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- Creators: Wang, Xiao
- Creators: Rogers, Bradley
- Status: Published
Description
This dissertation treats a number of related problems in control and data analysis of complex networks.
First, in existing linear controllability frameworks, the ability to steer a network from any initiate state toward any desired state is measured by the minimum number of driver nodes. However, the associated optimal control energy can become unbearably large, preventing actual control from being realized. Here I develop a physical controllability framework and propose strategies to turn physically uncontrollable networks into physically controllable ones. I also discover that although full control can be guaranteed by the prevailing structural controllability theory, it is necessary to balance the number of driver nodes and control energy to achieve actual control, and my work provides a framework to address this issue.
Second, in spite of recent progresses in linear controllability, controlling nonlinear dynamical networks remains an outstanding problem. Here I develop an experimentally feasible control framework for nonlinear dynamical networks that exhibit multistability. The control objective is to apply parameter perturbation to drive the system from one attractor to another. I introduce the concept of attractor network and formulate a quantifiable framework: a network is more controllable if the attractor network is more strongly connected. I test the control framework using examples from various models and demonstrate the beneficial role of noise in facilitating control.
Third, I analyze large data sets from a diverse online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors: linear, “S”-shape and exponential growths. Inspired by cell population growth model in microbial ecology, I construct a base growth model for meme popularity in OSNs. Then I incorporate human interest dynamics into the base model and propose a hybrid model which contains a small number of free parameters. The model successfully predicts the various distinct meme growth dynamics.
At last, I propose a nonlinear dynamics model to characterize the controlling of WNT signaling pathway in the differentiation of neural progenitor cells. The model is able to predict experiment results and shed light on the understanding of WNT regulation mechanisms.
First, in existing linear controllability frameworks, the ability to steer a network from any initiate state toward any desired state is measured by the minimum number of driver nodes. However, the associated optimal control energy can become unbearably large, preventing actual control from being realized. Here I develop a physical controllability framework and propose strategies to turn physically uncontrollable networks into physically controllable ones. I also discover that although full control can be guaranteed by the prevailing structural controllability theory, it is necessary to balance the number of driver nodes and control energy to achieve actual control, and my work provides a framework to address this issue.
Second, in spite of recent progresses in linear controllability, controlling nonlinear dynamical networks remains an outstanding problem. Here I develop an experimentally feasible control framework for nonlinear dynamical networks that exhibit multistability. The control objective is to apply parameter perturbation to drive the system from one attractor to another. I introduce the concept of attractor network and formulate a quantifiable framework: a network is more controllable if the attractor network is more strongly connected. I test the control framework using examples from various models and demonstrate the beneficial role of noise in facilitating control.
Third, I analyze large data sets from a diverse online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors: linear, “S”-shape and exponential growths. Inspired by cell population growth model in microbial ecology, I construct a base growth model for meme popularity in OSNs. Then I incorporate human interest dynamics into the base model and propose a hybrid model which contains a small number of free parameters. The model successfully predicts the various distinct meme growth dynamics.
At last, I propose a nonlinear dynamics model to characterize the controlling of WNT signaling pathway in the differentiation of neural progenitor cells. The model is able to predict experiment results and shed light on the understanding of WNT regulation mechanisms.
ContributorsWang, Lezhi (Author) / Lai, Ying-Cheng (Thesis advisor) / Wang, Xiao (Thesis advisor) / Papandreoou-Suppappola, Antonia (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2017
Description
Synthetic biology is an emerging field which melds genetics, molecular biology, network theory, and mathematical systems to understand, build, and predict gene network behavior. As an engineering discipline, developing a mathematical understanding of the genetic circuits being studied is of fundamental importance. In this dissertation, mathematical concepts for understanding, predicting, and controlling gene transcriptional networks are presented and applied to two synthetic gene network contexts. First, this engineering approach is used to improve the function of the guide ribonucleic acid (gRNA)-targeted, dCas9-regulated transcriptional cascades through analysis and targeted modification of the RNA transcript. In so doing, a fluorescent guide RNA (fgRNA) is developed to more clearly observe gRNA dynamics and aid design. It is shown that through careful optimization, RNA Polymerase II (Pol II) driven gRNA transcripts can be strong enough to exhibit measurable cascading behavior, previously only shown in RNA Polymerase III (Pol III) circuits. Second, inherent gene expression noise is used to achieve precise fractional differentiation of a population. Mathematical methods are employed to predict and understand the observed behavior, and metrics for analyzing and quantifying similar differentiation kinetics are presented. Through careful mathematical analysis and simulation, coupled with experimental data, two methods for achieving ratio control are presented, with the optimal schema for any application being dependent on the noisiness of the system under study. Together, these studies push the boundaries of gene network control, with potential applications in stem cell differentiation, therapeutics, and bio-production.
ContributorsMenn, David J (Author) / Wang, Xiao (Thesis advisor) / Kiani, Samira (Committee member) / Haynes, Karmella (Committee member) / Nielsen, David (Committee member) / Marshall, Pamela (Committee member) / Arizona State University (Publisher)
Created2018
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
It remains unquestionable that space-based technology is an indispensable component of modern daily lives. Success or failure of space missions is largely contingent upon the complex system analysis and design methodologies exerted in converting the initial idea
into an elaborate functioning enterprise. It is for this reason that this dissertation seeks to contribute towards the search for simpler, efficacious and more reliable methodologies and tools that accurately model and analyze space systems dynamics. Inopportunely, despite the inimical physical hazards, space systems must endure a perturbing dynamical environment that persistently disorients spacecraft attitude, dislodges spacecraft from their designated orbital locations and compels spacecraft to follow undesired orbital trajectories. The ensuing dynamics’ analytical models are complexly structured, consisting of parametrically excited nonlinear systems with external periodic excitations–whose analysis and control is not a trivial task. Therefore, this dissertation’s objective is to overcome the limitations of traditional approaches (averaging and perturbation, linearization) commonly used to analyze and control such dynamics; and, further obtain more accurate closed-form analytical solutions in a lucid and broadly applicable manner. This dissertation hence implements a multi-faceted methodology that relies on Floquet theory, invariant center manifold reduction and normal forms simplification. At the heart of this approach is an intuitive system state augmentation technique that transforms non-autonomous nonlinear systems into autonomous ones. Two fitting representative types of space systems dynamics are investigated; i) attitude motion of a gravity gradient stabilized spacecraft in an eccentric orbit, ii) spacecraft motion in the vicinity of irregularly shaped small bodies. This investigation demonstrates how to analyze the motion stability, chaos, periodicity and resonance. Further, versal deformation of the normal forms scrutinizes the bifurcation behavior of the gravity gradient stabilized attitude motion. Control laws developed on transformed, more tractable analytical models show that; unlike linear control laws, nonlinear control strategies such as sliding mode control and bifurcation control stabilize the intricate, unwieldy astrodynamics. The pitch attitude dynamics are stabilized; and, a regular periodic orbit realized in the vicinity of small irregularly shaped bodies. Importantly, the outcomes obtained are unconventionally realized as closed-form analytical solutions obtained via the comprehensive approach introduced by this dissertation.
into an elaborate functioning enterprise. It is for this reason that this dissertation seeks to contribute towards the search for simpler, efficacious and more reliable methodologies and tools that accurately model and analyze space systems dynamics. Inopportunely, despite the inimical physical hazards, space systems must endure a perturbing dynamical environment that persistently disorients spacecraft attitude, dislodges spacecraft from their designated orbital locations and compels spacecraft to follow undesired orbital trajectories. The ensuing dynamics’ analytical models are complexly structured, consisting of parametrically excited nonlinear systems with external periodic excitations–whose analysis and control is not a trivial task. Therefore, this dissertation’s objective is to overcome the limitations of traditional approaches (averaging and perturbation, linearization) commonly used to analyze and control such dynamics; and, further obtain more accurate closed-form analytical solutions in a lucid and broadly applicable manner. This dissertation hence implements a multi-faceted methodology that relies on Floquet theory, invariant center manifold reduction and normal forms simplification. At the heart of this approach is an intuitive system state augmentation technique that transforms non-autonomous nonlinear systems into autonomous ones. Two fitting representative types of space systems dynamics are investigated; i) attitude motion of a gravity gradient stabilized spacecraft in an eccentric orbit, ii) spacecraft motion in the vicinity of irregularly shaped small bodies. This investigation demonstrates how to analyze the motion stability, chaos, periodicity and resonance. Further, versal deformation of the normal forms scrutinizes the bifurcation behavior of the gravity gradient stabilized attitude motion. Control laws developed on transformed, more tractable analytical models show that; unlike linear control laws, nonlinear control strategies such as sliding mode control and bifurcation control stabilize the intricate, unwieldy astrodynamics. The pitch attitude dynamics are stabilized; and, a regular periodic orbit realized in the vicinity of small irregularly shaped bodies. Importantly, the outcomes obtained are unconventionally realized as closed-form analytical solutions obtained via the comprehensive approach introduced by this dissertation.
ContributorsWASWA, PETER (Author) / Redkar, Sangram (Thesis advisor) / Rogers, Bradley (Committee member) / Sugar, Thomas (Committee member) / Arizona State University (Publisher)
Created2019
Description
Complex dynamical systems are the kind of systems with many interacting components that usually have nonlinear dynamics. Those systems exist in a wide range of disciplines, such as physical, biological, and social fields. Those systems, due to a large amount of interacting components, tend to possess very high dimensionality. Additionally, due to the intrinsic nonlinear dynamics, they have tremendous rich system behavior, such as bifurcation, synchronization, chaos, solitons. To develop methods to predict and control those systems has always been a challenge and an active research area.
My research mainly concentrates on predicting and controlling tipping points (saddle-node bifurcation) in complex ecological systems, comparing linear and nonlinear control methods in complex dynamical systems. Moreover, I use advanced artificial neural networks to predict chaotic spatiotemporal dynamical systems. Complex networked systems can exhibit a tipping point (a “point of no return”) at which a total collapse occurs. Using complex mutualistic networks in ecology as a prototype class of systems, I carry out a dimension reduction process to arrive at an effective two-dimensional (2D) system with the two dynamical variables corresponding to the average pollinator and plant abundances, respectively. I demonstrate that, using 59 empirical mutualistic networks extracted from real data, our 2D model can accurately predict the occurrence of a tipping point even in the presence of stochastic disturbances. I also develop an ecologically feasible strategy to manage/control the tipping point by maintaining the abundance of a particular pollinator species at a constant level, which essentially removes the hysteresis associated with tipping points.
Besides, I also find that the nodal importance ranking for nonlinear and linear control exhibits opposite trends: for the former, large degree nodes are more important but for the latter, the importance scale is tilted towards the small-degree nodes, suggesting strongly irrelevance of linear controllability to these systems. Focusing on a class of recurrent neural networks - reservoir computing systems that have recently been exploited for model-free prediction of nonlinear dynamical systems, I uncover a surprising phenomenon: the emergence of an interval in the spectral radius of the neural network in which the prediction error is minimized.
My research mainly concentrates on predicting and controlling tipping points (saddle-node bifurcation) in complex ecological systems, comparing linear and nonlinear control methods in complex dynamical systems. Moreover, I use advanced artificial neural networks to predict chaotic spatiotemporal dynamical systems. Complex networked systems can exhibit a tipping point (a “point of no return”) at which a total collapse occurs. Using complex mutualistic networks in ecology as a prototype class of systems, I carry out a dimension reduction process to arrive at an effective two-dimensional (2D) system with the two dynamical variables corresponding to the average pollinator and plant abundances, respectively. I demonstrate that, using 59 empirical mutualistic networks extracted from real data, our 2D model can accurately predict the occurrence of a tipping point even in the presence of stochastic disturbances. I also develop an ecologically feasible strategy to manage/control the tipping point by maintaining the abundance of a particular pollinator species at a constant level, which essentially removes the hysteresis associated with tipping points.
Besides, I also find that the nodal importance ranking for nonlinear and linear control exhibits opposite trends: for the former, large degree nodes are more important but for the latter, the importance scale is tilted towards the small-degree nodes, suggesting strongly irrelevance of linear controllability to these systems. Focusing on a class of recurrent neural networks - reservoir computing systems that have recently been exploited for model-free prediction of nonlinear dynamical systems, I uncover a surprising phenomenon: the emergence of an interval in the spectral radius of the neural network in which the prediction error is minimized.
ContributorsJiang, Junjie (Author) / Lai, Ying-Cheng (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / Wang, Xiao (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2020
Description
The inherent behavior of many real world applications tends to exhibit complex or chaotic patterns. A novel technique to reduce and analyze such complex systems is introduced in this work, and its applications to multiple perturbed systems are discussed comprehensively. In this work, a unified approach between the Floquet theory for time periodic systems and the Poincare theory of Normal Forms is proposed to analyze time varying systems. The proposed unified approach is initially verified for linear time periodic systems with the aid of an intuitive state augmentation and the method of Time Independent Normal Forms (TINF). This approach also resulted in the closed form expressions for the State Transition Matrix (STM) and Lyapunov-Floquet (L-F) transformation for linear time periodic systems. The application of theory towards stability analysis is further demonstrated with the system of Suction Stabilized Floating (SSF) platform. Additionally, multiple control strategies are discussed and implemented to drive an unstable time periodic system to a desired stable point or orbit efficiently and optimally. The computed L-F transformation is further utilized to analyze nonlinear and externally excited systems with deterministic and stochastic time periodic coefficients. The central theme of this work is to verify the extension of Floquet theory towards time varying systems with periodic coefficients comprising of incommensurate frequencies or quasi-periodic systems. As per Floquet theory, a Lyapunov-Perron (L-P) transformation converts a time-varying quasi-periodic system to a time-invariant form. A class of commutative quasi-periodic systems is introduced to demonstrate the proposed theory and its applications analytically. An extension of the proposed unified approach towards analyzing the linear quasi-periodic system is observed to provide good results, computationally less complex and widely applicable for strongly excited systems. The computed L-P transformation using the unified theory is applied to analyze both commutative and non-commutative linear quasi-periodic systems with nonlinear terms and external excitation terms. For highly nonlinear quasi-periodic systems, the implementation of multiple order reduction techniques and their performance comparisons are illustrated in this work. Finally, the robustness and stability analysis of nonlinearly perturbed and stochastically excited quasi-periodic systems are performed using Lyapunov's direct method and Infante's approach.
ContributorsCherangara Subramanian, Susheelkumar (Author) / Redkar, Sangram (Thesis advisor) / Rogers, Bradley (Committee member) / Sugar, Thomas (Committee member) / Arizona State University (Publisher)
Created2021