We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices.

A subset S⊆V in a graph G=(V,E) is a [j,k]-set if, for every vertex vεV\-S, j≤|N(v)\∩S|≤k for non-negative integers j and k, that is, every vertex vεV\-S is adjacent to at least j but not more than k vertices in S. In this paper, we focus on small j and k, and relate the concept of [j,k]-sets to a host of other concepts in domination theory, including perfect domination, efficient domination, nearly perfect sets, 2-packings, and k-dependent sets. We also determine bounds on the cardinality of minimum [1, 2]-sets, and investigate extremal graphs achieving these bounds. This study has implications for restrained domination as well. Using a result for [1, 3]-sets, we show that, for any grid graph G, the restrained domination number is equal to the domination number of G.

A subset S⊆V in a graph G=(V,E) is a [j,k]-set if, for every vertex vεV\-S, j≤|N(v)\∩S|≤k for non-negative integers j and k, that is, every vertex vεV\-S is adjacent to at least j but not more than k vertices in S. In this paper, we focus on small j and k, and relate the concept of [j,k]-sets to a host of other concepts in domination theory, including perfect domination, efficient domination, nearly perfect sets, 2-packings, and k-dependent sets. We also determine bounds on the cardinality of minimum [1, 2]-sets, and investigate extremal graphs achieving these bounds. This study has implications for restrained domination as well. Using a result for [1, 3]-sets, we show that, for any grid graph G, the restrained domination number is equal to the domination number of G.

Every graph G = (V, E) has a dominating set S ⊆ V(G) such that any vertex not in S is adjacent to a vertex in S. We define a paired-dominating set S to be a dominating set S = {v1, v2,..., v2t-1, v2t} where M = {v1v2, v3v4, ..., v2t-1v2t} is a perfect matching in 〈S〉, the subgraph induced by S. The domination number of a graph G is the smallest cardinality of any dominating set of G, and the paired-domination number is the smallest cardinality of any paired-dominating set. Determining the domination number for grid graphs is a well-known open problem in graph theory. Not surprisingly, determining the paired-domination number for grid graphs is also a difficult problem. In this thesis, we survey past research in domination, paired-domination and grid graphs to obtain background for our study of paired-domination in grid graphs. We determine the paired-domination number for grid graphs Gr,c where r ∈ {2,3}, for infinite dimensional grid graphs, and for the complement of a grid graph.

As introduced by Slater in 2008, liar's domination provides a way of modeling protection devices where one may be faulty. Assume each vertex of a graph G is the possible location for an intruder such as a thief. A protection device at a vertex v is assumed to be able to detect the intruder at any vertex in its closed neighborhood N[v] and identify at which vertex in N[v] the intruder is located. A dominating set is required to identify any intruder's location in the graph G, and if any one device can fail to detect the intruder, then a double-dominating set is necessary. Stronger still, a liar's dominating set can identify an intruder's location even when any one device in the neighborhood of the intruder vertex can lie, that is, any one device in the neighborhood of the intruder vertex can misidentify any vertex in its closed neighborhood as the intruder location or fail to report an intruder in its closed neighborhood. In this thesis, we present the liar's domination number for the finite ladders, infinite ladder, and infinite P_3 x P_infty. We also give bounds for other grid graphs.

We consider a variety of types of vertex sequences, which are defined in terms of a requirement that the next vertex in the sequence must meet. For example, let S = (v1, v2, …, vk ) be a sequence of distinct vertices in a graph G such that every vertex vi in S dominates at least one vertex in V that is not dominated by any of the vertices preceding it in the sequence S. Such a sequence of maximal length is called a dominating sequence since the set {v1, v2, …, vk } must be a dominating set of G. In this paper we survey the literature on dominating and other related sequences, and propose for future study several new types of vertex sequences, which suggest the beginning of a theory of vertex sequences in graphs.