Applied Mathematics Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Asymptotic Cones Of Quadratically Defined Sets And Their Applications To Qcqps, Alexander Joyce

All Dissertations

Quadratically constrained quadratic programs (QCQPs) are a set of optimization problems defined by a quadratic objective function and quadratic constraints. QCQPs cover a diverse set of problems, but the nonconvexity and unboundedness of quadratic constraints lead to difficulties in globally solving a QCQP. This thesis covers properties of unbounded quadratic constraints via a description of the asymptotic cone of a set defined by a single quadratic constraint. A description of the asymptotic cone is provided, including properties such as retractiveness and horizon directions.

Using the characterization of the asymptotic cone, we generalize existing results for bounded quadratically defined regions with …

On Variants Of Sliding And Frank-Wolfe Type Methods And Their Applications In Video Co-Localization, Seyed Hamid Nazari

All Dissertations

In this dissertation, our main focus is to design and analyze first-order methods for computing approximate solutions to convex, smooth optimization problems over certain feasible sets. Specifically, our goal in this dissertation is to explore some variants of sliding and Frank-Wolfe (FW) type algorithms, analyze their convergence complexity, and examine their performance in numerical experiments. We achieve three accomplishments in our research results throughout this dissertation. First, we incorporate a linesearch technique to a well-known projection-free sliding algorithm, namely the conditional gradient sliding (CGS) method. Our proposed algorithm, called the conditional gradient sliding with linesearch (CGSls), does not require the …

Advancements In Gaussian Process Learning For Uncertainty Quantification, John C. Nicholson

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Gaussian processes are among the most useful tools in modeling continuous processes in machine learning and statistics. The research presented provides advancements in uncertainty quantification using Gaussian processes from two distinct perspectives. The first provides a more fundamental means of constructing Gaussian processes which take on arbitrary linear operator constraints in much more general framework than its predecessors, and the other from the perspective of calibration of state-aware parameters in computer models. If the value of a process is known at a finite collection of points, one may use Gaussian processes to construct a surface which interpolates these values to …

An Algorithm For Biobjective Mixed Integer Quadratic Programs, Pubudu Jayasekara Merenchige

All Dissertations

Multiobjective quadratic programs (MOQPs) are appealing since convex quadratic programs have elegant mathematical properties and model important applications. Adding mixed-integer variables extends their applicability while the resulting programs become global optimization problems. Thus, in this work, we develop a branch and bound (BB) algorithm for solving biobjective mixed-integer quadratic programs (BOMIQPs). An algorithm of this type does not exist in the literature.

The algorithm relies on five fundamental components of the BB scheme: calculating an initial set of efficient solutions with associated Pareto points, solving node problems, fathoming, branching, and set dominance. Considering the properties of the Pareto set of …