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Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…
A graph class is monotone if it is closed under taking subgraphs. It is known that a monotone class defined by finitely many obstructions has bounded treewidth if and only if one of the obstructions is a so-called tripod, that is, a…
We propose high-order hypergraph walks as a framework to generalize graph-based network science techniques to hypergraphs. Edge incidence in hypergraphs is quantitative, yielding hypergraph walks with both length and width. Graph methods…
We study the computational complexity of routing multiple objects through a network in such a way that only few collisions occur: Given a graph $G$ with two distinct terminal vertices and two positive integers $p$ and $k$, the question is…
Patchy colloids are promising candidates for building blocks in directed self-assembly. To be successful the surface patterns need to both be simple enough to be synthesized, while feature-rich enough to cause the colloids to self-assemble…
We study the motion of random walkers with residence time bias between first and subsequent visits to a site, as a model for synthetic molecular walkers composed of coupled DNAzyme legs known as molecular spiders. The mechanism of the…
Let $\mathcal{D}$ be a set of straight-line segments in the plane, potentially crossing, and let $c$ be a positive integer. We denote by $P$ the union of the endpoints of the straight-line segments of $\mathcal{D}$ and of the intersection…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
Let G=(V,E) be a graph. A vertex dominates itself and all its neighbors, i.e., every vertex v in V dominates its closed neighborhood N[v]. A vertex set D in G is an efficient dominating (e.d.) set for G if for every vertex v in V, there is…
In this work, we present a simple and efficient generator of polymeric linear chains, based on a random self-avoiding walk process. The chains are generated using a discrete process of growth, in cubic networks and in a finite time, without…
We consider two possible extensions of a theorem of Thomassen characterizing the graphs admitting a 2-vertex-connected orientation. First, we show that the problem of deciding whether a mixed graph has a 2-vertex-connected orientation is…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The…
In this paper we study the fixed-parameter tractability of the problem of deciding whether a given temporal graph admits a temporal walk that visits all vertices (temporal exploration) or, in some problem variants, a certain subset of the…
We consider the problem of embedding the nodes of a hypergraph into Euclidean space under the assumption that the interactions arose through closeness to unknown hyperedge centres. In this way, we tackle the inverse problem associated with…
The restoration lemma by Afek, Bremler-Barr, Kaplan, Cohen, and Merritt [Dist. Comp. '02] proves that, in an undirected unweighted graph, any replacement shortest path avoiding a failing edge can be expressed as the concatenation of two…
We study high order random walks in high dimensional expanders; namely, in complexes which are local spectral expanders. Recent works have studied the spectrum of high order walks and deduced fast mixing. However, the spectral gap of high…