The field of spintronics deals with the use of the spin degree of freedom of the electron and the spin current that arises from it. There are many static and dynamic applications for spin current whether it is supplied by spin polarized electric current from a magnetic layer or from pure spin current arising from spin orbit interaction such as the spin Hall effect. This dissertation focuses on the later where the spin Hall effect in platinum supplies a spin torque on an adjacent ferromagnetic layer and thereby excites auto-oscillations of its magnetization. Previous studies of magnetization dynamics excited by direct spin currents have demonstrated the existence of phase coherent auto-oscillations of magnetization in the 0-dimensional structures and its absence in the 2D case therefore the 1D case, a ferromagnetic nanowire, is presented here. This will cover the first instance of a micrometer scale STO and will show the excited modes are the edge and bulk spin wave eigenmodes of the nanowire. Additionally, the evolution of the auto-oscillation characteristics as the width of the wire is increased is shown which reveals the mechanisms of the auto-oscillation suppression as the system effective dimensionality crosses of over from the 1D to the 2D regime. Lastly, a novel type of spin torque oscillator with easy plane magnetic anisotropy is discussed; its properties are predicted via micromagnetic simulations and initial experimental data on this type of oscillator are presented.

Blumberg and Hill defined categories of equivariant spectra interpolating between the equivariant stable categories indexed by universes. Indexed by an N∞ operad O, these O-spectra are characterized by what transfers they admit between their fixed points. We study structural properties of the O-incomplete equvariant stable categories. We first show an analog of a theorem of Guillou and May, giving an equivalence between O-spectra and spectrally enriched presheaves on a spectral enhancement of the incomplete Burnside category. Using this, we define the smash product and geometric fixed points of O-spectra in terms of Kan extensions and show that O-spectra can be recovered from gluing diagrams between their geometric fixed points. Finally, we apply this to give Mayer-Vietoris sequences describing the Picard group of O-spectra. In the presence of an appropriate Segal conjecture, we compare this to the Picard group of invertible abelian Mackey functors, giving a partial generalization of a theorem by Fausk, Lewis, and May.

Central to the comparison between language and music is what Theodor Adorno termed a “wordless syntax,” such that the elements of a work of art might be held in relation to one another, rather than fixed relative to a static hierarchical form. In music, this syntax creates a tension between the expressive, voice-like aspects of melody, and the abstract, syntactical structures of harmony. The use of linguistic material further complicates the musical syntax, as there are multiple competing hierarchical structures at play. As an alternative to the word “hierarchy” in relation to musical form, the composer James Tenney offered “holarchy” as a replacement which sets elements in relation to one another, rather than to a fixed structure. The friction and instability created by multiple syntactical systems and the material nature of the music generates what I call in this dissertation holarchic flux.

In addition to a theoretical overview of holarchic flux and its relation to language and music, this essay outlines a novel algorithm for interval and chord rationalization, using Tenney’s metric of harmonic distance. This essay also describes a number of compositions of mine, including a solo voice work How to Get There From Here and ensemble compositions We remember not the word, but the sound of the word, and Terrain, with regard to the concepts of holarchic flux and musical syntax.

The field of spintronics deals with the use of the spin degree of freedom of the electron and the spin current that arises from it. There are many static and dynamic applications for spin current whether it is supplied by spin polarized electric current from a magnetic layer or from spin orbit torques. This dissertation will focus on the later cases where the spin Hall effect present in platinum supplies a spin torque on an adjacent permalloy layer creating a spin torque oscillator(STO). Previous studies have demonstrated the existence of STOs in the 0-dimensional case and its absence in the 2D case therefore the 1D case, a ferromagnetic nanowire, is tackled here. This will cover the first instance of a micrometer scale STO and will show the excited modes are the edge and bulk spin wave eigenmodes of the nanowire.

This work describes advances in nanopore sequencing technology as they apply to RNA. RNAs in the cellular environment have a wide range of functions and structures, by nature being much more dynamic in their activities than their chemical counterpart, DNA. The diversity of activities and functions that RNAs assume in the cell is reflected in the diverse research interests of those who study RNA. Any effort to develop nanopore-based direct RNA sequencing applications requires accounting for this diversity.

Given the spectrum of interests in RNA biology, much of this dissertation attempts to address a fundamental challenge in directly analyzing RNAs by nanopore - how to deliver and read diverse classes of RNA at single-nucleotide resolution using a nanopore sequencer? The introductory first chapter describes background on nanopores as sequencing sensors and samples of some biology surrounding this diverse class of molecules. The state of the art and challenges in RNA sequencing in general are discussed.

The second chapter of this work demonstrates a method specifically preparing tRNA for nanopore sequencing. The primary challenge in this effort is to be able to consistently load a single tRNA end and process the tRNA strand through the pore in a linear order. A molecular adapter composed of double-stranded DNA ligated to the tRNA termini facilitates this process. The adapter specifically targets tRNA by hybridizing to the universally conserved CCA tail of tRNA. It also provides a binding site for ϕ29 DNA polymerase, which acts a molecular brake on RNA under non-catalytic conditions. These two features allow for discrimination between two tRNA species from E. coli. This work demonstrates that it is possible to use a nanopore to analyze individual tRNAs as linear strands, which is a necessary prerequisite for nanopore-based tRNA sequencing.

The third chapter of this work describes applying the Oxford Nanopore MinION sequencer to directly sequence 16S ribosomal RNA (16S rRNA). Demonstration of direct RNA sequencing of poly-adenylated RNA by Oxford Nanopore in August of 2016 was a critical development towards direct sequencing of RNA in general. The work described in Chapter 3 again involves designing an adapter, but this time specific for prokaryotic 16S rRNA. This adapter can be used with the existing Oxford Nanopore direct RNA sequencing kit. Sequencing of 16S rRNA from E. coli and other three other microbial species is demonstrated. The data and confirmatory experiments show that it is possible to directly detect modified ribonucleotides in nanopore-based sequencing data, which has long been a promised benefit of direct RNA sequencing methods. The 16S rRNA adapter is designed to hybridize to conserved 3′-end sequence of E. coli 16S rRNA. It could be generalized to all prokaryotic 16S rRNA, which would be desirable for rapid identification of prokaryotic microbes in a clinical or environmental setting.

The appendices cover unpublished work on helicase proteins to control RNA strand movement through a nanopore. The appendices also contain protocols for preparing different classes of RNA for nanopore sequencing and preparation of the helicase fragment of the SV40 Large T-antigen.