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Statistical analysis of a graph often starts with embedding, the process of representing its nodes as points in space. How to choose the embedding dimension is a nuanced decision in practice, but in theory a notion of true dimension is…
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…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
A fundamental characteristic of matter is its ability to form ordered structures under the right thermodynamic conditions. Predicting these structures - and their properties - from the attributes of a material's building blocks is the holy…
Ubiquitous geometric objects can be precisely and efficiently represented as polyhedra. The transformation of a polyhedron into a vector, known as polyhedra representation learning, is crucial for manipulating these shapes with mathematical…
We study the asymptotics of large directed graphs, constrained to have certain densities of edges and/or outward $p$-stars. Our models are close cousins of exponential random graph models (ERGMs), in which edges and certain other subgraph…
A polyhedron is a graph $G$ which is simple, planar and 3-connected. In this note, we classify the family of strongly involutive self-dual polyhedra. The latter is done by using a well-known result due to Tutte characterizing 3-connected…
We report experiments, modeling and numerical simulations of the self--assembly of particle patterns obtained from a nanometric metallic square grid. Initially, nickel filaments of rectangular cross section are patterned on a SiO$_2$ flat…
We address the problem of defining graph transformations by the simultaneous application of direct transformations even when these cannot be applied independently of each other. An algebraic approach is adopted, with production rules of the…
Graph embedding methods produce unsupervised node features from graphs that can then be used for a variety of machine learning tasks. Modern graphs, particularly in industrial applications, contain billions of nodes and trillions of edges,…
Recently, it has been found experimentally that hydrated nacre exhibits a nonlinear mechanical response. While mechanical nonlinearity has been shown to be important in other biological structures, such as spider webs, the implications of…
We introduce a new regression framework designed to deal with large-scale, complex data that lies around a low-dimensional manifold with noises. Our approach first constructs a graph representation, referred to as the skeleton, to capture…
In this paper, our goal is to characterize two graph classes based on the properties of minimal vertex (edge) separators. We first present a structural characterization of graphs in which every minimal vertex separator is a stable set. We…
We introduce graphcodes, a novel multi-scale summary of the topological properties of a dataset that is based on the well-established theory of persistent homology. Graphcodes handle datasets that are filtered along two real-valued scale…
An instance of a strongly stable matching problem (SSMP) is an undirected bipartite graph $G=(A \cup B, E)$, with an adjacency list of each vertex being a linearly ordered list of ties, which are subsets of vertices equally good for a given…
The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous…
We present a novel method to perform numerical integration over curved polyhedra enclosed by high-order parametric surfaces. Such a polyhedron is first decomposed into a set of triangular and/or rectangular pyramids, whose certain faces…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
In this paper we construct all strongly regular graphs, with at most 600 vertices, admitting a transitive action of the orthogonal group $O^+(6,2)$ or $O^-(6,2)$. Consequently, we prove the existence of strongly regular graphs with…
The full potential of graphene in integrated circuits can only be realized with a reliable ultra-thin high-{\kappa} top-gate dielectric. Here, we report the first statistical analysis of the breakdown characteristics of dielectrics on…