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Hamiltonian Sets of Polygonal Paths in Assembly Graphs

A. Guterman, N. Jonoska, E. Kreines, A. Maksaev, N. Ostroukhova

Abstract

We provide four equivalent combinatorial conditions for a simple assembly graph (rigid vertex graph where all vertices are of degree 1 or 4) to have the largest number of Hamiltonian sets of polygonal paths relative its size. These conditions serve to prove the conjecture that such maximum, which is equal to $F_{2n+1}-1$, where $F_k$ denotes the $k$th Fibonacci number, is achieved only for special assembly graphs, called tangled cords.

Hamiltonian Sets of Polygonal Paths in Assembly Graphs

Abstract

We provide four equivalent combinatorial conditions for a simple assembly graph (rigid vertex graph where all vertices are of degree 1 or 4) to have the largest number of Hamiltonian sets of polygonal paths relative its size. These conditions serve to prove the conjecture that such maximum, which is equal to , where denotes the th Fibonacci number, is achieved only for special assembly graphs, called tangled cords.
Paper Structure (4 sections, 10 theorems, 19 equations, 9 figures)

This paper contains 4 sections, 10 theorems, 19 equations, 9 figures.

Key Result

Theorem 3.1

Four_Reg_Graphs_w_Rigid_Vert_DNA_Rec_2013 Let $\Gamma$ be a simple assembly graph, $\mathcal{V}(\Gamma)=n$, and $\mathcal{C}$ be a collection of Hamiltonian sets of polygonal paths in $\Gamma$. Then $|\mathcal{C}| \leqslant F_{2n+1}-1.$

Figures (9)

  • Figure 1: Some diagrams for a rigid vertex $v$ of degree 4.
  • Figure 2: Consecutevily drawing transverse path $v_0\,e_0\,v_1\,e_1\,v_1\,e_2\,v_2\,e_3\,v_3\,e_4\,v_3\,e_5\,v_2\,e_6\,v_4$.
  • Figure 3: An example of Hamiltonian set of polygonal paths with three paths: $\{v_1 e_1 v_2 e_{15} v_7, \, v_5 e_4 v_4 e_{13} v_8 e_{10} v_3, \,v_6\}$. Note that $v_6$ is a singleton.
  • Figure 4: How the tangled cord $TC_{n}$ is inductively constructed from $TC_{n-1}$. The visualization provides the 'correct' cyclic order of half-edges in each rigid vertex.
  • Figure 5: Enumerated edges in a graph with the assembly word $112323$
  • ...and 4 more figures

Theorems & Definitions (25)

  • Conjecture 1.1
  • Definition 2.1
  • Definition 2.2
  • Example 2.3
  • Definition 2.4
  • Remark 2.5
  • Theorem 3.1
  • Definition 3.2
  • Example 3.3
  • Definition 3.4
  • ...and 15 more