topological features. We implement our methods in MATLAB and test the algorithm on pseudoknotted structures from the bpRNA-1m database. Our findings confirm that genus is a robust quantifier of pseudoknot complexity.

q-bio.BM↗
arXiv2025

On gluing and splitting series invariants of plumbed 3-manifolds

We study series invariants for plumbed 3-manifolds and knot complements twisted by a root lattice. Our series recover recent results of Gukov-Pei-Putrov-Vafa, Gukov-Manolescu, Park, and Ri and apply more generally to 3-manifolds which are not necessarily negative definite. We show that our series verify certain gluing and splitting properties related to the corresponding operations on 3-manifolds. We conclude with an explicit description of the case of lens spaces and Brieskorn spheres.

math.GT↗
arXiv2024

Root lattices and invariant series for plumbed 3-manifolds

We study formal series which are invariants of plumbed 3-manifolds twisted by root lattices. These series extend the BPS $q$-series $\widehat{Z}(q)$ recently defined in Gukov-Pei-Putrov-Vafa, Gukov-Manolescu, Park, and further refined in Ri. We show that the series $\widehat{Z}(q)$ is unique in an appropriate sense and decomposes as the average of related series which are themselves invariant under the five Neumann moves amongst plumbing trees. Explicit computations are presented in the case of Brieskorn spheres and a non-Seifert manifold.

math.GT↗
arXiv2024

Signature, slicing foams, and crossing changes of Klein graphs

A totally oriented Klein graph is a trivalent spatial graph in the 3-sphere with a 3-coloring of its edges and an orientation on each bicolored link. A totally oriented Klein foam is a 3-colored 2-complex in the 4-ball whose boundary is a Klein foam and whose bicolored surfaces are oriented. We extend Gille-Robert's signature for 3-Hamiltonian Klein graphs to all totally oriented Klein graphs and develop an analogy of Murasugi's bounds relating the signature, slice genus and unknotting number of knots. In particular, we show that the signature of a totally oriented Klein graph produces a lower bound on the negative orbifold Euler characteristic of certain totally oriented Klein foams bounded by $Γ$. When $Γ$ is abstractly planar, these negative Euler characteristics, in turn, produce a lower bound on a certain natural unknotting number for $Γ$. Mutatis mutandi, we produce lower bounds on the corresponding Gordian distance between two totally oriented Klein graphs that can be related by a sequence of crossing changes. We also give examples of theta-curves for which our lower bounds on unknotting number improve on previously known bounds.

math.GT↗
arXiv2023

Adjacency of three-manifolds and Brunnian links

We introduce the notion of adjacency in three-manifolds. A three-manifold $Y$ is $n$-adjacent to another three-manifold $Z$ if there exists an $n$-component link in $Y$ and surgery slopes for that link such that performing Dehn surgery along any nonempty sublink yields $Z$. We characterize adjacencies from three-manifolds to the three-sphere, providing an analogy to Askitas and Kalfagianni's results on $n$-adjacency in knots.

math.GT↗
arXiv2022

Determinants of Simple Theta Curves and Symmetric Graphs

A theta curve is a spatial embedding of the $θ$-graph in the three-sphere, taken up to ambient isotopy. We define the determinant of a theta curve as an integer-valued invariant arising from the first homology of its Klein cover. When a theta curve is simple, containing a constituent unknot, we prove that the determinant of the theta curve is the product of the determinants of the constituent knots. Our proofs are combinatorial, relying on Kirchhoff's Matrix Tree Theorem and spanning tree enumeration results for symmetric, signed, planar graphs.

math.GT↗
arXiv2021

Knot Graphs and Gromov Hyperbolicity

We define a broad class of graphs that generalize the Gordian graph of knots. These knot graphs take into account unknotting operations, the concordance relation, and equivalence relations generated by knot invariants. We prove that overwhelmingly, the knot graphs are not Gromov hyperbolic, with the exception of a particular family of quotient knot graphs. We also investigate the property of homogeneity, and prove that the concordance knot graph is homogeneous. Finally, we prove that that for any $n$, there exists a knot $K$ such that the ball of radius $n$ in the Gordian graph centered at $K$ contains no connected sum of torus knots.

math.GT↗
arXiv2021

Quotients of the Gordian and H(2)-Gordian graphs

The Gordian graph and H(2)-Gordian graphs of knots are abstract graphs whose vertex sets represent isotopy classes of unoriented knots, and whose edge sets record whether pairs of knots are related by crossing changes or H(2)-moves, respectively. We investigate quotients of these graphs under equivalence relations defined by several knot invariants including the determinant, the span of the Jones polynomial, and an invariant related to tricolorability. We show, in all cases considered, that the quotient graphs are Gromov hyperbolic. We then prove a collection of results about the graph isomorphism type of the quotient graphs. In particular, we find that the H(2)-Gordian graph of links modulo the relation induced by the span of the Jones polynomial is isomorphic with the complete graph on infinitely many vertices.

math.GT↗
arXiv2021

Cosmetic operations and Khovanov multicurves

We prove an equivariant version of the Cosmetic Surgery Conjecture for strongly invertible knots. Our proof combines a recent result of Hanselman with the Khovanov multicurve invariants $\widetilde{\operatorname{Kh}}$ and $\widetilde{\operatorname{BN}}$. We apply the same techniques to reprove a result of Wang about the Cosmetic Crossing Conjecture and split links. Along the way, we show that $\widetilde{\operatorname{Kh}}$ and $\widetilde{\operatorname{BN}}$ detect if a Conway tangle is split.

math.GT↗
arXiv2020

Triple linking numbers and Heegaard Floer homology

We establish some new relationships between Milnor invariants and Heegaard Floer homology. This includes a formula for the Milnor triple linking number from the link Floer complex, detection results for the Whitehead link and Borromean rings, and a structural property of the $d$-invariants of surgeries on certain algebraically split links.

math.GT↗
arXiv2020

A note on band surgery and the signature of a knot

Band surgery is an operation relating pairs of knots or links in the three-sphere. We prove that if two quasi-alternating knots $K$ and $K'$ of the same square-free determinant are related by a band surgery, then the absolute value of the difference in their signatures is either 0 or 8. This obstruction follows from a more general theorem about the difference in the Heegaard Floer $d$-invariants for pairs of L-spaces that are related by distance one Dehn fillings and satisfy a certain condition in first homology. These results imply that $T(2, 5)$ is the only torus knot $T(2, m)$ with $m$ square-free that admits a chirally cosmetic banding, i.e. a band surgery operation to its mirror image. We conclude with a discussion on the scarcity of chirally cosmetic bandings.

math.GT↗
arXiv2019

Surgery on links of linking number zero and the Heegaard Floer $d$-invariant

We study Heegaard Floer homology and various related invariants (such as the $h$-function) for two-component L-space links with linking number zero. For such links, we explicitly describe the relationship between the $h$-function, the Sato-Levine invariant and the Casson invariant. We give a formula for the Heegaard Floer $d$-invariants of integral surgeries on two-component L-space links of linking number zero in terms of the $h$-function, generalizing a formula of Ni and Wu. As a consequence, for such links with unknotted components, we characterize L-space surgery slopes in terms of the $ν^{+}$-invariants of the knots obtained from blowing down the components. We give a proof of a skein inequality for the $d$-invariants of $+1$ surgeries along linking number zero links that differ by a crossing change. We also describe bounds on the smooth four-genus of links in terms of the $h$-function, expanding on previous work of the second author, and use these bounds to calculate the four-genus in several examples of links.

math.GT↗
arXiv2019

Distance one lens space fillings and band surgery on the trefoil knot

We prove that if the lens space $L(n, 1)$ is obtained by a surgery along a knot in the lens space $L(3,1)$ that is distance one from the meridional slope, then $n$ is in $\{-6, \pm 1, \pm 2, 3, 4, 7\}$. This result yields a classification of the coherent and non-coherent band surgeries from the trefoil to $T(2, n)$ torus knots and links. The main result is proved by studying the behavior of the Heegaard Floer $d$-invariants under integral surgery along knots in $L(3,1)$. The classification of band surgeries between the trefoil and torus knots and links is motivated by local reconnection processes in nature, which are modeled as band surgeries. Of particular interest is the study of recombination on circular DNA molecules.

math.GT↗
arXiv2018

Recent advances on the non-coherent band surgery model for site-specific recombination

Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the sites prior to recombination. Mathematically, site-specific recombination is modeled as coherent (knot to link) or non-coherent (knot to knot) banding. We here survey recent developments in the study of non-coherent bandings on knots and discuss biological implications.

math.GT↗
arXiv2018

Symmetric unions without cosmetic crossing changes

A symmetric union of two knots is a classical construction in knot theory which generalizes connected sum, introduced by Kinoshita and Terasaka in the 1950s. We study this construction for the purpose of finding an infinite family of hyperbolic non-fibered three-bridge knots of constant determinant which satisfy the well-known cosmetic crossing conjecture. This conjecture asserts that the only crossing changes which preserve the isotopy type of a knot are nugatory.

math.GT↗
arXiv2015

Cosmetic surgery in L-spaces and nugatory crossings

The cosmetic crossing conjecture (also known as the "nugatory crossing conjecture") asserts that the only crossing changes that preserve the oriented isotopy class of a knot in the 3-sphere are nugatory. We use the Dehn surgery characterization of the unknot to prove this conjecture for knots in integer homology spheres whose branched double covers are L-spaces satisfying a homological condition. This includes as a special case all alternating and quasi-alternating knots with square-free determinant. As an application, we prove the cosmetic crossing conjecture holds for all knots with at most nine crossings and provide new examples of knots, including pretzel knots, non-arborescent knots and symmetric unions for which the conjecture holds.

math.GT↗