Matching Items (101)
161497-Thumbnail Image.png
Description
The Pathways of Distinction Analysis (PoDA) program calculates relationships between a given group of genes contained within a pathway, and a disease state. It was used here to investigate liver cancer, and to explore how genetic variability may contribute to the different rates of development of the disease in males

The Pathways of Distinction Analysis (PoDA) program calculates relationships between a given group of genes contained within a pathway, and a disease state. It was used here to investigate liver cancer, and to explore how genetic variability may contribute to the different rates of development of the disease in males and females. The goal of the study was to identify germline variation that differs by sex in hepatocellular carcinoma. Using the program, multiple pathways and genes were identified to have significant differences in their relationship to liver cancer in males and females. In animal studies, the genes which were identified using the PoDA analysis have been shown to impact liver cancer, often with different results for males and females. While these genes are often the focus in animal models, they are absent from current Genome Wide Association Studies (GWAS) catalogs for humans. By working to bridge the results of animal studies and human studies, the results help to identify the causes of liver cancer, and more specifically, the reason the disease affects males at much higher rates. The differences in pathways identified to be significant for the two sexes indicate the germline variance may play sex-specific roles in the development of hepatocellular carcinoma. Additionally, these results reinforce the capacity of the PoDA analysis to identify genes that may be missed by more traditional GWAS methods. This study lays the groundwork for further investigations into the identified genes and pathways, and how they behave differently within males and females.
ContributorsOlson, Erik Jon (Author) / Buetow, Kenneth (Thesis advisor) / Wilson, Melissa (Committee member) / Cartwright, Reed (Committee member) / Arizona State University (Publisher)
Created2021
161797-Thumbnail Image.png
Description
This dissertation aims to study the electron and spin transport, scattering in two dimensional pseudospin-1 lattice systems, hybrid systems of topological insulator and magnetic insulators, and molecule chain systems. For pseudospin-1 systems, the energy band consists of a pair of Dirac cones and a flat band through the connecting point

This dissertation aims to study the electron and spin transport, scattering in two dimensional pseudospin-1 lattice systems, hybrid systems of topological insulator and magnetic insulators, and molecule chain systems. For pseudospin-1 systems, the energy band consists of a pair of Dirac cones and a flat band through the connecting point of the cones. First, contrary to the conditional wisdom that flatband can localize electrons, I find that in a non-equilibrium situation where a constant electric field is suddenly switched on, the flat band can enhance the resulting current in both the linear and nonlinear response regimes compared to spin-1/2 system. Second, in the setup of massive pseudospin-1 electron scattering over a gate potential scatterer, I discover the large resonant skew scattering called super skew scattering, which does not arise in the corresponding spin-1/2 system and massless pseudospin-1 system. Third, by applying an appropriate gate voltage to generate a cavity in an alpha-T3 lattice, I find the exponential decay of the quasiparticles from a chaotic cavity, with a one-to-one correspondence between the exponential decay rate and the Berry phase for the entire family of alpha-T3 materials. Based on the hybrid system of a ferromagnetic insulator on top of a topological insulator, I first investigate the magnetization dynamics of a pair of ferromagnetic insulators deposited on the surface of a topological insulator. The spin polarized current on the surface of topological insulator can affect the magnetization of the two ferromagnetic insulators through proximity effect, which in turn modulates the electron transport, giving rise to the robust phase locking between the two magnetization dynamics. Second, by putting a skyrmion structure on top of a topological insulator, I find robust electron skew scattering against skyrmion structure even with deformation, due to the emergence of resonant modes. The chirality of molecule can lead to spin polarized transport due to the spin orbit interaction. I investigate spin transport through a chiral polyacetylene molecule and uncover the emergence of spin Fano resonances as a manifestation of the chiral induced spin selectivity effect.
ContributorsWang, Chengzhen (Author) / Lai, Ying-Cheng (Thesis advisor) / Yu, Hongbin (Committee member) / Wang, Chao (Committee member) / Zhao, Yuji (Committee member) / Arizona State University (Publisher)
Created2021
129561-Thumbnail Image.png
Description

Extreme events, a type of collective behavior in complex networked dynamical systems, often can have catastrophic consequences. To develop effective strategies to control extreme events is of fundamental importance and practical interest. Utilizing transportation dynamics on complex networks as a prototypical setting, we find that making the network “mobile” can

Extreme events, a type of collective behavior in complex networked dynamical systems, often can have catastrophic consequences. To develop effective strategies to control extreme events is of fundamental importance and practical interest. Utilizing transportation dynamics on complex networks as a prototypical setting, we find that making the network “mobile” can effectively suppress extreme events. A striking, resonance-like phenomenon is uncovered, where an optimal degree of mobility exists for which the probability of extreme events is minimized. We derive an analytic theory to understand the mechanism of control at a detailed and quantitative level, and validate the theory numerically. Implications of our finding to current areas such as cybersecurity are discussed.

ContributorsChen, Yu-Zhong (Author) / Huang, Zi-Gang (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-08-18
129568-Thumbnail Image.png
Description

We develop a completely data-driven approach to reconstructing coupled neuronal networks that contain a small subset of chaotic neurons. Such chaotic elements can be the result of parameter shift in their individual dynamical systems and may lead to abnormal functions of the network. To accurately identify the chaotic neurons may

We develop a completely data-driven approach to reconstructing coupled neuronal networks that contain a small subset of chaotic neurons. Such chaotic elements can be the result of parameter shift in their individual dynamical systems and may lead to abnormal functions of the network. To accurately identify the chaotic neurons may thus be necessary and important, for example, applying appropriate controls to bring the network to a normal state. However, due to couplings among the nodes, the measured time series, even from non-chaotic neurons, would appear random, rendering inapplicable traditional nonlinear time-series analysis, such as the delay-coordinate embedding method, which yields information about the global dynamics of the entire network. Our method is based on compressive sensing. In particular, we demonstrate that identifying chaotic elements can be formulated as a general problem of reconstructing the nodal dynamical systems, network connections and all coupling functions, as well as their weights. The working and efficiency of the method are illustrated by using networks of non-identical FitzHugh–Nagumo neurons with randomly-distributed coupling weights.

ContributorsSu, Riqi (Author) / Lai, Ying-Cheng (Author) / Wang, Xiao (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-07-01
129524-Thumbnail Image.png
Description

The relation between flux and fluctuation is fundamental to complex physical systems that support and transport flows. A recently obtained law predicts monotonous enhancement of fluctuation as the average flux is increased, which in principle is valid but only for large systems. For realistic complex systems of small sizes, this

The relation between flux and fluctuation is fundamental to complex physical systems that support and transport flows. A recently obtained law predicts monotonous enhancement of fluctuation as the average flux is increased, which in principle is valid but only for large systems. For realistic complex systems of small sizes, this law breaks down when both the average flux and fluctuation become large. Here we demonstrate the failure of this law in small systems using real data and model complex networked systems, derive analytically a modified flux-fluctuation law, and validate it through computations of a large number of complex networked systems. Our law is more general in that its predictions agree with numerics and it reduces naturally to the previous law in the limit of large system size, leading to new insights into the flow dynamics in small-size complex systems with significant implications for the statistical and scaling behaviors of small systems, a topic of great recent interest.

ContributorsHuang, Zi-Gang (Author) / Dong, Jia-Qi (Author) / Huang, Liang (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-10-27
129462-Thumbnail Image.png
Description

We develop a general framework to analyze the controllability of multiplex networks using multiple-relation networks and multiple-layer networks with interlayer couplings as two classes of prototypical systems. In the former, networks associated with different physical variables share the same set of nodes and in the latter, diffusion processes take place.

We develop a general framework to analyze the controllability of multiplex networks using multiple-relation networks and multiple-layer networks with interlayer couplings as two classes of prototypical systems. In the former, networks associated with different physical variables share the same set of nodes and in the latter, diffusion processes take place. We find that, for a multiple-relation network, a layer exists that dominantly determines the controllability of the whole network and, for a multiple-layer network, a small fraction of the interconnections can enhance the controllability remarkably. Our theory is generally applicable to other types of multiplex networks as well, leading to significant insights into the control of complex network systems with diverse structures and interacting patterns.

ContributorsYuan, Zhengzhong (Author) / Zhao, Chen (Author) / Wang, Wen-Xu (Author) / Di, Zengru (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-10-24
129477-Thumbnail Image.png
Description

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

ContributorsCheng, Hongyan (Author) / Yao, Nan (Author) / Huang, Zi-Gang (Author) / Park, Junpyo (Author) / Do, Younghae (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-12-15
129346-Thumbnail Image.png
Description

An outstanding and fundamental problem in contemporary physics is to include and probe the many-body effect in the study of relativistic quantum manifestations of classical chaos. We address this problem using graphene systems described by the Hubbard Hamiltonian in the setting of resonant tunneling. Such a system consists of two

An outstanding and fundamental problem in contemporary physics is to include and probe the many-body effect in the study of relativistic quantum manifestations of classical chaos. We address this problem using graphene systems described by the Hubbard Hamiltonian in the setting of resonant tunneling. Such a system consists of two symmetric potential wells separated by a potential barrier, and the geometric shape of the whole domain can be chosen to generate integrable or chaotic dynamics in the classical limit. Employing a standard mean-field approach to calculating a large number of eigenenergies and eigenstates, we uncover a class of localized states with near-zero tunneling in the integrable systems. These states are not the edge states typically seen in graphene systems, and as such they are the consequence of many-body interactions. The physical origin of the non-edge-state type of localized states can be understood by the one-dimensional relativistic quantum tunneling dynamics through the solutions of the Dirac equation with appropriate boundary conditions. We demonstrate that, when the geometry of the system is modified to one with chaos, the localized states are effectively removed, implying that in realistic situations where many-body interactions are present, classical chaos is capable of facilitating greatly quantum tunneling. This result, besides its fundamental importance, can be useful for the development of nanoscale devices such as graphene-based resonant-tunneling diodes.

ContributorsYing, Lei (Author) / Wang, Guanglei (Author) / Huang, Liang (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-12-16
129347-Thumbnail Image.png
Description

Dynamical systems based on the minority game (MG) have been a paradigm for gaining significant insights into a variety of social and biological behaviors. Recently, a grouping phenomenon has been unveiled in MG systems of multiple resources (strategies) in which the strategies spontaneously break into an even number of groups,

Dynamical systems based on the minority game (MG) have been a paradigm for gaining significant insights into a variety of social and biological behaviors. Recently, a grouping phenomenon has been unveiled in MG systems of multiple resources (strategies) in which the strategies spontaneously break into an even number of groups, each exhibiting an identical oscillation pattern in the attendance of game players. Here we report our finding of spontaneous breakup of resources into three groups, each exhibiting period-three oscillations. An analysis is developed to understand the emergence of the striking phenomenon of triple grouping and period-three oscillations. In the presence of random disturbances, the triple-group/period-three state becomes transient, and we obtain explicit formula for the average transient lifetime using two methods of approximation. Our finding indicates that, period-three oscillation, regarded as one of the most fundamental behaviors in smooth nonlinear dynamical systems, can also occur in much more complex, evolutionary-game dynamical systems. Our result also provides a plausible insight for the occurrence of triple grouping observed, for example, in the U.S. housing market.

ContributorsDong, Jia-Qi (Author) / Huang, Zi-Gang (Author) / Huang, Liang (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-12-23
129362-Thumbnail Image.png
Description

The interplay between individual behaviors and epidemic dynamics in complex networks is a topic of recent interest. In particular, individuals can obtain different types of information about the disease and respond by altering their behaviors, and this can affect the spreading dynamics, possibly in a significant way. We propose a

The interplay between individual behaviors and epidemic dynamics in complex networks is a topic of recent interest. In particular, individuals can obtain different types of information about the disease and respond by altering their behaviors, and this can affect the spreading dynamics, possibly in a significant way. We propose a model where individuals' behavioral response is based on a generic type of local information, i.e., the number of neighbors that has been infected with the disease. Mathematically, the response can be characterized by a reduction in the transmission rate by a factor that depends on the number of infected neighbors. Utilizing the standard susceptible-infected-susceptible and susceptible-infected-recovery dynamical models for epidemic spreading, we derive a theoretical formula for the epidemic threshold and provide numerical verification. Our analysis lays on a solid quantitative footing the intuition that individual behavioral response can in general suppress epidemic spreading. Furthermore, we find that the hub nodes play the role of “double-edged sword” in that they can either suppress or promote outbreak, depending on their responses to the epidemic, providing additional support for the idea that these nodes are key to controlling epidemic spreading in complex networks.

ContributorsZhang, Haifeng (Author) / Xie, Jia-Rong (Author) / Tang, Ming (Author) / Lai, Ying-Cheng (Author) / Ira A. Fulton Schools of Engineering (Contributor)
Created2014-12-01