The Border Gateway Protocol (BGP) facilitates communication between parts of the Internet by determining paths by which data can get from one network to any other. Just as IP is used ubiquitously as an addressing scheme, BGP is used ubiquitously...
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...
Robustness to genetic perturbations is a fundamental property of all living things. The genetic code is degenerate, RNA secondary structure is robust to sequence changes, and protein structure is robust to amino acid substitutions. Complex systems...
Digital integrated circuits -- Testing. Digital integrated circuits -- Testing -- Mathematical models. Digital integrated circuits -- Design and construction.
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,...
We have a limited understanding of how an opinion is originated, how an opinion and information supporting and explaining it gets conveyed, and how the communicated opinion is perceived and processed by others. One direction of current research...
At the heart of computer games and computer generated films lies 3D content creation. A student wanting to learn how to create and edit 3D meshes can quickly find thousands of videos explaining the workflow process. These videos are a popular...
In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient...
This thesis centers around a generalization of the classical discrete Fourier transform. We first present a general diagrammatic approach to the construction of efficient algorithms for computing the Fourier transform of a function on a finite...
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...
In large and complex networks such as the Internet and road networks, traffic routing is typically decentralized. Users in the network choose their routes independently to minimize their own delay, leading to complicated and nonintuitive outcomes...
We begin with a presentation of the current state of Poljak and Turzik's conjecture that a matroid is sticky if and only if it is modular as described in [5] and [1]. We show that all graphic, cographic, and regular matroids must satisfy the...
We consider a problem of information overload: the conflict between vast amounts of data available in electronic form and inadequate tools for finding relevant information. To alleviate this problem we look at the information organization:...
Multimedia systems -- Mathematical models. ; Information storage and retrieval systems. ; Machinery -- Alignment.
This thesis introduces multiple media correlation, a new technology for the automatic alignment of multiple media objects such as text, audio, and video. This research began with the question: what can be learned when multiple multimedia components...
In the late 1960s, Ihara began work that led to the Ihara zeta function, a zeta function which is defined on a finite graph. This function is an interesting graph invariant which gives information on expansion properties of the graph. It also...
For a local field K, we study the affine buildings Ξ n and Δ n naturally associated to SL n ( K ) and Sp n ( K ), respectively. Since Sp n ( K ) is a subgroup of SL 2 n ( K ), we investigate properties of a natural embedding of Δ n in Ξ 2 n ....
Proteins, the basic structural and functional building blocks of cellular machinery, evolve under significant constraint. Evolutionary pressures limit the acceptable variation and covariation of amino acids in a protein. As such, these evolutionary...
Graph algorithms. Nuclear magnetic resonance spectroscopy -- Data processing. Proteins -- Structure -- Mathematical models. Proteins -- Crosslinking -- Mathematical models. Protein folding -- Mathematical models.
The study of three-dimensional protein structures produces insights into protein function at the molecular level. Graphs provide a natural representation of protein structures and associated experimental data, and enable the development of graph...
We examine variations of cops and robbers games on graphs. Our goals are to introduce some randomness into their study, and to estimate (expected) capture time. We show that a cop chasing a random walker can capture him in expected time n + o(n)....