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- Creators: Arizona State University
- Creators: Danvers, Alexander
- Status: Published
Description
Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.
ContributorsGlembo, Tyler J (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
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
The tools developed for the use of investigating dynamical systems have provided critical understanding to a wide range of physical phenomena. Here these tools are used to gain further insight into scalar transport, and how it is affected by mixing. The aim of this research is to investigate the efficiency of several different partitioning methods which demarcate flow fields into dynamically distinct regions, and the correlation of finite-time statistics from the advection-diffusion equation to these regions.
For autonomous systems, invariant manifold theory can be used to separate the system into dynamically distinct regions. Despite there being no equivalent method for nonautonomous systems, a similar analysis can be done. Systems with general time dependencies must resort to using finite-time transport barriers for partitioning; these barriers are the edges of Lagrangian coherent structures (LCS), the analog to the stable and unstable manifolds of invariant manifold theory. Using the coherent structures of a flow to analyze the statistics of trapping, flight, and residence times, the signature of anomalous diffusion are obtained.
This research also investigates the use of linear models for approximating the elements of the covariance matrix of nonlinear flows, and then applying the covariance matrix approximation over coherent regions. The first and second-order moments can be used to fully describe an ensemble evolution in linear systems, however there is no direct method for nonlinear systems. The problem is only compounded by the fact that the moments for nonlinear flows typically don't have analytic representations, therefore direct numerical simulations would be needed to obtain the moments throughout the domain. To circumvent these many computations, the nonlinear system is approximated as many linear systems for which analytic expressions for the moments exist. The parameters introduced in the linear models are obtained locally from the nonlinear deformation tensor.
For autonomous systems, invariant manifold theory can be used to separate the system into dynamically distinct regions. Despite there being no equivalent method for nonautonomous systems, a similar analysis can be done. Systems with general time dependencies must resort to using finite-time transport barriers for partitioning; these barriers are the edges of Lagrangian coherent structures (LCS), the analog to the stable and unstable manifolds of invariant manifold theory. Using the coherent structures of a flow to analyze the statistics of trapping, flight, and residence times, the signature of anomalous diffusion are obtained.
This research also investigates the use of linear models for approximating the elements of the covariance matrix of nonlinear flows, and then applying the covariance matrix approximation over coherent regions. The first and second-order moments can be used to fully describe an ensemble evolution in linear systems, however there is no direct method for nonlinear systems. The problem is only compounded by the fact that the moments for nonlinear flows typically don't have analytic representations, therefore direct numerical simulations would be needed to obtain the moments throughout the domain. To circumvent these many computations, the nonlinear system is approximated as many linear systems for which analytic expressions for the moments exist. The parameters introduced in the linear models are obtained locally from the nonlinear deformation tensor.
ContributorsWalker, Phillip (Author) / Tang, Wenbo (Thesis advisor) / Kostelich, Eric (Committee member) / Mahalov, Alex (Committee member) / Moustaoui, Mohamed (Committee member) / Platte, Rodrigo (Committee member) / Arizona State University (Publisher)
Created2018
Description
The growth of energy demands in recent years has been increasing faster than the expansion of transmission facility construction. This tendency cooperating with the continuous investing on the renewable energy resources drives the research, development, and construction of HVDC projects to create a more reliable, affordable, and environmentally friendly power grid.
Constructing the hybrid AC-HVDC grid is a significant move in the development of the HVDC techniques; the form of dc system is evolving from the point-to-point stand-alone dc links to the embedded HVDC system and the multi-terminal HVDC (MTDC) system. The MTDC is a solution for the renewable energy interconnections, and the MTDC grids can improve the power system reliability, flexibility in economic dispatches, and converter/cable utilizing efficiencies.
The dissertation reviews the HVDC technologies, discusses the stability issues regarding the ac and HVDC connections, proposes a novel power oscillation control strategy to improve system stability, and develops a nonlinear voltage droop control strategy for the MTDC grid.
To verify the effectiveness the proposed power oscillation control strategy, a long distance paralleled AC-HVDC transmission test system is employed. Based on the PSCAD/EMTDC platform simulation results, the proposed power oscillation control strategy can improve the system dynamic performance and attenuate the power oscillations effectively.
To validate the nonlinear voltage droop control strategy, three droop controls schemes are designed according to the proposed nonlinear voltage droop control design procedures. These control schemes are tested in a hybrid AC-MTDC system. The hybrid AC-MTDC system, which is first proposed in this dissertation, consists of two ac grids, two wind farms and a five-terminal HVDC grid connecting them. Simulation studies are performed in the PSCAD/EMTDC platform. According to the simulation results, all the three design schemes have their unique salient features.
Constructing the hybrid AC-HVDC grid is a significant move in the development of the HVDC techniques; the form of dc system is evolving from the point-to-point stand-alone dc links to the embedded HVDC system and the multi-terminal HVDC (MTDC) system. The MTDC is a solution for the renewable energy interconnections, and the MTDC grids can improve the power system reliability, flexibility in economic dispatches, and converter/cable utilizing efficiencies.
The dissertation reviews the HVDC technologies, discusses the stability issues regarding the ac and HVDC connections, proposes a novel power oscillation control strategy to improve system stability, and develops a nonlinear voltage droop control strategy for the MTDC grid.
To verify the effectiveness the proposed power oscillation control strategy, a long distance paralleled AC-HVDC transmission test system is employed. Based on the PSCAD/EMTDC platform simulation results, the proposed power oscillation control strategy can improve the system dynamic performance and attenuate the power oscillations effectively.
To validate the nonlinear voltage droop control strategy, three droop controls schemes are designed according to the proposed nonlinear voltage droop control design procedures. These control schemes are tested in a hybrid AC-MTDC system. The hybrid AC-MTDC system, which is first proposed in this dissertation, consists of two ac grids, two wind farms and a five-terminal HVDC grid connecting them. Simulation studies are performed in the PSCAD/EMTDC platform. According to the simulation results, all the three design schemes have their unique salient features.
ContributorsYu, Jicheng (Author) / Karady, George G. (Thesis advisor, Committee member) / Qin, Jiangchao (Thesis advisor, Committee member) / Ayyanar, Raja (Committee member) / Holbert, Keith E. (Committee member) / Lei, Qin (Committee member) / Arizona State University (Publisher)
Created2017
Description
Basilisk lizards are often studied for their unique ability to run across the surface of
water. Due to the complicated fluid dynamics of this process, the forces applied on the
water’s surface cannot be measured using traditional methods. This thesis presents a
novel technique of measuring the forces using a fluid dynamic force platform (FDFP),
a light, rigid box immersed in water. This platform, along with a motion capture
system, can be used to characterize the kinematics and dynamics of a basilisk lizard
running on water. This could ultimately lead to robots that can run on water in a
similar manner.
water. Due to the complicated fluid dynamics of this process, the forces applied on the
water’s surface cannot be measured using traditional methods. This thesis presents a
novel technique of measuring the forces using a fluid dynamic force platform (FDFP),
a light, rigid box immersed in water. This platform, along with a motion capture
system, can be used to characterize the kinematics and dynamics of a basilisk lizard
running on water. This could ultimately lead to robots that can run on water in a
similar manner.
ContributorsSweeney, Andrew Joseph (Author) / Marvi, Hamidreza (Thesis advisor) / Lentink, David (Committee member) / Lee, Hyunglae (Committee member) / Arizona State University (Publisher)
Created2019
Description
When children allege sexual abuse, there is rarely medical evidence or eyewitnesses, making their testimony in trial a primary factor in assessing their credibility. However, little is known about what may be unclear to jury members making verdict decisions. In some districts, jury members are allowed to ask questions of the child witness at the end of their testimony. The current study utilizes a sample of trial transcripts from Maricopa County, Arizona where children ages 5-17 years old have alleged some form of sexual abuse; a jurisdiction where jury members are permitted to ask written questions. Cases were analyzed to assess: 1) if jury questions were asked and how often these questions occurred, 2) what content they asked about, and 3) whether occurrence or frequency of jury questions related to case characteristics (i.e. child age, child-perpetrator relationship, severity of abuse, frequency of abuse). It was hypothesized that 1) juries would ask questions mostly about the dynamics of abuse and disclosure, 2) these questions would primarily clarify information previously discussed by attorneys during direct- and cross-examination (instead of asking new inquiries that went undiscussed during testimony), 3) there would be more jury questions as child age increases and 4) more serious cases (based on case characteristics) would have more jury questions. Results were mixed. Jury members often asked about the dynamics of abuse and disclosure (abuse details, statements regarding abuse, the child’s subjective reactions), but case characteristics of child age, child-perpetrator relationship, and severity of abuse did not have a relationship with the presence of jury questions. However, cases where children alleged multiple instances of abuse were more likely to receive jury questions, which may allude to the misconception that children would disclose abuse right away and not let multiple instances occur. Although the sample size is small for generalization, it is an important first step for future research to further examine jury questions, improve attorney questioning techniques, and better educate the general public about the dynamics of child sexual abuse cases.
ContributorsGarcia-Johnson, Anastacia M (Author) / Stolzenberg, Stacia N. (Thesis advisor) / Fox, Kathleen A. (Committee member) / Chamberlain, Alyssa W. (Committee member) / Arizona State University (Publisher)
Created2019
Description
Sport is a widespread phenomenon across human cultures and history. Unfortunately, positive emotions in sport have been long vaguely characterized as happy or pleasant, or ignored altogether. Recent emotion research has taken a differentiated approach, however, suggesting there are distinct positive emotions with diverse implications for behavior. The present study applied this evolutionarily informed approach in the context of sport to examine which positive emotions are associated with play. It was hypothesized that pride, amusement, and enthusiasm, but not contentment or awe, would increase in Ultimate Frisbee players during a practice scrimmage. Further, it was hypothesized that increases in pride and amusement during practice would be differentially associated with sport outcomes, including performance (scores, assists, and defenses), subjective social connectedness, attributions of success, and attitudes toward the importance of practice. It was found that all positive emotions decreased during practice. It was also found that increases in pride were associated with more scores and greater social connectedness, whereas increases in amusement were associated with more assists. The present study was one of the first to examine change in positive emotions during play and to relate them to specific performance outcomes. Future studies should expand to determine which came first: emotion or performance.
ContributorsKuna, Jacob Anthony (Author) / Shiota, Michelle (Thesis director) / Glenberg, Arthur (Committee member) / Danvers, Alexander (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2014-05
Description
The purpose of this study was to examine the effects of two positive discrete emotions, awe and nurturant love, on implicit prejudices. After completing an emotion induction task, participants completed Implicit Association Test blocks where they paired photos of Arab and White individuals with "good" and "bad" evaluations. We hypothesized that nurturant love would increase the strength of negative evaluations of Arab individuals and positive evaluations of White individuals, whereas awe would decrease the strength of these negative evaluations when compared to a neutral condition. However, we found that both awe and nurturant love increased negative implicit prejudices toward Arab individuals when compared to the neutral condition.
ContributorsCarrasco, Mia Annette (Author) / Shiota, Michelle (Thesis director) / O'Neil, Makenzie (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The parent-child relationship is one of the earliest and most formative experiences for social and emotional development. Synchrony, defined as the rhythmic patterning and quality of mutual affect, engagement, and physiological attunement, has been identified as a critical quality of a healthy mother-infant relationship. Although the salience of the quality of family interaction has been well-established, clinical and developmental research has varied widely in methods for observing and identifying influential aspects of synchrony. In addition, modern dynamic perspectives presume multiple factors converge in a complex system influenced by both nature and nurture, in which individual traits, behavior, and environment are inextricably intertwined within the system of dyadic relational units.
The present study aimed to directly examine and compare synchrony from three distinct approaches: observed microanalytic behavioral sequences, observed global dyadic qualities, and physiological attunement between mothers and infants. The sample consisted of 323 Mexican American mothers and their infants followed from the third trimester of pregnancy through the first year of life. Mothers were interviewed prenatally, observed at a home visit at 12 weeks postpartum, and were finally interviewed for child social-emotional problems at child age 12 months. Specific aspects of synchrony (microanalytical, global, and physiological) were examined separately as well as together to identify comparable and divergent qualities within the construct.
Findings indicated that multiple perspectives on synchrony are best examined together, but as independent qualities to account for varying characteristics captured by divergent systems. Dyadic relationships characterized by higher reciprocity, more time and flexibility in mutual non-negative engagement, and less tendency to enter negative or unengaged states were associated with fewer child social-emotional problems at child age 12 months. Lower infant cortisol was associated with higher levels of externalizing problems, and smaller differences between mother and child cortisol were associated with higher levels of child dysregulation. Results underscore the complex but important nature of synchrony as a salient mechanism underlying the social-emotional growth of children. A mutually engaged, non-negative, and reciprocal environment lays the foundation for the successful social and self-regulatory competence of infants in the first year of life.
The present study aimed to directly examine and compare synchrony from three distinct approaches: observed microanalytic behavioral sequences, observed global dyadic qualities, and physiological attunement between mothers and infants. The sample consisted of 323 Mexican American mothers and their infants followed from the third trimester of pregnancy through the first year of life. Mothers were interviewed prenatally, observed at a home visit at 12 weeks postpartum, and were finally interviewed for child social-emotional problems at child age 12 months. Specific aspects of synchrony (microanalytical, global, and physiological) were examined separately as well as together to identify comparable and divergent qualities within the construct.
Findings indicated that multiple perspectives on synchrony are best examined together, but as independent qualities to account for varying characteristics captured by divergent systems. Dyadic relationships characterized by higher reciprocity, more time and flexibility in mutual non-negative engagement, and less tendency to enter negative or unengaged states were associated with fewer child social-emotional problems at child age 12 months. Lower infant cortisol was associated with higher levels of externalizing problems, and smaller differences between mother and child cortisol were associated with higher levels of child dysregulation. Results underscore the complex but important nature of synchrony as a salient mechanism underlying the social-emotional growth of children. A mutually engaged, non-negative, and reciprocal environment lays the foundation for the successful social and self-regulatory competence of infants in the first year of life.
ContributorsCoburn, Shayna Skelley (Author) / Crnic, Keith A (Thesis advisor) / Dishion, Thomas J (Committee member) / Mackinnon, David P (Committee member) / Luecken, Linda J. (Committee member) / Arizona State University (Publisher)
Created2015
Description
Unmanned aerial vehicles have received increased attention in the last decade due to their versatility, as well as the availability of inexpensive sensors (e.g. GPS, IMU) for their navigation and control. Multirotor vehicles, specifically quadrotors, have formed a fast growing field in robotics, with the range of applications spanning from surveil- lance and reconnaissance to agriculture and large area mapping. Although in most applications single quadrotors are used, there is an increasing interest in architectures controlling multiple quadrotors executing a collaborative task. This thesis introduces a new concept of control involving more than one quadrotors, according to which two quadrotors can be physically coupled in mid-flight. This concept equips the quadro- tors with new capabilities, e.g. increased payload or pursuit and capturing of other quadrotors. A comprehensive simulation of the approach is built to simulate coupled quadrotors. The dynamics and modeling of the coupled system is presented together with a discussion regarding the coupling mechanism, impact modeling and additional considerations that have been investigated. Simulation results are presented for cases of static coupling as well as enemy quadrotor pursuit and capture, together with an analysis of control methodology and gain tuning. Practical implementations are introduced as results show the feasibility of this design.
ContributorsLarsson, Daniel (Author) / Artemiadis, Panagiotis (Thesis advisor) / Marvi, Hamidreza (Committee member) / Berman, Spring (Committee member) / Arizona State University (Publisher)
Created2016