Consider infecting a subset $A_0 \subseteq V(G)$ of the vertices of a graph $G$. Let an uninfected vertex $v \in V(G)$ become infected if $|N_G(v) \cap A_0| \geq r$, for some integer $r$. Define $A_t = A_{t-1} \cup \{v \in V(G) : |N_G(v) \cap A_{t-1}| \geq r \},$ and say that the set $A_0$ is \emph{lethal} under $r$-neighbor percolation if there exists a $t$ such that $A_t = V(G)$. For a graph $G$, let $m(G,r)$ be the size of the smallest lethal set in $G$ under $r$-neighbor percolation. The problem of determining $m(G,r)$ has been extensively studied for grids $G$ of various dimensions. We define $$m(a_1, \dots, a_d, r) = m\left (\prod_{i=1}^d [a_i], r\right )$$ for ease of notation. Famously, a lower bound of $m(a_1, \dots, a_d, d) \geq \frac{\sum_{j=1}^d \prod_{i \neq j} a_i}{d}$ is given by a beautiful argument regarding the high-dimensional ``surface area" of $G = [a_1] \times \dots \times [a_d]$. While exact values of $m(G,r)$ are known in some specific cases, general results are difficult to come by. In this thesis, we introduce a novel technique for viewing $3$-neighbor lethal sets on three-dimensional grids in terms of lethal sets in two dimensions. We also provide a strategy for recursively building up large lethal sets from existing small constructions. Using these techniques, we determine the exact size of all lethal sets under 3-neighbor percolation in three-dimensional grids $[a_1] \times [a_2] \times [a_3]$, for $a_1,a_2,a_3 \geq 11$. The problem of determining $m(n,n,3)$ is discussed by Benevides, Bermond, Lesfari and Nisse in \cite{benevides:2021}. The authors determine the exact value of $m(n,n,3)$ for even $n$, and show that, for odd $n$, $$\ceil*{\frac{n^2+2n}{3}} \leq m(n,n,3) \leq \ceil*{\frac{n^2+2n}{3}} + 1.$$ We prove that $m(n,n,3) = \ceil*{\frac{n^2+2n}{3}}$ if and only if $n = 2^k-1$, for some $k >0$. Finally, we provide a construction to prove that for $a_1,a_2,a_3 \geq 12$, bounds on the minimum lethal set on the the torus $G = C_{a_1} \square C_{a_2} \square C_{a_3}$ are given by $$2 \le m(G,3) - \frac{a_1a_2 + a_2a_3 + a_3a_1 -2(a_1+a_2+a_3)}{3} \le 3.$$ / Graduate

No description available.

No description available.

No description available.

Functional genetics is the study of the genes present in a genome of an organism, the complex interplay of all genes and their environment being the primary focus of study. The motivation for such studies is the premise that gene expression patterns in a cell are characteristic of its current state. The availability of the entire genome for many organisms now allows scientists unparalleled opportunities to characterize, classify, and manipulate genes or gene networks involved in metabolism, cellular differentiation, development, and disease. System-wide studies of biological systems have been made possible by the advent of high-throughput and large-scale tools such as microarrays which are capable of measuring the mRNA levels of all genes in a genome. Tools and methods for the integration, visualization, and modeling of the large-scale data obtained in typical systems biology experiments are indispensable. Our work focuses on a method that integrates gene expression values obtained from microarray experiments with biological functional information related to the genes measured in order to make global comparisons of multiple experiments. In our method, the integrated data is represented as a lattice and, using appropriate measures, a reference experiment can be compared to samples from a database of similar experiments, and a ranking of similarity is returned. In this work, support for the validity of our method is demonstrated both theoretically and empirically: a mathematical description of the lattice structure with respect to the integrated information is developed and the method is applied to data sets of both simulated and reported microarray experiments. A fast algorithm for constructing the lattice representation is also developed. / Ph. D.

We prove the positivity of Lusztig's q-analogue of weight multiplicity in a purely combinatorial way for rank 2 Lie algebras. Each summand in the polynomial can be interpreted as a linear combination of positive roots. We prove that all negative coefficients are cancelled in the polynomial. Further, the analysis of the root systems allows us to state formulae for every coefficient in Lusztig's q-analogue for rank 2 Lie algebras. / Ph. D.

Generating unbiased permutations at run time has traditionally been accomplished through application specific optimized combinational logic and has been limited to very small permutations. For generating unbiased permutations of any larger size, variations of the memory dependent Fisher-Yates algorithm are known to be an optimal solution in software and have been relied on as a hardware solution even to this day. However, in hardware, this thesis proves Fisher-Yates to be a suboptimal solution. This thesis will show variations of Fisher-Yates to be suboptimal by proposing an alternate method that does not rely on memory and outperforms Fisher-Yates based permutation generators, while still able to scale to very large sized permutations. This thesis also proves that this proposed method is unbiased and requires a minimal input. Lastly, this thesis demonstrates a means to scale the proposed method to any sized permutations and also to produce optimal partial permutations. / Master of Science / In computing, some applications need the ability to shuffle or rearrange items based on run time information during their normal operations. A similar task is a partial shuffle where only an information dependent selection of the total items is returned in a shuffled order. Initially, there may be the assumption that these are trivial tasks. However, the applications that rely on this ability are typically related to security which requires repeatable, unbiased operations. These requirements quickly turn seemingly simple tasks to complex. Worse, often they are done incorrectly and only appear to meet these requirements, which has disastrous implications for security. A current and dominating method to shuffle items that meets these requirements was developed over fifty years ago and is based on an even older algorithm refer to as Fisher-Yates, after its original authors. Fisher-Yates based methods shuffle items in memory, which is seen as advantageous in software but only serves as a disadvantage in hardware since memory access is significantly slower than other operations. Additionally, when performing a partial shuffle, Fisher-Yates methods require the same resources as when performing a complete shuffle. This is due to the fact that, with Fisher-Yates methods, each element in a shuffle is dependent on all of the other elements. Alternate methods to meet these requirements are known but are only able to shuffle a very small number of items before they become too slow for practical use. To combat the disadvantages current methods of shuffling possess, this thesis proposes an alternate approach to performing shuffles. This alternate approach meets the previously stated requirements while outperforming current methods. This alternate approach is also able to be extended to shuffling any number of items while maintaining a useable level of performance. Further, unlike current popular shuffling methods, the proposed method has no inter-item dependency and thus offers great advantages over current popular methods with partial shuffles.

The Kostka-Foulkes polynomials describe the change of basis between Schur polynomials and Hall-Littlewood polynomials. In this paper, we extend this idea to the family of BCn Macdonald spherical functions, with multiparameter Kostka-Foulkes polynomials acting as the change of basis from the BC_n spherical functions to the type Cn Schur polynomials. We develop a Kato-Lusztig formula that describes the multiparameter BCn-Kostka-Foulkes polynomials. / Master of Science

We study graph parameters arising from different types of colourings of random graphs, defined broadly as an assignment of colours to either the vertices or the edges of a graph. The chromatic number X(G) of a graph is the minimum number of colours required for a vertex colouring where no two adjacent vertices are coloured the same. Determining the chromatic number is one of the classic challenges in random graph theory. In Chapter 3, we give new upper and lower bounds for the chromatic number of the dense random graph G(n,p)) where p ∈ (0,1) is constant. These bounds are the first to match up to an additive term of order o(1) in the denominator, and in particular, they determine the average colour class size in an optimal colouring up to an additive term of order o(1). In Chapter 4, we study a related graph parameter called the equitable chromatic number. This is defined as the minimum number of colours needed for a vertex colouring where no two adjacent vertices are coloured the same and, additionally, all colour classes are as equal in size as possible. We prove one point concentration of the equitable chromatic number of the dense random graph G(n,m) with m = pn(n-1)/2, p < 1-1/e² constant, on a subsequence of the integers. We also show that whp, the dense random graph G(n,p) allows an almost equitable colouring with a near optimal number of colours. We call an edge colouring of a graph G a rainbow colouring if every pair of vertices is joined by a rainbow path, which is a path where no colour is repeated. The least number of colours where this is possible is called the rainbow connection number rc(G). Since its introduction in 2008 as a new way to quantify how well connected a given graph is, the rainbow connection number has attracted the attention of a great number of researchers. For any graph G, rc(G)≥diam(G), where diam(G) denotes the diameter. In Chapter 5, we will see that in the random graph G(n,p), rainbow connection number 2 is essentially equivalent to diameter 2. More specifically, we consider G ~ G(n,p) close to the diameter 2 threshold and show that whp rc(G) = diam(G) ∈ {2,3}. Furthermore, we show that in the random graph process, whp the hitting times of diameter 2 and of rainbow connection number 2 coincide. In Chapter 6, we investigate sharp thresholds for the property rc(G)≤=r where r is a fixed integer. The results of Chapter 6 imply that for r=2, the properties rc(G)≤=2 and diam(G)≤=2 share the same sharp threshold. For r≥3, the situation seems quite different. We propose an alternative threshold and prove that this is an upper bound for the sharp threshold for rc(G)≤=r where r≥3.

Le but de cette thèse est d'établir des résultats énumératifs sur certaines classes de chemins et d'animaux. Ces résultats sont obtenus en appliquant la théorie des empilements de pièces développée par Viennot. Nous étudions les excursions discrètes (ou chemins de Dyck généralisés) de hauteur bornée; nous obtenons des résultats énumératifs qui interprètent combinatoirement et étendent des résultats de Banderier, Flajolet et Bousquet-Mélou. Nous décrivons et énumérons plusieurs classes de chemins auto-évitants, dits chemins faiblement dirigés. Ces chemins sont plus nombreux que les chemins prudents qui forment la classe naturelle la plus grande jusqu'alors. Nous calculons le périmètre de site moyen des animaux dirigés, prouvant des conjectures de Conway et Le Borgne. Enfin, nous obtenons des résultats nouveaux sur l'énumération des animaux de Klarner et les animaux multi-dirigés de Bousquet-Mélou et Rechnitzer. / The goal of this thesis is to prove enumerative results on some classes of lattice walks and animals. These results are applications of the theory of heaps of pieces developed by Viennot. We study discrete excursions (or generalized Dyck paths) with bounded height; we obtain enumerative results that give a combinatorial interpretation and extend results by Banderier, Flajolet and Bousquet-Mélou. We describe and enumerate several classes of self-avoiding walks called weakly directed walks. These classes are larger than the class of prudent walks, the largest natural class enumerated so far. We compute the average site perimeter of directed animals, proving conjectures by Conway and Le Borgne. Finally, we obtain new results on the enumeration of Klarner animals and multi-directed animals defined by Bousquet-Mélou and Rechnitzer.