Partially ordered sets and permutations are combinatorial structures having vast applications in theoretical computer science. In this thesis, we study various computational and algorithmic problems related to these structures. The first chapter of...
Antibodies are known to be a primary correlate of protection in almost all current vaccines, and thus evaluating the antibody response is of critical importance in attempting to predict the efficacy of novel vaccine candidates. Historically...
Arctic soils in the permafrost region store substantially more carbon than is contained in the atmosphere, and are undergoing rapid change associated with anthropogenic climate change. Soil decomposition is an important component of ecosystem...
Genome sequencing technology has enabled the identification of genetic variants that are linked with cancer phenotypes, whether these are somatically acquired mutations or common inherited single nucleotide polymorphisms (SNPs). Whereas coding...
For many scientific applications, the data set cannot entirely fit in main memory. The data must reside out-of-core, i.e., on parallel disks. For many basic data-movement operations such as permuting, if the programmer does not design efficient...
In the past decade, the use of ordinal patterns in the analysis of time series and dynamical systems has become an important tool. Ordinal patterns (otherwise known as a permutation patterns) are found in time series by taking n data points at...
The ionosphere is the primary source for heavy ions which are ubiquitous in the terrestrial magnetosphere. Low-altitude energization in the auroral ionosphere results in bulk heating and transverse acceleration of ions, which begin to upwell and/or...
'Orthogonal modular forms are algebraic modular forms arising from lattices in quadratic spaces. In this thesis, we define orthogonal modular forms, establish their basic properties, and then apply them to a case of ternary quadratic spaces to...
We start by introducing avoidance coupling of Markov chains, with an overview of existing results. We then introduce and motivate a new notion, uniform coupling. We show that the only Markovian avoidance coupling on a cycle is of this type, and...
The identification of molecular alterations present in cancer is critical to better understand carcinogenesis as well as the clinical trajectories of patients with malignant tumors. Early detection and application of appropriate treatment...
Nuclear magnetic resonance spectroscopy -- Data processing. ; Proteins -- Analysis -- Mathematical models. ; Computer algorithms.
Our aim is to enhance high-throughput applications of Nuclear Magnetic Resonance (NMR) through the development of efficient computational methods that operate on sparse (minimal) sets of experimental NMR data. We have developed a family of four...
Mobile agents (Computer software). ; Electronic data processing -- Distributed processing. ; Sequential processing (Computer science) -- Mathematical models.
Mobile agents have received much attention recently as a way to efficiently access distributed resources in a low bandwidth network. Planning allows mobile agents to make the best use of the available resources. This thesis studies several planning...
Most current multiprocessor file systems are designed to use multiple disks in parallel, using the high aggregate bandwidth to meet the growing I/O requirements of parallel scientific applications. Most multiprocessor file systems provide...
Digital integrated circuits -- Testing. Digital integrated circuits -- Testing -- Mathematical models. Digital integrated circuits -- Design and construction.
We describe a set of natural image statistics that are built upon two multi-scale image decompositions, the quadrature mirror filter pyramid decomposition and the local angular harmonic decomposition. These image statistics consist of first- and...
Evolutionary Computation (EC) is one of the most advanced computational techniques. It has been frequently and successfully used to find good solutions to many complicated optimization problems with limited computational resources. EC is the...
The ctx and tcp genes that encode cholera toxin and the toxin co-regulated pilus, the major virulence determinants of Vibrio cholerae, are repressed by the nucleoid-associated protein H-NS and activated by the AraC-like transcriptional regulator...
The ability to resist highly tempting reward impulses is a struggle that all humans face on a daily basis, one that gives rise to many societal problems such as obesity and drug addiction. This form of self-regulation involves a critical balance...
Lungs -- Cancer -- New Hampshire. Bladder -- Cancer -- New Hampshire. Cancer -- Epidemiology. Cancer -- Environmental aspects -- New Hampshire. Cancer -- Genetic aspects
Complex diseases such as lung cancer are most commonly the result of environmental variables acting on an individual's genetic background. Those environmental variables may be found in the external environment, such as exposures to carcinogenic...
Subject Protein kinases. Aldosterone -- Physiological effect. Sodium -- Physiological transport. Sodium channels. Epithelial cells. Glucocorticoids. Medical Term Sgk protein.
It is well established that SGK1 plays a role in aldosterone mediated sodium transport. The intracellular localization of SGK1 has recently been demonstrated as mitochondrial. The studies described here evaluate the hypothesis that SGK1...
Self-reconfiguring (SR) robots are modular systems that can autonomously change shape, or reconfigure , for increased versatility and adaptability in unknown environments. In this thesis, we investigate planning and control for systems of...
We study the bijective combinatorics of reduced words. These are fundamental objects in the study of Coxeter groups. We restrict our focus to reduced words of permutations and signed permutations. Our results can all be situated within the context...
Computer input-output equipment. ; Computational grids (Computer systems). ; High performance computing. ; Electronic data processing -- Distributed processing.
High-performance computing increasingly occurs on computational grids composed of heterogeneous and geographically distributed systems of computers, networks, and storage devices that collectively act as a single virtual computer. A key challenge...
The demand for novel molecularly targeted drugs will continue to rise as we make progress toward personalizing cancer treatments to the molecular signatures of individual tumors. While the collection and analysis of genomic data has become routine,...
Although genome-wide association studies (GWAS) and other high-throughput initiatives have led to an information explosion in human genetics and genetic epidemiology, the mapping from genotype to phenotype remains challenging as most of the...
Polynomials. Finite fields (Algebra). Algebraic functions. Number theory.
The ring of univariate polynomials over a finite field shares many foundational arithmetic properties with the ring of rational integers. This similarity makes it possible for many problems in elementary number theory to be translated 'through the...
The Border Gateway Protocol (BGP) that manages inter-domain routing on the Internet lacks security. Protective measures using public key cryptography introduce complexities and costs. To support authentication and other security functionality in...