Related papers: Antiparallel d-stable Traces and a Stronger Versio…
A novel self-assembly strategy for polypeptide nanostructure design was presented in [Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments, Nature Chemical Biology 9 (2013) 362--366]. The first mathematical…
For a graph $G$ and $E \subseteq E(G)$, $E$-restricted strong trace is a closed walk which traverses every edge from $E$ once in each direction and every other edge twice in the same direction. In addition, every time a strong trace come to…
Recently designed biomolecular approaches to build single chain polypeptide polyhedra as molecular origami nanostructures have risen high interest in various double traces of the underlying graphs of these polyhedra. Double traces are walks…
A parallel $d$-stable trace is a closed walk which traverses every edge of a graph exactly twice in the same direction and for every vertex $v$, there is no subset $X \subseteq N(v)$ with $1 \leq |N| \leq d$ such that every time the walk…
The circuits of a polyhedron are a superset of its edge directions. Circuit walks, a sequence of steps along circuits, generalize edge walks and are "short" if they have few steps or small total length. Both interpretations of short are…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
Simultaneous Geometric Embedding (SGE) asks whether, for a given collection of graphs on the same vertex set V, there is an embedding of V in the plane that admits a crossing-free drawing with straightline edges for each of the given…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Graph vertex embeddings based on random walks have become increasingly influential in recent years, showing good performance in several tasks as they efficiently transform a graph into a more computationally digestible format while…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
This paper develops a structural theory of unique shortest paths in real-weighted graphs. Our main goal is to characterize exactly which sets of node sequences, which we call path systems, can be realized as unique shortest paths in a graph…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
We consider a Hamiltonian decomposition problem of partitioning a regular graph into edge-disjoint Hamiltonian cycles. It is known that verifying vertex non-adjacency in the 1-skeleton of the symmetric and asymmetric traveling salesperson…
In 2009, Jonoska, Seeman and Wu showed that every graph admits a route for a DNA reporter strand, that is, a closed walk covering every edge either once or twice, in opposite directions if twice, and passing through each vertex in a…
In this paper we revisit the classical Edge Disjoint Paths (EDP) problem, where one is given an undirected graph G and a set of terminal pairs P and asks whether G contains a set of pairwise edge-disjoint paths connecting every terminal…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
A directed acyclic graph $G=(V,E)$ is said to be $(e,d)$-depth robust if for every subset $S \subseteq V$ of $|S| \leq e$ nodes the graph $G-S$ still contains a directed path of length $d$. If the graph is $(e,d)$-depth-robust for any $e,d$…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
\textsc{Directed Token Sliding} asks, given a directed graph and two sets of pairwise nonadjacent vertices, whether one can reach from one set to the other by repeatedly applying a local operation that exchanges a vertex in the current set…