Fast construction of assembly trees for molecular graphs
A number of modeling and simulation algorithms using internal coordinates rely on hierarchical representations of molecular systems. Given the potentially complex topologies of molecular systems, though, automatically generating such hierarchical decompositions may be difficult. In this article, we present a fast general algorithm for the complete construction of a hierarchical representation of a molecular system. This two-step algorithm treats the input molecular system as a graph in which vertices represent atoms or pseudo-atoms, and edges represent covalent bonds. The first step contracts all cycles in the input graph. The second step builds an assembly tree from the reduced graph. We analyze the complexity of this algorithm and show that the first step is linear in the number of edges in the input graph, whereas the second one is linear in the number of edges in the graph without cycles, but dependent on the branching factor of the molecular graph. We demonstrate the performance of our algorithm on a set of specifically tailored difficult cases as well as on a large subset of molecular graphs extracted from the protein data bank. In particular, we experimentally show that both steps behave linearly in the number of edges in the input graph (the branching factor is fixed for the second step). Finally, we demonstrate an application of our hierarchy construction algorithm to adaptive torsion-angle molecular mechanics.
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A graph G is k-critical if G is not (k − 1)-colorable, but every proper subgraph of G is (k − 1)-colorable. A graph G is k-choosable if G has an L-coloring from every list assignment L with |L(v)|=k for all v, and a graph G is k-list-critical if G is not (k−1)-choosable, but every proper subgraph of G is (k−1)-choosable. The problem of determining the minimum number of edges in a k-critical graph with n vertices has been widely studied, starting with work of Gallai and culminating with the seminal results of Kostochka and Yancey, who essentially solved the problem. In this paper, we improve the best known lower bound on the number of edges in a k-list-critical graph. In fact, our result on k-list-critical graphs is derived from a lower bound on the number of edges in a graph with Alon–Tarsi number at least k. Our proof uses the discharging method, which makes it simpler and more modular than previous work in this area.
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The study of cyclic graphs has always been a hot topic in the field of graph theory and has received widespread attention from graph theory practitioners. If an n-order graph G exactly contains cycles of all lengths from 3 to n, then the graph is called a pan cycle graph. This article proves that, after excluding some special cases, when the number of edges in graph G is greater than or equal to C2n-3+12, graph G must be a pan cyclic graph.
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