Physical Sciences and Mathematics Commons^™

Differential Equation Models And Numerical Methods For Reverse Engineering Genetic Regulatory Networks, Mi Un Yoon

Doctoral Dissertations

This dissertation develops and analyzes differential equation-based mathematical models and efficient numerical methods and algorithms for genetic regulatory network identification. The primary objectives of the dissertation are to design, analyze, and test a general variational framework and numerical methods for seeking its approximate solutions for reverse engineering genetic regulatory networks from microarray datasets using the approach based on differential equation modeling. In the proposed variational framework, no structure assumption on the genetic network is presumed, instead, the network is solely determined by the microarray profile of the network components and is identified through a well chosen variational principle which minimizes …

Analytical Computation Of Proper Orthogonal Decomposition Modes And N-Width Approximations For The Heat Equation With Boundary Control, Tasha N. Fernandez

Masters Theses

Model reduction is a powerful and ubiquitous tool used to reduce the complexity of a dynamical system while preserving the input-output behavior. It has been applied throughout many different disciplines, including controls, fluid and structural dynamics. Model reduction via proper orthogonal decomposition (POD) is utilized for of control of partial differential equations. In this thesis, the analytical expressions of POD modes are derived for the heat equation. The autocorrelation function of the latter is viewed as the kernel of a self adjoint compact operator, and the POD modes and corresponding eigenvalues are computed by solving homogeneous integral equations of the …

Spatiotemporal Dynamics In A Lower Montane Tropical Rainforest, Robert Michael Lawton

Doctoral Dissertations

Disturbance in a forest’s canopy, whether caused by treefall, limbfall, landslide, or fire determines not only the distribution of well-lit patches at any given time, but also the ways in which the forest changes over time. In this dissertation, I use a 25 year record of treefall gap formation find a novel and highly patterned process of forest disturbance and regeneration, providing a local mechanism by examining the factors that influence the likelihood of treefall. I then develop a stochastic cellular automaton for disturbance and regeneration based on the analysis of this long term data set and illustrate the potential …

Propagation Of Periodic Waves Using Wave Confinement, Paula Cysneiros Sanematsu

Masters Theses

This thesis studies the behavior of the Eulerian scheme, with "Wave Confinement" (WC), when propagating periodic waves. WC is a recently developed method that was derived from the scheme "vorticity confinement" used in fluid mechanics, and it efficiently solves the linear wave equation. This new method is applicable for numerous simulations such as radio wave propagation, target detection, cell phone and satellite communications.

The WC scheme adds a nonlinear term to the discrete wave equation that adds stability with negative and positive diffusion, conserves integral quantities such as total amplitude and wave speed, and it allows wave propagation over long …

Nonlinear Acoustics Of Piston-Driven Gas-Column Oscillations, Andrew William Wilson

Masters Theses

The piston-driven oscillator is traditionally modeled by directly applying boundary conditions to the acoustic wave equations; with better models re-deriving the wave equations but retaining nonlinear and viscous effects. These better models are required as the acoustic solution exhibits singularity near the natural frequencies of the cavity, with an unbounded (and therefore unphysical) solution. Recently, a technique has been developed to model general pressure oscillations in propulsion systems and combustion devices. Here, it is shown that this technique applies equally well to the piston-driven gas-column oscillator; and that the piston experiment provides strong evidence for the validity of the general …

Optimal Control Of Species Augmentation Conservation Strategies, Erin Nicole Bodine

Doctoral Dissertations

Species augmentation is a method of reducing species loss via augmenting declining or threatened populations with individuals from captive-bred or stable, wild populations. In this dissertation, species augmentation is analyzed in an optimal control setting to determine the optimal augmentation strategies given various constraints and settings. In each setting, we consider the effects on both the target/endangered population and a reserve population from which the individuals translocated in the augmentation are harvested. Four different optimal control formulations are explored. The first two optimal control formulations model the underlying population dynamics with a system of ordinary differential equations. Each of these …

Theoretical Models For Wall Injected Duct Flows, Tony Saad

Doctoral Dissertations

This dissertation is concerned with the mathematical modeling of the flow in a porous cylinder with a focus on applications to solid rocket motors. After discussing the historical development and major contributions to the understanding of wall injected flows, we present an inviscid rotational model for solid and hybrid rockets with arbitrary headwall injection. Then, we address the problem of pressure integration and find that for a given divergence free velocity field, unless the vorticity transport equation is identically satisfied, one cannot find an analytic expression for the pressure by direct integration of the Navier-Stokes equations. This is followed by …