Danielle O'Donnol

Oklahoma State University | Oklahoma State · Department of Mathematics

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 Klei...

We show that if a composite $\theta$-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 $\theta$-curve. We also prove similar results for 2-strand tangles and knotoids.

During DNA replication in living cells some DNA knots are inadvertently produced by DNA topoisomerases facilitating progression of replication forks. The types of DNA knots formed are conditioned by the 3D organization of replicating DNA molecules. Therefore, by characterizing formed DNA knots it is possible to infer the 3D arrangement of replicati...

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...

We classify topologically trivial Legendrian $\Theta$-graphs and identify the complete family of nondestabilizeable Legendrian realizations in this topological class. In contrast to all known results for Legendrian knots, this is an infinite family of graphs. We also show that any planar graph that contains a subdivision of a $\Theta$-graph or $S^1...

We classify topologically trivial Legendrian $\Theta$-graphs and identify the complete family of nondestabilizeable Legendrian realizations in this topological class. In contrast to all known results for Legendrian knots, this is an infinite family of graphs. We also show that any planar graph that contains a subdivision of a $\Theta$-graph or $S^1...

We prove two results on the classification of trivial Legendrian embeddings $g: G \rightarrow (S^3,\xi_{std})$ of planar graphs. First, the oriented Legendrian ribbon $R_g$ and rotation invariant $\text{rot}_g$ are a complete set of invariants. Second, if $G$ is 3-connected or contains $K_4$ as a minor, then the unique trivial embedding of $G$ is L...

We study the Thurston-Bennequin number of complete and complete bipartite Legendrian graphs. We define a new invariant called the total Thurston-Bennequin number of the graph. We show that this invariant is determined by the Thurston-Bennequin numbers of 3-cycles for complete graphs and by the Thurston-Bennequin number of 4-cycles for complete bipa...

This paper introduces a number of new intrinsically 3-linked graphs through five new constructions. We then prove that intrinsic 3-linkedness is not preserved by $\text{Y}\nabla$ moves. We will see that the graph $M$, which is obtained through a $\text{Y}\nabla$ move on $(PG)^*_*(PG)$, is not intrinsically 3-linked.

We use a semisupervised learning algorithm based on a topological data analysis approach to assign functional categories to yeast proteins using similarity graphs. This new approach to analyzing biological networks yields results that are as good as or better than state of the art existing approaches.

In this article we give necessary and suficient conditions for two triples of integers to be realized as the Thurston-Bennequin number and the rotation number of a Legendrian theta-graph with all cycles unknotted. We show that these invariants are not enough to determine the Legendrian class of a topologically planar theta-graph. We define the tran...

We investigate Legendrian graphs in $(\R^3, \xi_{std})$. We extend the classical invariants, Thurston-Bennequin number and rotation number to Legendrian graphs. We prove that a graph can be Legendrian realized with all its cycles Legendrian unknots with $tb=-1$ and $rot=0$ if and only if it does not contain $K_4$ as a minor. We show that the pair $...

This paper focuses on the graphs in the Petersen family, the set of minor minimal intrinsically linked graphs. We prove there is a relationship between algebraic linking of an embedding and knotting in an embedding. We also present a more explicit relationship for the graph $K_{3,3,1}$ between knotting and linking, which relates the sum of the squa...

In this paper we examine the question: given $n>1$, find a function $f:\mathbf{N}\rightarrow \mathbf{N}$ where $m=f(n)$ is the smallest integer such that $K_m$ is intrinsically $n$-linked. We prove that for $n>1$, every embedding of $K_{\lfloor \frac{7}{2}n\rfloor}$ in $\mathbf{R}^3$ contains a non-splittable link of $n$ components. We also prove a...

We prove that every embedding of $K_{2n+1,2n+1}$ into $\R^3$ contains a non-split link of $n$-components. Further, given an embedding of $K_{2n+1,2n+1}$ in $\R^3$, every edge of $K_{2n+1,2n+1}$ is contained in a non-split $n$-component link in $K_{2n+1,2n+1}$.

Polar development and cell division in Caulobacter crescentus are controlled and coordinated by multiple signal transduction proteins. divJ encodes a histidine kinase. A null mutation in divJ results in a reduced growth rate, cell filamentation, and mislocalized stalks. Suppressor analysis of divJ identified mutations in genes encoding the tyrosine...

The expression of the flagellin proteins in Caulobacter crescentus is regulated by the progression of flagellar assembly both at the transcriptional and post-transcriptional levels. An early basal body structure is required for the transcription of flagellin genes, whereas the ensuing assembly of a hook structure is required for flagellin protein s...

In Caulobacter crescentus, stalk biosynthesis is regulated by cell cycle cues and by extracellular phosphate concentration. Phosphate-starved cells undergo dramatic stalk elongation to produce stalks as much as 30 times as long as those of cells growing in phosphate-rich medium. To identify genes involved in the control of stalk elongation, transpo...