A General Framework for Complex Network Applications

Complex network theory has been applied to solving practical problems from different domains. In this paper, we present a general framework for complex network applications. The keys of a successful application are a thorough understanding of the real system and a correct mapping of complex network theory to practical problems in the system. Despite of certain limitations discussed in this paper, complex network theory provides a foundation on which to develop powerful tools in analyzing and optimizing large interconnected systems.Comment: 8 page

Reduced-order modeling of power electronics components and systems

This dissertation addresses the seemingly inevitable compromise between modeling fidelity and simulation speed in power electronics. Higher-order effects are considered at the component and system levels. Order-reduction techniques are applied to provide insight into accurate, computationally efficient component-level (via reduced-order physics-based model) and system-level simulations (via multiresolution simulation). Proposed high-order models, verified with hardware measurements, are, in turn, used to verify the accuracy of final reduced-order models for both small- and large-signal excitations. At the component level, dynamic high-fidelity magnetic equivalent circuits are introduced for laminated and solid magnetic cores. Automated linear and nonlinear order-reduction techniques are introduced for linear magnetic systems, saturated systems, systems with relative motion, and multiple-winding systems, to extract the desired essential system dynamics. Finite-element models of magnetic components incorporating relative motion are set forth and then reduced. At the system level, a framework for multiresolution simulation of switching converters is developed. Multiresolution simulation provides an alternative method to analyze power converters by providing an appropriate amount of detail based on the time scale and phenomenon being considered. A detailed full-order converter model is built based upon high-order component models and accurate switching transitions. Efficient order-reduction techniques are used to extract several lower-order models for the desired resolution of the simulation. This simulation framework is extended to higher-order converters, converters with nonlinear elements, and closed-loop systems. The resulting rapid-to-integrate component models and flexible simulation frameworks could form the computational core of future virtual prototyping design and analysis environments for energy processing units

Systematic development of equivalent circuits for synchronous machines.

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Energy-based Analysis of Biochemical Cycles using Bond Graphs

Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks

Analogue Hawking Radiation and Sine-Gordon Soliton in a Superconducting Circuit

We propose the use of a waveguide-like transmission line based on direct-current superconducting quantum interference devices (dc-SQUID) and study the sine-Gordon (SG) equation which characterises the dynamical behavior of the superconducting phase in this transmission line. Guided by the duality between black holes in Jackiw-Teitelboim (JT) dilaton gravity and solitons in sine-Gordon field theory, we show how to, in our setup, realize 1 + 1 dimensional black holes as solitons of the sine-Gordon equation. We also study the analogue Hawking radiation in terms of the quantum soliton evaporation, and analyze its feasibility within current circuit quantum electrodynamics (cQED) technology. Our results may not only facilitate experimentally understanding the relation between Jackiw-Teitelboim dilaton gravity and sine-Gordon field theory, but also pave a new way, in principle, for the exploration of analogue quantum gravitational effects.Comment: 6 pages, 2 figure

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Magnetoelectric effects in Josephson junctions

The review is devoted to the fundamental aspects and characteristic features of the magnetoelectric effects, reported in the literature on Josephson junctions (JJs). The main focus of the review is on the manifestations of the direct and inverse magnetoelectric effects in various types of Josephson systems. They provide a coupling of the magnetization in superconductor/ferromagnet/superconductor JJs to the Josephson current. The direct magnetoelectric effect is a driving force of spin torques acting on the ferromagnet inside the JJ. Therefore it is of key importance for the electrical control of the magnetization. The inverse magnetoelectric effect accounts for the back action of the magnetization dynamics on the Josephson subsystem, in particular, making the JJ to be in the resistive state in the presence of the magnetization dynamics of any origin. The perspectives of the coupling of the magnetization in JJs with ferromagnetic interlayers to the Josephson current via the magnetoelectric effects are discussed

Paradigm and paradox in power networks

Well known in the theory of network flows, Braess paradox states that adding path(s) to a congested road network may increase overall journey time. In transportation networks, the phenomenon results from selfish routing. In power systems, an analogous increase in congestion can arise as a consequence of Kirchhoff's laws, suggesting opportunities to optimize grid topology. The thesis starts with the discussion of Braess-like congestion phenomena in linear circuits. We prove that adding electrical path(s) always increases congestion in networks powered by voltage sources, while the opposite in networks driven by current sources. Although such predictability is not present in networks controlled by a mixture of voltage and current sources, our results offer a clean decomposition that completely separates the effect of current sources and voltage sources on total loss. The culmination of this research is a set of four equivalent methods of computing I^2R loss in mixed-source networks. We go on to explore network decomposition in combination with greedy sequential line switching heuristics to address the NP-hardness of power grid topology control. By means of some low order examples, it is shown that within a reasonably large class of greedy heuristics, none can be found that perform better than the others across all grid topologies. Despite this cautionary tale, statistical evidence indicates that, among three most representative heuristics, the global greedy heuristic is most computationally intensive but has the best chance of reducing generation cost while enforcing connectivity. The final part of the thesis presents a new approach to grid decomposition using vertex cut sets. We show that each vertex cut set and corresponding grid decomposition establishes a natural upper bound on the interactions between subgrids as nodal injections are regulated within each. Using such decomposition, it becomes possible to isolate congestion effects to a relatively small subgrid. A fast grid decomposition heuristic based on vertex cut sets and locational marginal prices is then proposed and studied through simulations on IEEE 118-bus system. On average, the computational cost is significantly reduced and the generation cost saving is similar to what is obtained with a global greedy algorithm