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Full-Text Articles in Other Applied Mathematics
Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel
Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel
Department of Mathematics: Dissertations, Theses, and Student Research
The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to …
The Neural Ring: Using Algebraic Geometry To Analyze Neural Codes, Nora Youngs
The Neural Ring: Using Algebraic Geometry To Analyze Neural Codes, Nora Youngs
Department of Mathematics: Dissertations, Theses, and Student Research
Neurons in the brain represent external stimuli via neural codes. These codes often arise from stimulus-response maps, associating to each neuron a convex receptive field. An important problem confronted by the brain is to infer properties of a represented stimulus space without knowledge of the receptive fields, using only the intrinsic structure of the neural code. How does the brain do this? To address this question, it is important to determine what stimulus space features can - in principle - be extracted from neural codes. This motivates us to define the neural ring and a related neural ideal, algebraic objects …
Random Search Models Of Foraging Behavior: Theory, Simulation, And Observation., Ben C. Nolting
Random Search Models Of Foraging Behavior: Theory, Simulation, And Observation., Ben C. Nolting
Department of Mathematics: Dissertations, Theses, and Student Research
Many organisms, from bacteria to primates, use stochastic movement patterns to find food. These movement patterns, known as search strategies, have recently be- come a focus of ecologists interested in identifying universal properties of optimal foraging behavior. In this dissertation, I describe three contributions to this field. First, I propose a way to extend Charnov's Marginal Value Theorem to the spatially explicit framework of stochastic search strategies. Next, I describe simulations that compare the efficiencies of sensory and memory-based composite search strategies, which involve switching between different behavioral modes. Finally, I explain a new behavioral analysis protocol for identifying the …