Matching Items (100)
Description
In this thesis I introduce a new direction to computing using nonlinear chaotic dynamics. The main idea is rich dynamics of a chaotic system enables us to (1) build better computers that have a flexible instruction set, and (2) carry out computation that conventional computers are not good at it. Here I start from the theory, explaining how one can build a computing logic block using a chaotic system, and then I introduce a new theoretical analysis for chaos computing. Specifically, I demonstrate how unstable periodic orbits and a model based on them explains and predicts how and how well a chaotic system can do computation. Furthermore, since unstable periodic orbits and their stability measures in terms of eigenvalues are extractable from experimental times series, I develop a time series technique for modeling and predicting chaos computing from a given time series of a chaotic system. After building a theoretical framework for chaos computing I proceed to architecture of these chaos-computing blocks to build a sophisticated computing system out of them. I describe how one can arrange and organize these chaos-based blocks to build a computer. I propose a brand new computer architecture using chaos computing, which shifts the limits of conventional computers by introducing flexible instruction set. Our new chaos based computer has a flexible instruction set, meaning that the user can load its desired instruction set to the computer to reconfigure the computer to be an implementation for the desired instruction set. Apart from direct application of chaos theory in generic computation, the application of chaos theory to speech processing is explained and a novel application for chaos theory in speech coding and synthesizing is introduced. More specifically it is demonstrated how a chaotic system can model the natural turbulent flow of the air in the human speech production system and how chaotic orbits can be used to excite a vocal tract model. Also as another approach to build computing system based on nonlinear system, the idea of Logical Stochastic Resonance is studied and adapted to an autoregulatory gene network in the bacteriophage λ.
ContributorsKia, Behnam (Author) / Ditto, William (Thesis advisor) / Huang, Liang (Committee member) / Lai, Ying-Cheng (Committee member) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2011
Description
Speciation is the fundamental process that has generated the vast diversity of life on earth. The hallmark of speciation is the evolution of barriers to gene flow. These barriers may reduce gene flow either by keeping incipient species from hybridizing at all (pre-zygotic), or by reducing the fitness of hybrids (post-zygotic). To understand the genetic architecture of these barriers and how they evolve, I studied a genus of wasps that exhibits barriers to gene flow that act both pre- and post-zygotically. Nasonia is a genus of four species of parasitoid wasps that can be hybridized in the laboratory. When two of these species, N. vitripennis and N. giraulti are mated, their offspring suffer, depending on the generation and cross examined, up to 80% mortality during larval development due to incompatible genic interactions between their nuclear and mitochondrial genomes. These species also exhibit pre-zygotic isolation, meaning they are more likely to mate with their own species when given the choice. I examined these two species and their hybrids to determine the genetic and physiological bases of both speciation mechanisms and to understand the evolutionary forces leading to them. I present results that indicate that the oxidative phosphorylation (OXPHOS) pathway, an essential pathway that is responsible for mitochondrial energy generation, is impaired in hybrids of these two species. These results indicate that this impairment is due to the unique evolutionary dynamics of the combined nuclear and mitochondrial origin of this pathway. I also present results showing that, as larvae, these hybrids experience retarded growth linked to the previously observed mortality and I explore possible physiological mechanisms for this. Finally, I show that the pre-mating isolation is due to a change in a single pheromone component in N. vitripennis males, that this change is under simple genetic control, and that it evolved neutrally before being co-opted as a species recognition signal. These results are an important addition to our overall understanding of the mechanisms of speciation and showcase Nasonia as an emerging model for the study of the genetics of speciation.
ContributorsGibson, Joshua D (Author) / Gadau, Jürgen (Thesis advisor) / Harrison, Jon (Committee member) / Pratt, Stephen (Committee member) / Verrelli, Brian (Committee member) / Willis, Wayne (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation investigates the condition of skeletal muscle insulin resistance using bioinformatics and computational biology approaches. Drawing from several studies and numerous data sources, I have attempted to uncover molecular mechanisms at multiple levels. From the detailed atomistic simulations of a single protein, to datamining approaches applied at the systems biology level, I provide new targets to explore for the research community. Furthermore I present a new online web resource that unifies various bioinformatics databases to enable discovery of relevant features in 3D protein structures.
ContributorsMielke, Clinton (Author) / Mandarino, Lawrence (Committee member) / LaBaer, Joshua (Committee member) / Magee, D. Mitchell (Committee member) / Dinu, Valentin (Committee member) / Willis, Wayne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Complex dynamical systems consisting interacting dynamical units are ubiquitous in nature and society. Predicting and reconstructing nonlinear dynamics of units and the complex interacting networks among them serves the base for the understanding of a variety of collective dynamical phenomena. I present a general method to address the two outstanding problems as a whole based solely on time-series measurements. The method is implemented by incorporating compressive sensing approach that enables an accurate reconstruction of complex dynamical systems in terms of both nodal equations that determines the self-dynamics of units and detailed coupling patterns among units. The representative advantages of the approach are (i) the sparse data requirement which allows for a successful reconstruction from limited measurements, and (ii) general applicability to identical and nonidentical nodal dynamics, and to networks with arbitrary interacting structure, strength and sizes. Another two challenging problem of significant interest in nonlinear dynamics: (i) predicting catastrophes in nonlinear dynamical systems in advance of their occurrences and (ii) predicting the future state for time-varying nonlinear dynamical systems, can be formulated and solved in the framework of compressive sensing using only limited measurements. Once the network structure can be inferred, the dynamics behavior on them can be investigated, for example optimize information spreading dynamics, suppress cascading dynamics and traffic congestion, enhance synchronization, game dynamics, etc. The results can yield insights to control strategies design in the real-world social and natural systems. Since 2004, there has been a tremendous amount of interest in graphene. The most amazing feature of graphene is that there exists linear energy-momentum relationship when energy is low. The quasi-particles inside the system can be treated as chiral, massless Dirac fermions obeying relativistic quantum mechanics. Therefore, the graphene provides one perfect test bed to investigate relativistic quantum phenomena, such as relativistic quantum chaotic scattering and abnormal electron paths induced by klein tunneling. This phenomenon has profound implications to the development of graphene based devices that require stable electronic properties.
ContributorsYang, Rui (Author) / Lai, Ying-Cheng (Thesis advisor) / Duman, Tolga M. (Committee member) / Akis, Richard (Committee member) / Huang, Liang (Committee member) / Arizona State University (Publisher)
Created2012
Description
Salmonella enterica is a gastrointestinal (GI) pathogen that can cause systemic diseases. It invades the host through the GI tract and can induce powerful immune responses in addition to disease. Thus, it is considered as a promising candidate to use as oral live vaccine vectors. Scientists have been making great efforts to get a properly attenuated Salmonella vaccine strain for a long time, but could not achieve a balance between attenuation and immunogenicity. So the regulated delayed attenuation/lysis Salmonella vaccine vectors were proposed as a design to seek this balance. The research work is progressing steadily, but more improvements need to be made. As one of the possible improvements, the cyclic adenosine monophosphate (cAMP) -independent cAMP receptor protein (Crp*) is expected to protect the Crp-dependent crucial regulator, araC PBAD, in these vaccine designs from interference by glucose, which decreases synthesis of cAMP, and enhance the colonizing ability by and immunogenicity of the vaccine strains. In this study, the cAMP-independent crp gene mutation, crp-70, with or without araC PBAD promoter cassette, was introduced into existing Salmonella vaccine strains. Then the plasmid stability, growth rate, resistance to catabolite repression, colonizing ability, immunogenicity and protection to challenge of these new strains were compared with wild-type crp or araC PBAD crp strains using western blots, enzyme-linked immunosorbent assays (ELISA) and animal studies, so as to evaluate the effects of the crp-70 mutation on the vaccine strains. The performances of the crp-70 strains in some aspects were closed to or even exceeded the crp+ strains, but generally they did not exhibit the expected advantages compared to their wild-type parents. Crp-70 rescued the expression of araC PBAD fur from catabolite repression. The strain harboring araC PBAD crp-70 was severely affected by its slow growth, and its colonizing ability and immunogenicity was much weaker than the other strains. The Pcrp crp-70 strain showed relatively good ability in colonization and immune stimulation. Both the araC PBAD crp-70 and the Pcrp crp-70 strains could provide certain levels of protection against the challenge with virulent pneumococci, which were a little lower than for the crp+ strains.
ContributorsShao, Shihuan (Author) / Curtiss, Roy (Thesis advisor) / Arizona State University (Publisher)
Created2012
Description
What can classical chaos do to quantum systems is a fundamental issue highly relevant to a number of branches in physics. The field of quantum chaos has been active for three decades, where the focus was on non-relativistic quantumsystems described by the Schr¨odinger equation. By developing an efficient method to solve the Dirac equation in the setting where relativistic particles can tunnel between two symmetric cavities through a potential barrier, chaotic cavities are found to suppress the spread in the tunneling rate. Tunneling rate for any given energy assumes a wide range that increases with the energy for integrable classical dynamics. However, for chaotic underlying dynamics, the spread is greatly reduced. A remarkable feature, which is a consequence of Klein tunneling, arise only in relativistc quantum systems that substantial tunneling exists even for particle energy approaching zero. Similar results are found in graphene tunneling devices, implying high relevance of relativistic quantum chaos to the development of such devices. Wave propagation through random media occurs in many physical systems, where interesting phenomena such as branched, fracal-like wave patterns can arise. The generic origin of these wave structures is currently a matter of active debate. It is of fundamental interest to develop a minimal, paradigmaticmodel that can generate robust branched wave structures. In so doing, a general observation in all situations where branched structures emerge is non-Gaussian statistics of wave intensity with an algebraic tail in the probability density function. Thus, a universal algebraic wave-intensity distribution becomes the criterion for the validity of any minimal model of branched wave patterns. Coexistence of competing species in spatially extended ecosystems is key to biodiversity in nature. Understanding the dynamical mechanisms of coexistence is a fundamental problem of continuous interest not only in evolutionary biology but also in nonlinear science. A continuous model is proposed for cyclically competing species and the effect of the interplay between the interaction range and mobility on coexistence is investigated. A transition from coexistence to extinction is uncovered with a non-monotonic behavior in the coexistence probability and switches between spiral and plane-wave patterns arise. Strong mobility can either promote or hamper coexistence, while absent in lattice-based models, can be explained in terms of nonlinear partial differential equations.
ContributorsNi, Xuan (Author) / Lai, Ying-Cheng (Thesis advisor) / Huang, Liang (Committee member) / Yu, Hongbin (Committee member) / Akis, Richard (Committee member) / Arizona State University (Publisher)
Created2012
Description
Thirty six percent of Americans are obese and thirty three percent are overweight; obesity has become a known killer in the U.S. yet its prevalence has maintained a firm grasp on the U.S. population and continues to spread across the globe as other countries slowly adopt the American lifestyle. A survey was compiled collecting demographic and body mass index (BMI) information, as well as Tanofsky-Kraff’s (2009) “Assess Eating in the Absence of Hunger” survey questions. The survey used for this study was emailed out to Arizona State University students in Barrett, The Honors College, and the ASU School of Nutrition and Health Promotion listservs. A total of 457 participants completed the survey, 72 males and 385 females (mean age, 24.5±7.7 y; average body mass index (BMI), 23.4 ± 4.8 [a BMI of 25-29.9 is classified as overweight]). When comparing BMI with the living situation, 71% of obese students were living at home with family versus off campus with friends or alone. For comparison, 45% of normal weight students lived at home with family. These data could help structure prevention plans targeting college students by focusing on weight gain prevention at the family level. Results from the Tanofsky-Kraff (2009) survey revealed there was not a significant relationship between external or physical cues and BMI in men or women, but there was a significant positive correlation between emotional cues and BMI in women only. Anger and sadness were the emotional cues in women related to initiating consumption past satiation and consumption following several hours of fasting. Although BMI was inversely related to physical activity in this sample (r = -0.132; p=0.005), controlling for physical activity did not impact the significant associations of BMI with anger or sadness (P>0.05). This information is important in targeting prevention programs to address behavioral change and cognitive awareness of the effects of emotion on over-consumption.
ContributorsGarza, Andrea Marie (Author) / Johnston, Carol (Thesis director) / Jacobs, Mark (Committee member) / Coletta, Dawn (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
New-onset diabetes after kidney transplantation (NODAT) occurs in 20% of kidney transplant patients. In 5 patients who are at risk for new-onset diabetes after kidney transplantation, skeletal muscle gene expression profiling was performed both before and after kidney transplant. The differences in gene expression before and after transplant were compared in order to identify specific genes that could be linked to developing NODAT. These findings could open new avenues for future research.
ContributorsLowery, Clint Curtis (Author) / Coletta, Dawn (Thesis director) / Katsanos, Christos (Committee member) / Willis, Wayne (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / W. P. Carey School of Business (Contributor)
Created2014-05
Description
DNA methylation, a subset of epigenetics, has been found to be a significant marker associated with variations in gene expression and activity across the entire human genome. As of now, however, there is little to no information about how DNA methylation varies between different tissues inside a singular person's body. By using research data from a preliminary study of lean and obese clinical subjects, this study attempts to put together a profile of the differences in DNA methylation that can be observed between two particular body tissues from this subject group: blood and skeletal muscle. This study allows us to start describing the changes that occur at the epigenetic level that influence how differently these two tissues operate, along with seeing how these tissues change between individuals of different weight classes, especially in the context of the development of symptoms of Type 2 Diabetes.
ContributorsRappazzo, Micah Gabriel (Author) / Coletta, Dawn (Thesis director) / Katsanos, Christos (Committee member) / Dinu, Valentin (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor) / Department of Psychology (Contributor)
Created2013-12
DescriptionA novel and unconventional approach for delivering a eukaryotic apoptosis factor, TNF-related apoptosis-inducing ligand (TRAIL), to cancer cells within and around necrotizing tumors by utilizing a S. Typhimurium purine requiring auxotroph as a biological vector to develop two anticancer therapies with multiple modality and broad economic feasibility.
ContributorsKoons, Andrew (Author) / Curtiss, Roy (Thesis director) / Lake, Douglas (Committee member) / Janthakahalli, Nagaraj Vinay (Committee member) / Barrett, The Honors College (Contributor)
Created2013-12