A utilização de redes complexas para a descriçãoi de diversos sistemas naturais e artificias,compreendidos nas mais diversas áreas do conhecimento humano, tem se mostrado uma abordagem poderosa para a redução da complexidade inerente a tais sistemas. Em muitos casos, tal complexidade resulta do número de componentes envolvidos e de suas intrincadas relações. Uma forma de reduzir a complexidade associada a tais sistemas, consiste em identificar e agrupar componentes que possuam características similares. Sendo assim, desenvolvemos nesta tese métodos de identificação de comunidades em redes complexas. Tais métodos se baseiam na ideia de que comunidades surgem quando grupos de vértices possuem um número mais elevado de conexões entre os vértices do mesmo grupo do que com vértices externos à este grupo. Além disso, utilizamos a função modularidade como função objetivo e como forma de avaliação e comparação dos resultados obtidos nesta tese com resultados previamente reportados na literatura. Uma vez estabelecido um método de identificação de comunidades, utilizamos a abordagem de redes complexas para a determinação de domínios estruturais de proteínas. Para tal, criamos redes de contato entre os aminoácidos de uma proteí?na buscando representar apenas as ligações relevantes do ponto de vista topológico. Por meio destas representações, aplicamos os métodos de identificação de comunidades desenvolvidos nesta tese, no intuito de identificar domínios estruturais de cadeias proteicas. Por fim, desenvolvemos um método específico para a identificação de domínios em proteínas com dois domínios sequencias, concluindo desta forma, os objetivos propostos nesta tese. / The use of complex networks for the representation of various natural and artificial sys- tems in the most diverse fields of human knowledge, has proven to be a powerful approach for the reduction of the complexity in the study of such systems. In many cases, this complexity emerges from the number of components of the system and from the intricate relationship between them. A reduction in this complexity is made possible by the iden- tification and grouping of the components of the system with similar characteristics. In this way, we developed in this thesis, methods for community identification in complex networks. Such methods are based on the notion that communities arise when groups of vertices are more densely connected with vertices of their same group, than with ver- tices belonging to other groups in the network. Moreover, the modularity function has been used as an objective function, and as a score for the evaluation and comparison of the results obtained in this thesis with the results reported in the literature of complex networks. Upon the establishment of a method for community detection, we used the framework of complex networks to the determination of structural protein domains. The- refore, we have created contact networks of amino acids of protein chains, focusing on the representation of only the most relevant interactions between them, from a topological point of view. We have applied to these networks the methods for community identi- fication developed in this thesis, aiming to identify the structural domains of proteins. Finally, we have developed a specific method for the identification of protein domains in protein chains with two sequential domains, concluding in this way, the objectives proposed in this thesis.

In this dissertation we solve several combinatorial problems in different areas of mathematics: automata theory, combinatorics of partially ordered sets and extremal combinatorics. Firstly, we focus on some new automata that do not seem to have occurred much in the literature, that of solvability of mazes. For our model, a maze is a countable strongly connected digraph together with a proper colouring of its edges (without two edges leaving a vertex getting the same colour) and two special vertices: the origin and the destination. A pointer or robot starts in the origin of a maze and moves naturally between its vertices, according to a sequence of specific instructions from the set of all colours; if the robot is at a vertex for which there is no out-edge of the colour indicated by the instruction, it remains at that vertex and proceeds to execute the next instruction in the sequence. We call such a finite or infinite sequence of instructions an algorithm. In particular, one of the most interesting and very natural sets of mazes occurs when our maze is the square lattice Z2 as a graph with some of its edges removed. Obviously, we need to require that the origin and the destination vertices are in the same connected component and it is very natural to take the four instructions to be the cardinal directions. In this set-up, we make progress towards a beautiful problem posed by Leader and Spink in 2011 which asks whether there is an algorithm which solves the set of all such mazes. Next, we address a problem regarding symmetric chain decompositions of posets. We ask if there exists a symmetric chain decomposition of a 2 × 2 × ... × 2 × n cuboid (k 2’s) such that no chain has a subchain of the form (a1,...,ak,0) ≺ ... ≺ (a1,...,ak,n−1)? We show this is true precisely when k≥5 and n≥3. Thisquestion arises naturally when considering products of symmetric chain decompositions which induce orthogonal chain decompositions — the existence of the decompositions provided in this chapter unexpectedly resolves the most difficult case of previous work by Spink on almost orthogonal symmetric chain decompositions (2017) which makes progress on a conjecture of Shearer and Kleitman. Moreover, we generalize our methods to other finite graded posets. Finally, we address two different problems in extremal combinatorics related to mathematical physics. Firstly, we study metastable states in the Ising model. We propose a general model for 1-flip spin systems, and initiate the study of extremal properties of their stable states. By translating local stability conditions into Sperner- type conditions, we provide non-trivial upper bounds which are often tight for large classes of such systems. The last topic we consider is a deterministic bootstrap percolation type problem. More specifically, we prove several extremal results about fast 2-neighbour percolation on the two dimensional grid.

Neste trabalho, estudamos o problema de encontrar grafos extremais com rela c~ao a energia laplaciana sem sinal. Mais especi camente, procuramos grafos com a maior energia laplaciana sem sinal em determinadas classes. Nesse sentido, conjecturamos que o grafo unic clico conexo com a maior energia laplaciana sem sinal e o grafo formado por um tri^angulo com v ertices pendentes distribu dos balanceadamente e provamos parcialmente essa conjectura. Tal resultado foi provado tamb em para a energia laplaciana. Al em disso, conjecturamos que o grafo com a maior energia laplaciana sem sinal dentre todos os grafos com n v ertices e o grafo split completo com uma clique de [n+1/ 3] v ertices e provamos tal conjectura para algumas classes de grafos, em particular, para arvores, grafos unic clicos e bic clicos. / In this work, we study the problem of nding extremal graphs with relation to the signless Laplacian energy. More speci cally, we look for graphs with the largest signless Laplacian energy inside certains classes. In this sense, we conjecture that the connected unicyclic graph with the largest signless Laplacian energy is the graph consisting of a triangle with balanced distributed pendent vertices and we partially prove this conjecture. This result was also proved for the Laplacian energy. Moreover we conjecture that the graph with the largest signless Laplacian energy among all graphs with n vertices is the complete split graph with a clique of [n+1/ 3] vertices and we prove this conjecture for some classes of graphs, in particular, for trees, for unicyclic and bicyclic graphs.

In a 2011 paper by Beeler and Hoilman, the game of peg solitaire is generalized to arbitrary boards. These boards are treated as graphs in the combinatorial sense. An open problem from that paper is to determine the minimum number of edges necessary for a graph with a fixed number of vertices to be solvable. This thesis provides new bounds on this number. It also provides necessary and sufficient conditions for two families of graphs to be solvable, along with criticality results, and the maximum number of pegs that can be left in each of the two graph families.

Inverse problems naturally occur in many branches of science and mathematics. An inverse problem entails finding the values of one or more parameters using the values obtained from observed data. A typical example of an inverse problem is the inversion of the Radon transform. Here a function (for example of two variables) is deduced from its integrals along all possible lines. This problem is intimately connected with image reconstruction for X-ray computerized tomography. Moment problems are a special class of inverse problems. While the classical theory of moments dates back to the beginning of the 20th century, the systematic study of truncated moment problems began only a few years ago. In this dissertation we will first survey the elementary theory of truncated moment problems, and then focus on those problems with cubic column relations. For a degree 2n real d-dimensional multisequence β ≡ β (2n) ={β i}i∈Zd+,|i|≤2n to have a representing measure μ, it is necessary for the associated moment matrix Μ(n) to be positive semidefinite, and for the algebraic variety associated to β, Vβ, to satisfy rank Μ(n)≤ card Vβ as well as the following consistency condition: if a polynomial p(x)≡ ∑|i|≤2naixi vanishes on Vβ, then Λ(p):=∑|i|≤2naiβi=0. In 2005, Professor Raúl Curto collaborated with L. Fialkow and M. Möller to prove that for the extremal case (Μ(n)= Vβ), positivity and consistency are sufficient for the existence of a (unique, rank Μ(n)-atomic) representing measure. In joint work with Professor Raúl Curto we have considered cubic column relations in M(3) of the form (in complex notation) Z3=itZ+ubar Z, where u and t are real numbers. For (u,t) in the interior of a real cone, we prove that the algebraic variety Vβ consists of exactly 7 points, and we then apply the above mentioned solution of the extremal moment problem to obtain a necessary and sufficient condition for the existence of a representing measure. This requires a new representation theorem for sextic polynomials in Z and bar Z which vanish in the 7-point set Vβ. Our proof of this representation theorem relies on two successive applications of the Fundamental Theorem of Linear Algebra. Finally, we use the Division Algorithm from algebraic geometry to extend this result to other situations involving cubic column relations.

We study several extremal problems in graphs and hypergraphs. The first one is on list-colouring hypergraphs, which is a generalization of the ordinary colouring of hypergraphs. We discuss two methods for determining the list-chromatic number of hypergraphs. One method uses hypergraph polynomials, which invokes Alon's combinatorial nullstellensatz. This method usually requires computer power to complete the calculations needed for even a modest-sized hypergraph. The other method is elementary, and uses the idea of minimum improper colourings. We apply these methods to various classes of hypergraphs, including the projective planes. We focus on solving the list-colouring problem for Steiner triple systems (STS). It is not hard using either method to determine that Steiner triple systems of orders 7, 9 and 13 are 3-list-chromatic. For systems of order 15, we show that they are 4-list-colourable, but they are also ``almost'' 3-list-colourable. For all Steiner triple systems, we prove a couple of simple upper bounds on their list-chromatic numbers. Also, unlike ordinary colouring where a 3-chromatic STS exists for each admissible order, we prove using probabilistic methods that for every $s$, every STS of high enough order is not $s$-list-colourable. The second problem is on embedding nearly-spanning bounded-degree trees in sparse graphs. We determine sufficient conditions based on expansion properties for a sparse graph to embed every nearly-spanning tree of bounded degree. We then apply this to random graphs, addressing a question of Alon, Krivelevich and Sudakov, and determine a probability $p$ where the random graph $G_{n,p}$ asymptotically almost surely contains every tree of bounded degree. This $p$ is nearly optimal in terms of the maximum degree of the trees that we embed. Finally, we solve a problem that arises from quantum computing, which can be formulated as an extremal question about maximizing the size of a type of acyclic directed graph.

We study several extremal problems in graphs and hypergraphs. The first one is on list-colouring hypergraphs, which is a generalization of the ordinary colouring of hypergraphs. We discuss two methods for determining the list-chromatic number of hypergraphs. One method uses hypergraph polynomials, which invokes Alon's combinatorial nullstellensatz. This method usually requires computer power to complete the calculations needed for even a modest-sized hypergraph. The other method is elementary, and uses the idea of minimum improper colourings. We apply these methods to various classes of hypergraphs, including the projective planes. We focus on solving the list-colouring problem for Steiner triple systems (STS). It is not hard using either method to determine that Steiner triple systems of orders 7, 9 and 13 are 3-list-chromatic. For systems of order 15, we show that they are 4-list-colourable, but they are also ``almost'' 3-list-colourable. For all Steiner triple systems, we prove a couple of simple upper bounds on their list-chromatic numbers. Also, unlike ordinary colouring where a 3-chromatic STS exists for each admissible order, we prove using probabilistic methods that for every $s$, every STS of high enough order is not $s$-list-colourable. The second problem is on embedding nearly-spanning bounded-degree trees in sparse graphs. We determine sufficient conditions based on expansion properties for a sparse graph to embed every nearly-spanning tree of bounded degree. We then apply this to random graphs, addressing a question of Alon, Krivelevich and Sudakov, and determine a probability $p$ where the random graph $G_{n,p}$ asymptotically almost surely contains every tree of bounded degree. This $p$ is nearly optimal in terms of the maximum degree of the trees that we embed. Finally, we solve a problem that arises from quantum computing, which can be formulated as an extremal question about maximizing the size of a type of acyclic directed graph.

In this dissertation, a problem related to Hadwiger's conjecture has been studied. We first proved a conjecture of Jakobsen from 1983 which states that every simple graphs on $n$ vertices and at least (11n-35)/2 edges either has a minor isomorphic to K_8 with one edge deleted or is isomorphic to a graph obtained from disjoint copies of K_{1, 2, 2, 2, 2} and/or K_7 by identifying cliques of size five. We then studied the extremal functions for complete minors. We proved that every simple graph on nge9 vertices and at least 7n-27 edges either has a minor, or is isomorphic to K_{2, 2, 2, 3, 3}, or is isomorphic to a graph obtained from disjoint copies of K_{1, 2, 2, 2, 2, 2} by identifying cliques of size six. This result extends Mader's theorem on the extremal function for K_p minors, where ple7. We discussed the possibilities of extending our methods to K_{10} and K_{11} minors. We have also found the extremal function for K_7 plus a vertex minor.

Aligning two images by point to point correspondence is a hard optimization problem. It can be solved using t-Extremal Optimization or with a modification of this method called Fitness threshold accepting. In this work these two methods are tested and compared to see whether one of the methods should be preferred for image alignment. Since real image data is almost always noisy the performance of the methods under conditions like noisy and outlying data is analyzed too.

Let F0 be a fixed k-uniform hypergraph, and let H be a given k-uniform hypergraph on n vertices. An F0-packing of H is a family F of edge-disjoint copies of F0 which are subhypergraphs in H. Let nF0(H) denote the maximum size |F| of an F0-packing F of H. It is well-known that computing nF0(H) is NP-hard for nearly any choice of F0. In this thesis, we consider the special case when F0 is a linear hypergraph, that is, when no two edges of F0 overlap in more than one vertex. We establish for z > 0 and n &ge n0(z) sufficiently large, an algorithm which, in time polynomial in n, constructs an F0-packing F of H of size |F| ≥ nF0(H) - znk. A central direction in our proof uses so-called fractional F0-packings of H which are known to approximate nF0(H). The driving force of our argument, however, is the use and development of several tools within the theory of hypergraph regularity.