Interaction dynamics in small networks of nonlinear elements

We study a small circuit of coupled nonlinear elements to investigate general features of signal transmission through networks. The small circuit itself is perceived as building block for larger networks. Individual dynamics and coupling are motivated by neuronal systems: We consider two types of dynamical modes for an individual element, regular spiking and chattering and each individual element can receive excitatory and/or inhibitory inputs and is subjected to different feedback types (excitatory and inhibitory; forward and recurrent). Both, deterministic and stochastic simulations are carried out to study the input-output relationships of these networks. Major results for regular spiking elements include frequency locking, spike rate amplification for strong synaptic coupling, and inhibition-induced spike rate control which can be interpreted as a output frequency rectification. For chattering elements, spike rate amplification for low frequencies and silencing for large frequencies is characteristic

The critical role of intracavity dynamics in high-power mode-locked fiber lasers

We present a theoretical description of the generation of ultra-short, high-energy pulses in two laser cavities driven by periodic spectral filtering or dispersion management. Critical in driving the intra-cavity dynamics is the nontrivial phase profiles generated and their periodic modification from either spectral filtering or dispersion management. For laser cavities with a spectral filter, the theory gives a simple geometrical description of the intra-cavity dynamics and provides a simple and efficient method for optimizing the laser cavity performance. In the dispersion managed cavity, analysis shows the generated self-similar behavior to be governed by the porous media equation with a rapidly-varying, mean-zero diffusion coefficient whose solution is the well-known Barenblatt similarity solution with parabolic profile. © 2010 Copyright SPIE - The International Society for Optical Engineering.

Characterizing the transition dynamics for multi-pulsing in mode-locked lasers

We consider experimentally and theoretically a refined parameter space near the transition to multi-pulse modelocking. Near the transition, the onset of instability is initiated by a Hopf (periodic) bifurcation. As cavity energy is increased, the band of unstable, oscillatory modes generates a chaotic behavior between single- and multi-pulse operation. Both theory and experiment are in good qualitative agreement and they suggest that the phenomenon is of a universal nature in mode-locked lasers at the onset of multi-pulsing from N to N + 1 pulses per round trip. This is the first theoretical and experimental characterization of the transition behavior, made possible by a highly refined tuning of the gain pump level. © 2010 Copyright SPIE - The International Society for Optical Engineering.

Geographic Information Systems-Based Approaches to Study Congressional Redistricting in the United States

The ability for the citizens of a nation to determine their own representation has long been regarded as one of the most critical objectives of any electoral system. Without having the assurance of equality in representation, the fundamental nature and operation of the political system is severely undermined. Given the centuries of institutional reforms and population changes in the American system, Congressional Redistricting stands as an institution whereby this promise of effective representation can either be fulfilled or denied. The broad set of processes that encapsulate Congres- sional Redistricting have been discussed, experimented, and modified to achieve clear objectives and have long been understood to be important. Questions remain about how the dynamics which link all of these processes operate and what impact the real- ities of Congressional Redistricting hold for representation in the American system. This dissertation examines three aspects of how Congressional Redistricting in the Untied States operates in accordance with the principle of “One Person, One Vote.” By utilizing data and data analysis techniques of Geographic Information Systems (GIS), this dissertation seeks to address how Congressional Redistricting impacts the principle of one person, one vote from the standpoint of legislator accountability, redistricting institutions, and the promise of effective minority representation.

Dynamics of the Disk-Pendulum Coupled System With Vertical Excitation

This paper investigates the static and dynamic characteristics of the semi-elliptical rocking disk on which a pendulum pinned. This coupled system’s response is also analyzed analytically and numerically when a vertical harmonic excitation is applied to the bottom of the rocking disk. Lagrange’s Equation is used to derive the motion equations of the disk-pendulum coupled system. The second derivative test for the system’s potential energy shows how the location of the pendulum’s pivotal point affects the number and stability of equilibria, and the change of location presents different bifurcation diagrams for different geometries of the rocking disk. For both vertically excited and unforced cases, the coupled system shows chaos easily, but the proper chosen parameters can still help the system reach and keep the steady state. For the steady state of the vertically excited rocking disk without a pendulum, the variation of the excitation’s amplitude and frequency result in the hysteresis for the amplitude of the response. When a pendulum is pinned on the rocking disk, three major categories of steady states are presently in the numerical way.

Theory and Practice in Sustainability Science: Influence of Urban Form on the Urban Heat Island and Implications for Urban Systems

As the world population continues to grow past seven billion people and global challenges continue to persist including resource availability, biodiversity loss, climate change and human well-being, a new science is required that can address the integrated nature of these challenges and the multiple scales on which they are manifest. Sustainability science has emerged to fill this role. In the fifteen years since it was first called for in the pages of Science, it has rapidly matured, however its place in the history of science and the way it is practiced today must be continually evaluated. In Part I, two chapters address this theoretical and practical grounding. Part II transitions to the applied practice of sustainability science in addressing the urban heat island (UHI) challenge wherein the climate of urban areas are warmer than their surrounding rural environs. The UHI has become increasingly important within the study of earth sciences given the increased focus on climate change and as the balance of humans now live in urban areas.

In Chapter 2 a novel contribution to the historical context of sustainability is argued. Sustainability as a concept characterizing the relationship between humans and nature emerged in the mid to late 20th century as a response to findings used to also characterize the Anthropocene. Emerging from the human-nature relationships that came before it, evidence is provided that suggests Sustainability was enabled by technology and a reorientation of world-view and is unique in its global boundary, systematic approach and ambition for both well being and the continued availability of resources and Earth system function. Sustainability is further an ambition that has wide appeal, making it one of the first normative concepts of the Anthropocene.

Despite its widespread emergence and adoption, sustainability science continues to suffer from definitional ambiguity within the academe. In Chapter 3, a review of efforts to provide direction and structure to the science reveals a continuum of approaches anchored at either end by differing visions of how the science interfaces with practice (solutions). At one end, basic science of societally defined problems informs decisions about possible solutions and their application. At the other end, applied research directly affects the options available to decision makers. While clear from the literature, survey data further suggests that the dichotomy does not appear to be as apparent in the minds of practitioners.

In Chapter 4, the UHI is first addressed at the synoptic, mesoscale. Urban climate is the most immediate manifestation of the warming global climate for the majority of people on earth. Nearly half of those people live in small to medium sized cities, an understudied scale in urban climate research. Widespread characterization would be useful to decision makers in planning and design. Using a multi-method approach, the mesoscale UHI in the study region is characterized and the secular trend over the last sixty years evaluated. Under isolated ideal conditions the findings indicate a UHI of 5.3 ± 0.97 °C to be present in the study area, the magnitude of which is growing over time.

Although urban heat islands (UHI) are well studied, there remain no panaceas for local scale mitigation and adaptation methods, therefore continued attention to characterization of the phenomenon in urban centers of different scales around the globe is required. In Chapter 5, a local scale analysis of the canopy layer and surface UHI in a medium sized city in North Carolina, USA is conducted using multiple methods including stationary urban sensors, mobile transects and remote sensing. Focusing on the ideal conditions for UHI development during an anticyclonic summer heat event, the study observes a range of UHI intensity depending on the method of observation: 8.7 °C from the stationary urban sensors; 6.9 °C from mobile transects; and, 2.2 °C from remote sensing. Additional attention is paid to the diurnal dynamics of the UHI and its correlation with vegetation indices, dewpoint and albedo. Evapotranspiration is shown to drive dynamics in the study region.

Finally, recognizing that a bridge must be established between the physical science community studying the Urban Heat Island (UHI) effect, and the planning community and decision makers implementing urban form and development policies, Chapter 6 evaluates multiple urban form characterization methods. Methods evaluated include local climate zones (LCZ), national land cover database (NCLD) classes and urban cluster analysis (UCA) to determine their utility in describing the distribution of the UHI based on three standard observation types 1) fixed urban temperature sensors, 2) mobile transects and, 3) remote sensing. Bivariate, regression and ANOVA tests are used to conduct the analyses. Findings indicate that the NLCD classes are best correlated to the UHI intensity and distribution in the study area. Further, while the UCA method is not useful directly, the variables included in the method are predictive based on regression analysis so the potential for better model design exists. Land cover variables including albedo, impervious surface fraction and pervious surface fraction are found to dominate the distribution of the UHI in the study area regardless of observation method.

Chapter 7 provides a summary of findings, and offers a brief analysis of their implications for both the scientific discourse generally, and the study area specifically. In general, the work undertaken does not achieve the full ambition of sustainability science, additional work is required to translate findings to practice and more fully evaluate adoption. The implications for planning and development in the local region are addressed in the context of a major light-rail infrastructure project including several systems level considerations like human health and development. Finally, several avenues for future work are outlined. Within the theoretical development of sustainability science, these pathways include more robust evaluations of the theoretical and actual practice. Within the UHI context, these include development of an integrated urban form characterization model, application of study methodology in other geographic areas and at different scales, and use of novel experimental methods including distributed sensor networks and citizen science.

Role of Vinculin in Regulating Force-Sensitive Dynamics of Adherens Junctions During Collective Cell Migration

Dynamic processes such as morphogenesis and tissue patterning require the precise control of many cellular processes, especially cell migration. Historically, these processes are thought to be mediated by genetic and biochemical signaling pathways. However, recent advances have unraveled a previously unappreciated role of mechanical forces in regulating these homeostatic processes in of multicellular systems. In multicellular systems cells adhere to both deformable extracellular matrix (ECM) and other cells, which are sources of applied forces and means of mechanical support. Cells detect and respond to these mechanical signals through a poorly understood process called mechanotransduction, which can have profound effects on processes such as cell migration. These effects are largely mediated by the sub cellular structures that link cells to the ECM, called focal adhesions (FAs), or cells to other cells, termed adherens junctions (AJs).

Overall this thesis is comprised of my work on identifying a novel force dependent function of vinculin, a protein which resides in both FAs and AJs - in dynamic process of collective migration. Using a collective migration assay as a model for collective cell behavior and a fluorescence resonance energy transfer (FRET) based molecular tension sensor for vinculin I demonstrated a spatial gradient of tension across vinculin in the direction of migration. To define this novel force-dependent role of vinculin in collective migration I took advantage of previously established shRNA based vinculin knock down Marin-Darby Canine Kidney (MDCK) epithelial cells.

The first part of my thesis comprises of my work demonstrating the mechanosensitive role of vinculin at AJ’s in collectively migrating cells. Using vinculin knockdown cells and vinculin mutants, which specifically disrupt vinculin’s ability to bind actin (VinI997A) or disrupt its ability to localize to AJs without affecting its localization at FAs (VinY822F), I establish a role of force across vinculin in E-cadherin internalization and clipping. Furthermore by measuring E-cadherin dynamics using fluorescence recovery after bleaching (FRAP) analysis I show that vinculin inhibition affects the turnover of E-cadherin at AJs. Together these data reveal a novel mechanosensitive role of vinculin in E-cadherin internalization and turnover in a migrating cell layer, which is contrary to the previously identified role of vinculin in potentiating E-cadherin junctions in a static monolayer.

For the last part of my thesis I designed a novel tension sensor to probe tension across N-cadherin (NTS). N-cadherin plays a critical role in cardiomyocytes, vascular smooth muscle cells, neurons and neural crest cells. Similar to E-cadherin, N-cadherin is also believed to bear tension and play a role in mechanotransduction pathways. To identify the role of tension across N-cadherin I designed a novel FRET-based molecular tension sensor for N-cadherin. I tested the ability of NTS to sense molecular tension in vascular smooth muscle cells, cardiomyocytes and cancer cells. Finally in collaboration with the Horwitz lab we have been able to show a role of tension across N-cadherin in synaptogenesis of neurons.

Degeneracy of velocity constraints in rigid body systems

The equations governing the dynamics of rigid body systems with velocity constraints are singular at degenerate configurations in the constraint distribution. In this report, we describe the causes of singularities in the constraint distribution of interconnected rigid body systems with smooth configuration manifolds. A convention of defining primary velocity constraints in terms of orthogonal complements of one-dimensional subspaces is introduced. Using this convention, linear maps are defined and used to describe the space of allowable velocities of a rigid body. Through the definition of these maps, we present a condition for non-degeneracy of velocity constraints in terms of the one dimensional subspaces defining the primary velocity constraints. A method for defining the constraint subspace and distribution in terms of linear maps is presented. Using these maps, the constraint distribution is shown to be singular at configuration where there is an increase in its dimension.

Molecular docking and geographical information systems as tools to assess the potential impact of veterinary medicines on non-target organisms and the environment

Veterinary medicines (VMs) from agricultural industry can enter the environment in a number of ways. This includes direct exposure through aquaculture, accidental spillage and disposal, and indirect entry by leaching from manure or runoff after treatment. Many compounds used in animal treatments have ecotoxic properties that may have chronic or sometimes lethal effects when they come into contact with non-target organisms. VMs enter the environment in mixtures, potentially having additive effects. Traditional ecotoxicology tests are used to determine the lethal and sometimes reproductive effects on freshwater and terrestrial organisms. However, organisms used in ecotoxicology tests can be unrepresentative of the populations that are likely to be exposed to the compound in the environment. Most often the tests are on single compound toxicity but mixture effects may be significant and should be included in ecotoxicology testing. This work investigates the use, measured environmental concentrations (MECs) and potential impact of sea lice treatments on salmon farms in Scotland. Alternative methods for ecotoxicology testing including mixture toxicity, and the use of in silico techniques to predict the chronic impact of VMs on different species of aquatic organisms were also investigated. The Scottish Environmental Protection Agency (SEPA) provided information on the use of five sea lice treatments from 2008-2011 on Scottish salmon farms. This information was combined with the recently available data on sediment MECs for the years 2009-2012 provided by SEPA using ArcGIS 10.1. In depth analysis of this data showed that from a total of 55 sites, 30 sites had a MEC higher than the maximum allowable concentration (MAC) as set out by SEPA for emamectin benzoate and 7 sites had a higher MEC than MAC for teflubenzuron. A number of sites that were up to 16 km away from the nearest salmon farm reported as using either emamectin benzoate or teflubenzuron measured positive for the two treatments. There was no relationship between current direction and the distribution of the sea lice treatments, nor was there any evidence for alternative sources of the compounds e.g. land treatments. The sites that had MECs higher than the MAC could pose a risk to non-target organisms and disrupt the species dynamics of the area. There was evidence that some marine protected sites might be at risk of exposure to these compounds. To complement this work, effects on acute mixture toxicity of the 5 sea lice treatments, plus one major metabolite 3-phenoxybenzoic acid (3PBA), were measured using an assay using the bioluminescent bacteria Aliivibrio fischeri. When exposed to the 5 sea lice treatments and 3PBA A. fischeri showed a response to 3PBA, emamectin benzoate and azamethiphos as well as combinations of the three. In order to establish any additive effect of the sea lice treatments, the efficacy of two mixture prediction equations, concentration addition (CA) and independent action ii(IA) were tested using the results from single compound dose response curves. In this instance IA was the more effective prediction method with a linear regression confidence interval of 82.6% compared with 22.6% of CA. In silico molecular docking was carried out to predict the chronic effects of 15 VMs (including the five used as sea lice control). Molecular docking has been proposed as an alternative screening method for the chronic effects of large animal treatments on non-target organisms. Oestrogen receptor alpha (ERα) of 7 non-target bony fish and the African clawed frog Xenopus laevis were modelled using SwissModel. These models were then ‘docked’ to oestradiol, the synthetic oestrogen ethinylestradiol, two known xenoestrogens dichlorodiphenyltrichloroethane (DDT) and bisphenol A (BPA), the antioestrogen breast cancer treatment tamoxifen and 15 VMs using Auto Dock 4. Based on the results of this work, four VMs were identified as being possible xenoestrogens or anti-oestrogens; these were cypermethrin, deltamethrin, fenbendazole and teflubenzuron. Further investigation, using in vitro assays, into these four VMs has been suggested as future work. A modified recombinant yeast oestrogen screen (YES) was attempted using the cDNA of the ERα of the zebrafish Danio rerio and the rainbow trout Oncorhynchus mykiss. Due to time and difficulties in cloning protocols this work was unable to be completed. Use of such in vitro assays would allow for further investigation of the highlighted VMs into their oestrogenic potential. In conclusion, VMs used as sea lice treatments, such as teflubenzuron and emamectin benzoate may be more persistent and have a wider range in the environment than previously thought. Mixtures of sea lice treatments have been found to persist together in the environment, and effects of these mixtures on the bacteria A. fischeri can be predicted using the IA equation. Finally, molecular docking may be a suitable tool to predict chronic endocrine disrupting effects and identify varying degrees of impact on the ERα of nine species of aquatic organisms.

Projected equations of motion approach to hybrid quantum/classical dynamics in dielectric-metal composites

We introduce a hybrid method for dielectric-metal composites that describes the dynamics of the metallic system classically whilst retaining a quantum description of the dielectric. The time-dependent dipole moment of the classical system is mimicked by the introduction of projected equations of motion (PEOM) and the coupling between the two systems is achieved through an effective dipole-dipole interaction. To benchmark this method, we model a test system (semiconducting quantum dot-metal nanoparticle hybrid). We begin by examining the energy absorption rate, showing agreement between the PEOM method and the analytical rotating wave approximation (RWA) solution. We then investigate population inversion and show that the PEOM method provides an accurate model for the interaction under ultrashort pulse excitation where the traditional RWA breaks down.

A novel methodology for analysis of large scale interconnected power and gas systems

The European Union continues to exert a large influence on the direction of member states energy policy. The 2020 targets for renewable energy integration have had significant impact on the operation of current power systems, forcing a rapid change from fossil fuel dominated systems to those with high levels of renewable power. Additionally, the overarching aim of an internal energy market throughout Europe has and will continue to place importance on multi-jurisdictional co-operation regarding energy supply. Combining these renewable energy and multi-jurisdictional supply goals results in a complicated multi-vector energy system, where the understanding of interactions between fossil fuels, renewable energy, interconnection and economic power system operation is increasingly important. This paper provides a novel and systematic methodology to fully understand the changing dynamics of interconnected energy systems from a gas and power perspective. A fully realistic unit commitment and economic dispatch model of the 2030 power systems in Great Britain and Ireland, combined with a representative gas transmission energy flow model is developed. The importance of multi-jurisdictional integrated energy system operation in one of the most strategically important renewable energy regions is demonstrated.

Methods, Models & Systems for Dealing with Some Business, Management & Engineering Problems

This keynote presentation will report some of our research work and experience on the development and applications of relevant methods, models, systems and simulation techniques in support of different types and various levels of decision making for business, management and engineering. In particular, the following topics will be covered. Modelling, multi-agent-based simulation and analysis of the allocation management of carbon dioxide emission permits in China (Nanfeng Liu & Shuliang Li Agent-based simulation of the dynamic evolution of enterprise carbon assets (Yin Zeng & Shuliang Li) A framework & system for extracting and representing project knowledge contexts using topic models and dynamic knowledge maps: a big data perspective (Jin Xu, Zheng Li, Shuliang Li & Yanyan Zhang) Open innovation: intelligent model, social media & complex adaptive system simulation (Shuliang Li & Jim Zheng Li) A framework, model and software prototype for modelling and simulation for deshopping behaviour and how companies respond (Shawkat Rahman & Shuliang Li) Integrating multiple agents, simulation, knowledge bases and fuzzy logic for international marketing decision making (Shuliang Li & Jim Zheng Li) A Web-based hybrid intelligent system for combined conventional, digital, mobile, social media and mobile marketing strategy formulation (Shuliang Li & Jim Zheng Li) A hybrid intelligent model for Web & social media dynamics, and evolutionary and adaptive branding (Shuliang Li) A hybrid paradigm for modelling, simulation and analysis of brand virality in social media (Shuliang Li & Jim Zheng Li) Network configuration management: attack paradigms and architectures for computer network survivability (Tero Karvinen & Shuliang Li)

The Role of Corals on Tsunami Dynamics in an Island Setting: A Case Study of Tutuila Island

Thesis (Ph.D.)--University of Washington, 2016-07

Machine learning and data decompositions for complex networked dynamical systems

Thesis (Ph.D.)--University of Washington, 2016-08

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08