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Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
A tiling is a collection of vertex disjoint subgraphs called tiles. If the tiles are all isomorphic to a graph $H$ then the tiling is an $H$-tiling. If a graph $G$ has an $H$-tiling which covers all of the vertices of $G$ then the $H$-tiling is a perfect $H$-tiling or an $H$-factor. A goal of this study is to extend theorems on sufficient minimum degree conditions for perfect tilings in graphs to directed graphs. Corrádi and Hajnal proved that every graph $G$ on $3k$ vertices with minimum degree $delta(G)ge2k$ has a $K_3$-factor, where $K_s$ is the complete graph on $s$ vertices. The following theorem extends this result to directed graphs: If $D$ is a directed graph on $3k$ vertices with minimum total degree $delta(D)ge4k-1$ then $D$ can be partitioned into $k$ parts each of size $3$ so that all of parts contain a transitive triangle and $k-1$ of the parts also contain a cyclic triangle. The total degree of a vertex $v$ is the sum of $d^-(v)$ the in-degree and $d^+(v)$ the out-degree of $v$. Note that both orientations of $C_3$ are considered: the transitive triangle and the cyclic triangle. The theorem is best possible in that there are digraphs that meet the minimum degree requirement but have no cyclic triangle factor. The possibility of added a connectivity requirement to ensure a cycle triangle factor is also explored. Hajnal and Szemerédi proved that if $G$ is a graph on $sk$ vertices and $delta(G)ge(s-1)k$ then $G$ contains a $K_s$-factor. As a possible extension of this celebrated theorem to directed graphs it is proved that if $D$ is a directed graph on $sk$ vertices with $delta(D)ge2(s-1)k-1$ then $D$ contains $k$ disjoint transitive tournaments on $s$ vertices. We also discuss tiling directed graph with other tournaments. This study also explores minimum total degree conditions for perfect directed cycle tilings and sufficient semi-degree conditions for a directed graph to contain an anti-directed Hamilton cycle. The semi-degree of a vertex $v$ is $min{d^+(v), d^-(v)}$ and an anti-directed Hamilton cycle is a spanning cycle in which no pair of consecutive edges form a directed path.
ContributorsMolla, Theodore (Author) / Kierstead, Henry A (Thesis advisor) / Czygrinow, Andrzej (Committee member) / Fishel, Susanna (Committee member) / Hurlbert, Glenn (Committee member) / Spielberg, Jack (Committee member) / Arizona State University (Publisher)
Created2013
Description
In 1959, Iwasawa proved that the size of the $p$-part of the class groups of a $\mathbb{Z}_p$-extension grows as a power of $p$ with exponent ${\mu}p^m+{\lambda}\,m+\nu$ for $m$ sufficiently large. Broadly, I construct conditions to verify if a given $m$ is indeed sufficiently large. More precisely, let $CG_m^i$ (class group) be the $\epsilon_i$-eigenspace component of the $p$-Sylow subgroup of the class group of the field at the $m$-th level in a $\mathbb{Z}_p$-extension; and let $IACG^i_m$ (Iwasawa analytic class group) be ${\mathbb{Z}_p[[T]]/((1+T)^{p^m}-1,f(T,\omega^{1-i}))}$, where $f$ is the associated Iwasawa power series. It is expected that $CG_m^i$ and $IACG^i_m$ be isomorphic, providing us with a powerful connection between algebraic and analytic techniques; however, as of yet, this isomorphism is unestablished in general. I consider the existence and the properties of an exact sequence $$0\longrightarrow\ker{\longrightarrow}CG_m^i{\longrightarrow}IACG_m^i{\longrightarrow}\textrm{coker}\longrightarrow0.$$ In the case of a $\mathbb{Z}_p$-extension where the Main Conjecture is established, there exists a pseudo-isomorphism between the respective inverse limits of $CG_m^i$ and $IACG_m^i$. I consider conditions for when such a pseudo-isomorphism immediately gives the existence of the desired exact sequence, and I also consider work-around methods that preserve cardinality for otherwise. However, I primarily focus on constructing conditions to verify if a given $m$ is sufficiently large that the kernel and cokernel of the above exact sequence have become well-behaved, providing similarity of growth both in the size and in the structure of $CG_m^i$ and $IACG_m^i$; as well as conditions to determine if any such $m$ exists. The primary motivating idea is that if $IACG_m^i$ is relatively easy to work with, and if the relationship between $CG_m^i$ and $IACG_m^i$ is understood; then $CG_m^i$ becomes easier to work with. Moreover, while the motivating framework is stated concretely in terms of the cyclotomic $\mathbb{Z}_p$-extension of $p$-power roots of unity, all results are generally applicable to arbitrary $\mathbb{Z}_p$-extensions as they are developed in terms of Iwasawa-Theory-inspired, yet abstracted, algebraic results on maps between inverse limits.
ContributorsElledge, Shawn Michael (Author) / Childress, Nancy (Thesis advisor) / Bremner, Andrew (Committee member) / Fishel, Susanna (Committee member) / Jones, John (Committee member) / Paupert, Julien (Committee member) / Arizona State University (Publisher)
Created2013
Description
Research on combinatorics education is sparse when compared with other fields in mathematics education. This research attempted to contribute to the dearth of literature by examining students' reasoning about enumerative combinatorics problems and how students conceptualize the set of elements being counted in such problems, called the solution set. In particular, the focus was on the stable patterns of reasoning, known as ways of thinking, which students applied in a variety of combinatorial situations and tasks. This study catalogued students' ways of thinking about solution sets as they progressed through an instructional sequence. In addition, the relationships between the catalogued ways of thinking were explored. Further, the study investigated the challenges students experienced as they interacted with the tasks and instructional interventions, and how students' ways of thinking evolved as these challenges were overcome. Finally, it examined the role of instruction in guiding students to develop and extend their ways of thinking. Two pairs of undergraduate students with no formal experience with combinatorics participated in one of the two consecutive teaching experiments conducted in Spring 2012. Many ways of thinking emerged through the grounded theory analysis of the data, but only eight were identified as robust. These robust ways of thinking were classified into three categories: Subsets, Odometer, and Problem Posing. The Subsets category encompasses two ways of thinking, both of which ultimately involve envisioning the solution set as the union of subsets. The three ways of thinking in Odometer category involve holding an item or a set of items constant and systematically varying the other items involved in the counting process. The ways of thinking belonging to Problem Posing category involve spontaneously posing new, related combinatorics problems and finding relationships between the solution sets of the original and the new problem. The evolution of students' ways of thinking in the Problem Posing category was analyzed. This entailed examining the perturbation experienced by students and the resulting accommodation of their thinking. It was found that such perturbation and its resolution was often the result of an instructional intervention. Implications for teaching practice are discussed.
ContributorsHalani, Aviva (Author) / Roh, Kyeong Hah (Thesis advisor) / Fishel, Susanna (Committee member) / Saldanha, Luis (Committee member) / Thompson, Patrick (Committee member) / Zandieh, Michelle (Committee member) / Arizona State University (Publisher)
Created2013
Description
A central concept of combinatorics is partitioning structures with given constraints. Partitions of on-line posets and on-line graphs, which are dynamic versions of the more familiar static structures posets and graphs, are examined. In the on-line setting, vertices are continually added to a poset or graph while a chain partition or coloring (respectively) is maintained. %The optima of the static cases cannot be achieved in the on-line setting. Both upper and lower bounds for the optimum of the number of chains needed to partition a width $w$ on-line poset exist. Kierstead's upper bound of $\frac{5^w-1}{4}$ was improved to $w^{14 \lg w}$ by Bosek and Krawczyk. This is improved to $w^{3+6.5 \lg w}$ by employing the First-Fit algorithm on a family of restricted posets (expanding on the work of Bosek and Krawczyk) . Namely, the family of ladder-free posets where the $m$-ladder is the transitive closure of the union of two incomparable chains $x_1\le\dots\le x_m$, $y_1\le\dots\le y_m$ and the set of comparabilities $\{x_1\le y_1,\dots, x_m\le y_m\}$. No upper bound on the number of colors needed to color a general on-line graph exists. To lay this fact plain, the performance of on-line coloring of trees is shown to be particularly problematic. There are trees that require $n$ colors to color on-line for any positive integer $n$. Furthermore, there are trees that usually require many colors to color on-line even if they are presented without any particular strategy. For restricted families of graphs, upper and lower bounds for the optimum number of colors needed to maintain an on-line coloring exist. In particular, circular arc graphs can be colored on-line using less than 8 times the optimum number from the static case. This follows from the work of Pemmaraju, Raman, and Varadarajan in on-line coloring of interval graphs.
ContributorsSmith, Matthew Earl (Author) / Kierstead, Henry A (Thesis advisor) / Colbourn, Charles (Committee member) / Czygrinow, Andrzej (Committee member) / Fishel, Susanna (Committee member) / Hurlbert, Glenn (Committee member) / Arizona State University (Publisher)
Created2012
Description
In 1984, Sinnott used $p$-adic measures on $\mathbb{Z}_p$ to give a new proof of the Ferrero-Washington Theorem for abelian number fields by realizing $p$-adic $L$-functions as (essentially) the $Gamma$-transform of certain $p$-adic rational function measures. Shortly afterward, Gillard and Schneps independently adapted Sinnott's techniques to the case of $p$-adic $L$-functions associated to elliptic curves with complex multiplication (CM) by realizing these $p$-adic $L$-functions as $Gamma$-transforms of certain $p$-adic rational function measures. The results in the CM case give the vanishing of the Iwasawa $mu$-invariant for certain $mathbb{Z}_p$-extensions of imaginary quadratic fields constructed from torsion points of CM elliptic curves.
In this thesis, I develop the theory of $p$-adic measures on $mathbb{Z}_p^d$, with particular interest given to the case of $d>1$. Although I introduce these measures within the context of $p$-adic integration, this study includes a strong emphasis on the interpretation of $p$-adic measures as $p$-adic power series. With this dual perspective, I describe $p$-adic analytic operations as maps on power series; the most important of these operations is the multivariate $Gamma$-transform on $p$-adic measures.
This thesis gives new significance to product measures, and in particular to the use of product measures to construct measures on $mathbb{Z}_p^2$ from measures on $mathbb{Z}_p$. I introduce a subring of pseudo-polynomial measures on $mathbb{Z}_p^2$ which is closed under the standard operations on measures, including the $Gamma$-transform. I obtain results on the Iwasawa-invariants of such pseudo-polynomial measures, and use these results to deduce certain continuity results for the $Gamma$-transform. As an application, I establish the vanishing of the Iwasawa $mu$-invariant of Yager's two-variable $p$-adic $L$-function from measure theoretic considerations.
In this thesis, I develop the theory of $p$-adic measures on $mathbb{Z}_p^d$, with particular interest given to the case of $d>1$. Although I introduce these measures within the context of $p$-adic integration, this study includes a strong emphasis on the interpretation of $p$-adic measures as $p$-adic power series. With this dual perspective, I describe $p$-adic analytic operations as maps on power series; the most important of these operations is the multivariate $Gamma$-transform on $p$-adic measures.
This thesis gives new significance to product measures, and in particular to the use of product measures to construct measures on $mathbb{Z}_p^2$ from measures on $mathbb{Z}_p$. I introduce a subring of pseudo-polynomial measures on $mathbb{Z}_p^2$ which is closed under the standard operations on measures, including the $Gamma$-transform. I obtain results on the Iwasawa-invariants of such pseudo-polynomial measures, and use these results to deduce certain continuity results for the $Gamma$-transform. As an application, I establish the vanishing of the Iwasawa $mu$-invariant of Yager's two-variable $p$-adic $L$-function from measure theoretic considerations.
ContributorsZinzer, Scott Michael (Author) / Childress, Nancy (Thesis advisor) / Bremner, Andrew (Committee member) / Fishel, Susanna (Committee member) / Jones, John (Committee member) / Spielberg, John (Committee member) / Arizona State University (Publisher)
Created2015
Description
Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands.
Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
ContributorsChapman, Eric (Author) / Childers, Daniel L. (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Hall, Sharon J (Committee member) / Turetsky, Merritt (Committee member) / Arizona State University (Publisher)
Created2015
Description
In a large network (graph) it would be desirable to guarantee the existence of some local property based only on global knowledge of the network. Consider the following classical example: how many connections are necessary to guarantee that the network contains three nodes which are pairwise adjacent? It turns out that more than n^2/4 connections are needed, and no smaller number will suffice in general. Problems of this type fall into the category of ``extremal graph theory.'' Generally speaking, extremal graph theory is the study of how global parameters of a graph are related to local properties. This dissertation deals with the relationship between minimum degree conditions of a host graph G and the property that G contains a specified spanning subgraph (or class of subgraphs). The goal is to find the optimal minimum degree which guarantees the existence of a desired spanning subgraph. This goal is achieved in four different settings, with the main tools being Szemeredi's Regularity Lemma; the Blow-up Lemma of Komlos, Sarkozy, and Szemeredi; and some basic probabilistic techniques.
ContributorsDeBiasio, Louis (Author) / Kierstead, Henry A (Thesis advisor) / Czygrinow, Andrzej (Thesis advisor) / Hurlbert, Glenn (Committee member) / Kadell, Kevin (Committee member) / Fishel, Susanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
Gray codes are perhaps the best known structures for listing sequences of combinatorial objects, such as binary strings. Simply defined as a minimal change listing, Gray codes vary greatly both in structure and in the types of objects that they list. More specific types of Gray codes are universal cycles and overlap sequences. Universal cycles are Gray codes on a set of strings of length n in which the first n-1 letters of one object are the same as the last n-1 letters of its predecessor in the listing. Overlap sequences allow this overlap to vary between 1 and n-1. Some of our main contributions to the areas of Gray codes and universal cycles include a new Gray code algorithm for fixed weight m-ary words, and results on the existence of universal cycles for weak orders on [n]. Overlap cycles are a relatively new structure with very few published results. We prove the existence of s-overlap cycles for k-permutations of [n], which has been an open research problem for several years, as well as constructing 1- overlap cycles for Steiner triple and quadruple systems of every order. Also included are various other results of a similar nature covering other structures such as binary strings, m-ary strings, subsets, permutations, weak orders, partitions, and designs. These listing structures lend themselves readily to some classes of combinatorial objects, such as binary n-tuples and m-ary n-tuples. Others require more work to find an appropriate structure, such as k-subsets of an n-set, weak orders, and designs. Still more require a modification in the representation of the objects to fit these structures, such as partitions. Determining when and how we can fit these sets of objects into our three listing structures is the focus of this dissertation.
ContributorsHoran, Victoria E (Author) / Hurlbert, Glenn H. (Thesis advisor) / Czygrinow, Andrzej (Committee member) / Fishel, Susanna (Committee member) / Colbourn, Charles (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
The uncrossing partially ordered set $P_n$ is defined on the set of matchings on $2n$ points on a circle represented with wires. The order relation is $\tau'\leq \tau$ in $P_n$ if and only if $\tau'$ is obtained by resolving a crossing of $\tau$. %This partial order has been studied by Alman-Lian-Tran, Huang-Wen-Xie, Kenyon, and Lam. %The posets $P_n$ emerged from studies of circular planar electrical networks. Circular planar electrical networks are finite weighted undirected graphs embedded into a disk, with boundary vertices and interior vertices. By Curtis-Ingerman-Morrow and de Verdi\`ere-Gitler-Vertigan, the electrical networks can be encoded with response matrices. By Lam the space of response matrices for electrical networks has a cell structure, and this cell structure can be described by the uncrossing partial orders. %Lam proves that the posets can be identified with dual Bruhat order on affine permutations of type $(n,2n)$. Using this identification, Lam proves the poset $\hat{P}_n$, the uncrossing poset $P_n$ with a unique minimum element $\hat{0}$ adjoined, is Eulerian. This thesis consists of two sets of results: (1) flag enumeration in intervals in the uncrossing poset $P_n$ and (2) cyclic sieving phenomenon on the set $P_n$.
I identify elements in $P_n$ with affine permutations of type $(0,2n)$. %This identification enables us to explicitly describe the elements in $P_n$ with the elements in $\mathcal{MP}_n$.
Using this identification, I adapt a technique in Reading for finding recursions for the cd-indices of intervals in Bruhat order of Coxeter groups to the uncrossing poset $P_n$. As a result, I produce recursions for the cd-indices of intervals in the uncrossing poset $P_n$. I also obtain a recursion for the ab-indices of intervals in the poset $\hat{P}_n$, the poset $P_n$ with a unique minimum $\hat0$ adjoined. %We define an induced subposet $\mathcal{MP}_n$ of the affine permutations under Bruhat order.
Reiner-Stanton-White defined the cyclic sieving phenomenon (CSP) associated to a finite cyclic group action on a finite set and a polynomial. Sagan observed the CSP on the set of non-crossing matchings with the $q$-Catalan polynomial. Bowling-Liang presented similar results on the set of $k$-crossing matchings for $1\leq k \leq 3$. In this dissertation, I focus on the set of all matchings on $[2n]:=\{1,2,\dots,2n\}$. I find the number of matchings fixed by $\frac{2\pi}{d}$ rotations for $d|2n$. I then find the polynomial $X_n(q)$ such that the set of matchings together with $X_n(q)$ and the cyclic group of order $2n$ exhibits the CSP.
I identify elements in $P_n$ with affine permutations of type $(0,2n)$. %This identification enables us to explicitly describe the elements in $P_n$ with the elements in $\mathcal{MP}_n$.
Using this identification, I adapt a technique in Reading for finding recursions for the cd-indices of intervals in Bruhat order of Coxeter groups to the uncrossing poset $P_n$. As a result, I produce recursions for the cd-indices of intervals in the uncrossing poset $P_n$. I also obtain a recursion for the ab-indices of intervals in the poset $\hat{P}_n$, the poset $P_n$ with a unique minimum $\hat0$ adjoined. %We define an induced subposet $\mathcal{MP}_n$ of the affine permutations under Bruhat order.
Reiner-Stanton-White defined the cyclic sieving phenomenon (CSP) associated to a finite cyclic group action on a finite set and a polynomial. Sagan observed the CSP on the set of non-crossing matchings with the $q$-Catalan polynomial. Bowling-Liang presented similar results on the set of $k$-crossing matchings for $1\leq k \leq 3$. In this dissertation, I focus on the set of all matchings on $[2n]:=\{1,2,\dots,2n\}$. I find the number of matchings fixed by $\frac{2\pi}{d}$ rotations for $d|2n$. I then find the polynomial $X_n(q)$ such that the set of matchings together with $X_n(q)$ and the cyclic group of order $2n$ exhibits the CSP.
ContributorsKim, Younghwan (Author) / Fishel, Susanna (Thesis advisor) / Bremner, Andrew (Committee member) / Czygrinow, Andrzej (Committee member) / Kierstead, Henry (Committee member) / Paupert, Julien (Committee member) / Arizona State University (Publisher)
Created2018