arXiv subjects

Senja Barthel

Publications and source records attributed to Senja Barthel.

8 recordsLinked to original sources

arXiv2025

Linking number of grid models

This paper studies the linking numbers of random links within the grid model. The linking number is treated as a random variable on the isotopy classes of 2-component links, with the paper exploring its asymptotic growth as the diagram size increases. The main result is that the $u$th moment of the linking number for a random link is a polynomial in the grid size with degree $d\leq u$, and all odd moments vanishing. The limits of the moments of the normalized linking number are computed, and it is shown that the distribution of the normalized linking number converges weakly as the grid size tends to infinity.

math.GT↗

arXiv2024

Properties of leveled spatial graphs

We investigate the property of a spatial graph of having a leveled embedding and characterize the abstract graphs with this property. We show that all leveled embeddings are free and we compare leveled and paneled (also known as flat) embeddings. Two new graph invariants are introduced: the level number, an invariant for graphs that admit a leveled embedding, and the Hamiltonian level number, an invariant for Hamiltonian graphs. These invariants provide a measure on how far a graph is from being planar. We study the relation between the (Hamiltonian) level number and other graph invariants that minimize the decomposition of a graph in planar subgraphs, namely the thickness and the book thickness of a graph. We characterize graphs with low level number and determine both the level number and the Hamiltonian level number of complete graphs and of complete bipartite graphs.

math.CO↗

arXiv2024

Constructing embedded surfaces for cellular embeddings of leveled spatial graphs

For a given spatial graph $\mathcal{G} \subset \mathbb{R}^3$, we would like to find a closed orientable surface $\mathcal{S}$ embedded in $\mathbb{R}^3$ in which $\mathcal{G}$ is cellular embedded. However, for general $\mathcal{G}$ this is not possible. We therefore define a property of spatial graphs, called leveled, to show that for leveled spatial graphs with a small number of levels, a surface $\mathcal{S}$ can always be found. The argument is based on decomposing $\mathcal{G}$ into spatial subgraphs that can be placed on a sphere and on cylinders attached as handles, in such a way that the resulting surface contains a cellular embedding of $\mathcal{G}$. We generalize the procedure to an algorithm that, if successful, constructs $\mathcal{S}$ for leveled spatial graphs with any number of levels. We conjecture that all connected leveled embeddings can be cellular embedded with the presented algorithm.

math.GT↗

arXiv2022

SELFIES and the future of molecular string representations

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings -- most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100\% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chemistry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.

physics.chem-ph↗

arXiv2019

Toroidal embeddings of abstractly planar graphs are knotted or linked

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.

math.GT↗

arXiv2019

There exist no Minimally Knotted Planar Spatial Graphs on the Torus

We show that all nontrivial embeddings of planar graphs on the torus contain a nontrivial knot or a nonsplit link. This is equivalent to showing that no minimally knotted planar spatial graphs on the torus exist that contain neither a nontrivial knot nor a nonsplit link all of whose components are unknots.

math.GT↗

arXiv2018

Note on minimal number of skewed unit cells for periodic distance calculation

How many copies of a parallelepiped are needed to ensure that for every point in the parallelepiped a copy of each other point exists, such that the distance between them equals the distance of the pair of points when the opposite sites of the parallelepiped are identified? This question is answered in Euclidean space by constructing the smallest domain that fulfills the above condition. We also describe how to obtain all primitive cells of a lattice (i.e., closures of fundamental domains) that realise the smallest number of copies needed and give them explicitly in 2D and 3D.

cs.CG↗

arXiv2017

On chirality of toroidal embeddings of polyhedral graphs

We investigate properties of spatial graphs on the standard torus. It is known that nontrivial embeddings of planar graphs in the torus contain a nontrivial knot or a nonsplit link due to [1],[2]. Building on this and using the chirality of torus knots and links [3],[4], we prove that nontrivial embeddings of simple 3-connected planar graphs in the standard torus are chiral. For the case that the spatial graph contains a nontrivial knot, the statement was shown by Castle [5]. We give an alternative proof using minors instead of the Euler characteristic. To prove the case in which the graph embedding contains a nonsplit link, we show the chirality of Hopf ladders with at least three rungs, thus generalising a theorem of Simon [6].

math.GT↗