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Query: "author" (Tomaž Pisanski) .

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The Sierpiński product of graphs
Jurij Kovič, Tomaž Pisanski, Sara Sabrina Zemljič, Arjana Žitnik, 2023, original scientific article

Abstract: In this paper we introduce a product-like operation that generalizes the construction of the generalized Sierpiński graphs. Let $G$, $H$ be graphs and let $f: V(G) \to V(H)$ be a function. Then the Sierpiński product of graphs $G$ and $H$ with respect to $f$, denoted by $G\otimes_f H$, is defined as the graph on the vertex set $V(G) \times V(H)$, consisting of $|V(G)|$ copies of $H$; for every edge $\{g, g'\}$ of $G$ there is an edge between copies $gH$ and $g'H$ of form $\{(g, f(g'), (g', f(g))\}$. Some basic properties of the Sierpiński product are presented. In particular, we show that the graph $G\otimes_f H$ is connected if and only if both graphs $G$ and $H$ are connected and we present some conditions that $G, \, H$ must fulfill for $G\otimes_f H$ to be planar. As for symmetry properties, we show which automorphisms of $G$ and $H$ extend to automorphisms of $G\otimes_f H$. In several cases we can also describe the whole automorphism group of the graph $G\otimes_f H$. Finally, we show how to extend the Sierpiński product to multiple factors in a natural way. By applying this operation $n$ times to the same graph we obtain an alternative approach to the well-known $n$-th generalized Sierpiński graph.
Keywords: Sierpiński graphs, graph products, connectivity, planarity, symmetry
Published in DiRROS: 19.03.2024; Views: 117; Downloads: 42
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Design principles for rapid folding of knotted DNA nanostructures
Vid Kočar, John S. Schreck, Slavko Čeru, Helena Gradišar, Nino Bašić, Tomaž Pisanski, Jonathan P. K. Doye, Roman Jerala, 2016, original scientific article

Abstract: Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the "free-end" rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.
Published in DiRROS: 13.04.2016; Views: 4354; Downloads: 1425
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