Browsing College of Natural Science and Mathematics (CNSM) by Subject "mathematical models"
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Investigations in phylogenetics: tree inference and model identifiabilityThis thesis presents two projects in mathematical phylogenetics. The first presents a new, statistically consistent, fast method for inferring species trees from topological gene trees under the multispecies coalescent model. The algorithm of this method takes a collection of unrooted topological gene trees, computes a novel intertaxon distance from them, and outputs a metric species tree. The second establishes that numerical and nonnumerical parameters of a specic Prole Mixture Model of protein sequence evolution are generically identifiable. Algebraic techniques are used, especially a theorem of Kruskal on tensor decomposition.

On the KleinGordon equation originating on a curve and applications to the tsunami runup problemOur goal is to study the linear KleinGordon equation in matrix form, with initial conditions originating on a curve. This equation has applications to the CrossSectionally Averaged Shallow Water equations, i.e. a system of nonlinear partial differential equations used for modeling tsunami waves within narrow bays, because the general CarrierGreenspan transform can turn the CrossSectionally Averaged Shallow Water equations (for shorelines of constant slope) into a particular form of the matrix KleinGordon equation. Thus the matrix KleinGordon equation governs the runup of tsunami waves along shorelines of constant slope. If the narrow bay is Ushaped, the CrossSectionally Averaged Shallow Water equations have a known general solution via solving the transformed matrix KleinGordon equation. However, the initial conditions for our KleinGordon equation are given on a curve. Thus our goal is to solve the matrix KleinGordon equation with known conditions given along a curve. Therefore we present a method to extrapolate values on a line from conditions on a curve, via the Taylor formula. Finally, to apply our solution to the CrossSectionally Averaged Shallow Water equations, our numerical simulations demonstrate how Gaussian and Nwave profiles affect the runup of tsunami waves within various Ushaped bays.

Species network inference under the multispecies coalescent modelSpecies network inference is a challenging problem in phylogenetics. In this work, we present two results on this. The first shows that many topological features of a level1 network are identifable under the network multispecies coalescent model (NMSC). Specifcally, we show that one can identify from gene tree frequencies the unrooted semidirected species network, after suppressing all cycles of size less than 4. The second presents the theory behind a new, statistically consistent, practical method for the inference of level1 networks under the NMSC. The input for this algorithm is a collection of unrooted topological gene trees, and the output is an unrooted semidirected species network.