51. Knots and $\theta$-curves identification in polymeric chains and native proteins using neural networksFernando Bruno da Silva, Boštjan Gabrovšek, Marta Korpacz, Kamil Luczkiewicz, Szymon Niewieczerzal, Maciej Sikora, Joanna I. Sulkowska, 2024, izvirni znanstveni članek Povzetek: Entanglement in proteins is a fascinating structural motif that is neither easy to detect via traditional methods nor fully understood. Recent advancements in AI-driven models have predicted that millions of proteins could potentially have a nontrivial topology. Herein, we have shown that long short-term memory (LSTM)-based neural networks (NN) architecture can be applied to detect, classify, and predict entanglement not only in closed polymeric chains but also in polymers and protein-like structures with open knots, actual protein configurations, and also $\theta$-curves motifs. The analysis revealed that the LSTM model can predict classes (up to the $6_1$ knot) accurately for closed knots and open polymeric chains, resembling real proteins. In the case of open knots formed by protein-like structures, the model displays robust prediction capabilities with an accuracy of 99%. Moreover, the LSTM model with proper features, tested on hundreds of thousands of knotted and unknotted protein structures with different architectures predicted by AlphaFold 2, can distinguish between the trivial and nontrivial topology of the native state of the protein with an accuracy of 93%. Ključne besede: machine learning, topology, protein databases, entanglements, open knots, closed knots Objavljeno v DiRROS: 23.10.2024; Ogledov: 311; Prenosov: 496
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52. Mutual-visibility and general position in double graphs and in MycielskiansDhanya Roy, Sandi Klavžar, Aparna Lakshmanan S., 2025, izvirni znanstveni članek Povzetek: The general position problem in graphs is to find the largest possible set of vertices with the property that no three of them lie on a common shortest path. The mutual-visibility problem in graphs is to find the maximum number of vertices that can be selected such that every pair of vertices in the collection has a shortest path between them with no vertex from the collection as an internal vertex. Here, the general position problem and the mutual-visibility problem are investigated in double graphs and in Mycielskian graphs. Sharp general bounds are proved, in particular involving the total and the outer mutual-visibility number of base graphs. Several exact values are also determined, in particular the mutual-visibility number of the double graphs and of the Mycielskian of cycles. Ključne besede: general position, mutual-visibility, double graph, Mycielskian graph, outer mutual-visibility, total mutual-visibility Objavljeno v DiRROS: 23.10.2024; Ogledov: 248; Prenosov: 126
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53. A new approach to universal $F$-inverse monoids in enriched signatureGanna Kudryavtseva, Ajda Lemut Furlani, 2024, izvirni znanstveni članek Povzetek: We show that the universal $X$-generated $F$-inverse monoid $F(G)$, where ▫$G$▫ is an $X$-generated group, introduced by Auinger, Szendrei and the first-named author, arises as a quotient inverse monoid of the Margolis-Meakin expansion $M(G, X\cup \overline{G})$ of $G$, with respect to the extended generating set $X\cup \overline{G}$, where $\overline{G}$ is a bijective copy of $G$ which encodes the ▫$m$▫-operation in $F(G)$. The construction relies on a certain dual-closure operator on the semilattice of all finite and connected subgraphs containing the origin of the Cayley graph ${\rm Cay}(G, X\cup {\overline{G}})$ and leads to a new and simpler proof of the universal property of $F(G)$. Ključne besede: inverse monoid, F-inverse monoid, Margolis-Meakin expansion, group presentation, Cayley graph of a group, closure operator, dual-closure operator, partial action, partial action product Objavljeno v DiRROS: 21.10.2024; Ogledov: 275; Prenosov: 127
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54. Computation of leaky waves in layered structures coupled to unbounded media by exploiting multiparameter eigenvalue problemsHauke Gravenkamp, Bor Plestenjak, Daniel A. Kiefer, Elias Jarlebring, 2025, izvirni znanstveni članek Povzetek: We present a semi-analytical approach to compute quasi-guided elastic wave modes in horizontally layered structures radiating into unbounded fluid or solid media. This problem is of relevance, e.g., for the simulation of guided ultrasound in embedded plate structures or seismic waves in soil layers over an elastic half-space. We employ a semi-analytical formulation to describe the layers, thus discretizing the thickness direction by means of finite elements. For a free layer, this technique leads to a well-known quadratic eigenvalue problem for the mode shapes and corresponding horizontal wavenumbers. Incorporating the coupling conditions to account for the adjacent half-spaces gives rise to additional terms that are nonlinear in the wavenumber. We show that the resulting nonlinear eigenvalue problem can be cast in the form of a multiparameter eigenvalue problem whose solutions represent the wave numbers in the plate and in the half-spaces. The multiparameter eigenvalue problem is solved numerically using recently developed algorithms. Matlab implementations of the proposed methods are publicly available. Ključne besede: guided waves, plates, soil dynamics, half-space, leaky waves, semi-analytical method Objavljeno v DiRROS: 11.10.2024; Ogledov: 320; Prenosov: 2464
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55. Symmetries of the Woolly Hat graphsLeah Berman, Sergio Hiroki Koike Quintanar, Elías Mochán, Alejandra Ramos Rivera, Primož Šparl, Steve Wilson, 2024, izvirni znanstveni članek Povzetek: A graph is edge-transitive if the natural action of its automorphism group on its edge set is transitive. An automorphism of a graph is semiregular if all of the orbits of the subgroup generated by this automorphism have the same length. While the tetravalent edge-transitive graphs admitting a semiregular automorphism with only one orbit are easy to determine, those that admit a semiregular automorphism with two orbits took a considerable effort and were finally classified in 2012. Of the several possible different "types" of potential tetravalent edge-transitive graphs admitting a semiregular automorphism with three orbits, only one "type" has thus far received no attention. In this paper we focus on this class of graphs, which we call the Woolly Hat graphs. We prove that there are in fact no edge-transitive Woolly Hat graphs and classify the vertex-transitive ones. Ključne besede: edge-transitive, vertex-transitive, tricirculant, Woolly Hat graphs Objavljeno v DiRROS: 07.10.2024; Ogledov: 439; Prenosov: 170
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56. On the 2-rainbow independent domination numbers of some graphsBoštjan Gabrovšek, Aljoša Peperko, Janez Žerovnik, 2023, izvirni znanstveni članek Povzetek: By suitably adjusting the tropical algebra technique we compute the rainbow independent domination numbers of several infinite families of graphs including Cartesian products $C_n \Box P_m$ and $C_n \Box C_m$ for all $n$ and $m\le 5$, and generalized Petersen graphs $P(n,2)$ for $n \ge 3$. Ključne besede: graph theory, rainbow independent domination number, path algebra, tropical algebra Objavljeno v DiRROS: 03.10.2024; Ogledov: 482; Prenosov: 201
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57. Inequalities and equalities on the joint and generalized spectral and essential spectral radius of the Hadamard geometric mean of bounded sets of positive kernel operatorsKatarina Bogdanović, Aljoša Peperko, 2023, izvirni znanstveni članek Povzetek: We prove new inequalities and equalities for the generalized and the joint spectral radius (and their essential versions) of Hadamard (Schur) geometric means of bounded sets of positive kernel operators on Banach function spaces. In the case of nonnegative matrices that define operators on Banach sequences we obtain additional results. Our results extend results of several authors that appeared relatively recently. Ključne besede: Hadamard-Schur geometric mean, Hadamard-Schur product, joint and generalized spectral radius, essential spectral radius, measure of noncompactness, positive kernel operators, non-negative matrices, bounded sets of operators Objavljeno v DiRROS: 03.10.2024; Ogledov: 403; Prenosov: 206
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58. Covering the edges of a graph with trianglesCsilla Bujtás, Akbar Davoodi, Laihao Ding, Ervin Győri, Zsolt Tuza, Donglei Yang, 2025, izvirni znanstveni članek Povzetek: In a graph $G$, let $\rho_\triangle(G)$ denote the minimum size of a set of edges and triangles that cover all edges of $G$, and let $\alpha_1(G)$ be the maximum size of an edge set that contains at most one edge from each triangle. Motivated by a question of Erdős, Gallai, and Tuza, we study the relationship between $\rho_\triangle(G)$ and $\alpha_1(G)$ and establish a sharp upper bound on $\rho_\triangle(G)$. We also prove Nordhaus-Gaddum-type inequalities for the considered invariants. Ključne besede: edge-disjoint triangles, edge clique covering, Nordhaus-Gaddum inequality Objavljeno v DiRROS: 03.10.2024; Ogledov: 371; Prenosov: 200
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59. Vertex-primitive digraphs with large fixityMarco Barbieri, Primož Potočnik, 2024, izvirni znanstveni članek Povzetek: The relative fixity of a digraph $\Gamma$ is defined as the ratio between the largest number of vertices fixed by a nontrivial automorphism of $\Gamma$ and the number of vertices of $\Gamma$ .We characterize the vertex-primitive digraphs whose relative fixity is at least $1 \over 3$, and we show that there are only finitely many vertex-primitive digraphs of bounded out-valency and relative fixity exceeding a positive constant. Ključne besede: vertex-primitive digraphs, fixity, product action, graphs Objavljeno v DiRROS: 03.10.2024; Ogledov: 380; Prenosov: 180
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60. Fast winning strategies for Staller in the Maker-Breaker domination gameCsilla Bujtás, Pakanun Dokyeesun, 2024, izvirni znanstveni članek Povzetek: The Maker-Breaker domination game is played on a graph $G$ by two players, called Dominator and Staller, who alternately choose a vertex that has not been played so far. Dominator wins the game if his moves form a dominating set. Staller wins if she plays all vertices from a closed neighborhood of a vertex $v \in V(G)$. Dominator's fast winning strategies were studied earlier. In this work, we concentrate on the cases when Staller has a winning strategy in the game. We introduce the invariant $\gamma'_{\rm SMB}(G)$ (resp., $\gamma_{\rm SMB}(G)$) which is the smallest integer $k$ such that, under any strategy of Dominator, Staller can win the game by playing at most $k$ vertices, if Staller (resp., Dominator) plays first on the graph $G$. We prove some basic properties of $\gamma_{\rm SMB}(G)$ and $\gamma'_{\rm SMB}(G)$ and study the parameters' changes under some operators as taking the disjoint union of graphs or deleting a cut vertex. We show that the inequality $\delta(G)+1 \le \gamma'_{\rm SMB}(G) \le \gamma_{\rm SMB}(G)$ always holds and that for every three integers $r,s,t$ with $2\le r\le s\le t$, there exists a graph $G$ such that $\delta(G)+1 = r$, $\gamma'_{\rm SMB}(G) = s$, and $\gamma_{\rm SMB}(G) = t$. We prove exact formulas for $\gamma'_{\rm SMB}(G)$ where $G$ is a path, or it is a tadpole graph which is obtained from the disjoint union of a cycle and a path by adding one edge between them. Ključne besede: domination game, Maker–Breaker game, winning number, Maker-Breaker domination game, closed neighborhood hypergraph Objavljeno v DiRROS: 03.10.2024; Ogledov: 436; Prenosov: 188
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