We provide a theoretical model for a design involving a dc voltage biased Josephson junction (JJ) that strongly drives a high quality factor microwave cavity via the ac Josephson effect. We explore the rich classical dynamics of the resultant...
RUNX1 is a transcription factor regulating hematopoietic development. Study of the RUNX1 structure revealed two functional domains. The runt domain binds DNA and mediates interaction with CBFß. Sequences C terminal to the runt domain form the...
The advent of hypervisors revolutionized the computing industry in terms of malware prevention and detection, secure virtual machine managers, and cloud resilience. However, this has resulted in a disjointed response to handling known threats...
The performance of machine learning algorithms largely depends on data representation. As a critical step in machine learning, representation learning (feature learning) learns a transformation of training data to give a new representation that can...
Partially ordered sets and permutations are combinatorial structures having vast applications in theoretical computer science. In this thesis, we study various computational and algorithmic problems related to these structures. The first chapter of...
'Orthogonal modular forms are algebraic modular forms arising from lattices in quadratic spaces. In this thesis, we define orthogonal modular forms, establish their basic properties, and then apply them to a case of ternary quadratic spaces to...
The recognition of foreign peptides by MHC (Major Histocompatibility Complex) proteins is a critical step in the immune response mounted by higher vertebrates against pathogens. MHC proteins have many allelic variants, each recognizing different...
Robots -- Control systems. ; Robots -- Motion. ; Computer algorithms. ; Electronic data processing -- Distributed processing.
Self-reconfiguring robots are robots composed of many physically connected modules which can change their structural configuration to support multiple functionalities. We claim that self-reconfiguring robots are more versatile, extensible, and...
We study motion planning problems, finding trajectories that connect two configurations of a system, from two different perspectives: optimality and survivability. For the problem of finding optimal trajectories, we provide a model in which the...
An interval order is an ordered set whose elements are in correspondence with a collection of intervals in a linearly ordered set, with disjoint intervals ordered by their relative position. The order complex of an ordered set is the simplicial...
Scleroderma (systemic sclerosis; SSc) is a devastating autoimmune disease of unknown etiology for which there is no cure, and no truly effective therapies available. Immune dysfunction, fibrosis and vasculopathy are the three major features of the...
This thesis investigates a notion of Turing reducibility introduced by Winkler [8] that is total on all computably enumerable oracles. Groszek and Weber show in [7] that this is a new notion of reducibility and it is not transitive. They give su...
The overall scope of my thesis project is to determine effects of farnesol, a secreted factor produced by C. albicans , on P. aeruginosa virulence. These two organisms are frequently found with one another in mixed infections and our lab has...
We present designs, theory and the results of fabrication and testing for a novel parallel microrobotic assembly scheme using stress-engineered MEMS microrobots. The robots are 240-280 μm × 60 μm × 7-20 μm in size, each robot consist of a...
This thesis contains material relating to two separate subjects. The first section determines when the C*-algebra affiliated to a directed graph has continuous trace. We use groupoid methods and the focus is on producing conditions on a graph that...
Oligomers -- Structure -- Mathematical models. Nuclear magnetic resonance spectroscopy.
Medical Term: Nuclear Magnetic Resonance, Biomolecular.
Protein complexes play vital roles in the fundamental processes of life. In particular, homo-oligomers are involved in cell signaling, regulation, and transport. To make detailed studies of these symmetric proteins, they need to be discovered, and...
Electronic mail systems -- Security measures. Electronic mail systems -- Social aspects. Trust.
A secure system that cannot be used by real users to secure real-world processes is not really secure at all. While many believe that usability and security are diametrically opposed, a growing body of research from the field of Human-Computer...
This thesis approaches the problem of locating zero-day exploits used in network attacks. The hypothesis is that the advent of high-performance virtualization presents a unique opportunity to both discover these events and increase the attacker's...
In order to most effectively investigate protein structure and improve protein function, it is necessary to carefully plan appropriate experiments. The combinatorial number of possible experiment plans demands effective criteria and efficient...
Proteins -- Structure -- Data processing. Proteins -- Analysis -- Data processing. Nuclear magnetic resonance spectroscopy. Oligomers -- Analysis -- Data processing.
Symmetric homo-oligomers (protein complexes with similar subunits arranged symmetrically) play pivotal roles in complex biological processes such as ion transport and cellular regulation. Structure determination of these complexes is necessary in...
Polynomials. Finite fields (Algebra). Algebraic functions. Number theory.
The ring of univariate polynomials over a finite field shares many foundational arithmetic properties with the ring of rational integers. This similarity makes it possible for many problems in elementary number theory to be translated 'through the...
In Chapter 2 we look at the distribution of permutation statistics in the context of pattern-avoiding permutations. The first part of this chapter deals with a recursively defined bijection of Robertson [37] between 123- and 132-avoiding...
Novel biotherapeutics have reshaped drug discovery and promise a continued revolution in disease therapy, yet therapeutic proteins present unique design challenges. One distinguishing risk factor is the prospect of eliciting an adaptive immune...
Vibrio cholerae is the etiologic agent of cholera in humans. Intestinal colonization occurs via ingestion of contaminated food and water and results in symptoms that include the production of the characteristic rice water stool, vomiting, and...
This thesis considers the two special sensor networks for future sensor network design: mobile sensor networks and hybrid network of sensors and robots. To investigate two types of networks, we abstract two most important aspects that are ingrained...
Toxoplasma gondii is an obligate intracellular pathogen that is able to survive in a range of hosts due to its repertoire of secreted effector proteins. Utilizing the type I and type II Δku80 strains we engineered a collection of targeted knockout...
Access control is a core component of any information-security strategy. Researchers have spent tremendous energy over the past forty years defining abstract access-control models and proving various properties about them. However, surprisingly...