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Transmission expansion planning (TEP) is a complex decision making process that requires comprehensive analysis to determine the time, location, and number of electric power transmission facilities that are needed in the future power grid. This dissertation investigates the topic of solving TEP problems for large power systems. The dissertation can

Transmission expansion planning (TEP) is a complex decision making process that requires comprehensive analysis to determine the time, location, and number of electric power transmission facilities that are needed in the future power grid. This dissertation investigates the topic of solving TEP problems for large power systems. The dissertation can be divided into two parts. The first part of this dissertation focuses on developing a more accurate network model for TEP study. First, a mixed-integer linear programming (MILP) based TEP model is proposed for solving multi-stage TEP problems. Compared with previous work, the proposed approach reduces the number of variables and constraints needed and improves the computational efficiency significantly. Second, the AC power flow model is applied to TEP models. Relaxations and reformulations are proposed to make the AC model based TEP problem solvable. Third, a convexified AC network model is proposed for TEP studies with reactive power and off-nominal bus voltage magnitudes included in the model. A MILP-based loss model and its relaxations are also investigated. The second part of this dissertation investigates the uncertainty modeling issues in the TEP problem. A two-stage stochastic TEP model is proposed and decomposition algorithms based on the L-shaped method and progressive hedging (PH) are developed to solve the stochastic model. Results indicate that the stochastic TEP model can give a more accurate estimation of the annual operating cost as compared to the deterministic TEP model which focuses only on the peak load.
ContributorsZhang, Hui (Author) / Vittal, Vijay (Thesis advisor) / Heydt, Gerald T (Thesis advisor) / Mittelmann, Hans D (Committee member) / Hedman, Kory W (Committee member) / Arizona State University (Publisher)
Created2013
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Description
New OpenFlow switches support a wide range of network applications, such as firewalls, load balancers, routers, and traffic monitoring. While ternary content addressable memory (TCAM) allows switches to process packets at high speed based on multiple header fields, today's commodity switches support just thousands to tens of thousands of forwarding

New OpenFlow switches support a wide range of network applications, such as firewalls, load balancers, routers, and traffic monitoring. While ternary content addressable memory (TCAM) allows switches to process packets at high speed based on multiple header fields, today's commodity switches support just thousands to tens of thousands of forwarding rules. To allow for finer-grained policies on this hardware, efficient ways to support the abstraction of a switch are needed with arbitrarily large rule tables. To do so, a hardware-software hybrid switch is designed that relies on rule caching to provide large rule tables at low cost. Unlike traditional caching solutions, neither individual rules are cached (to respect rule dependencies) nor compressed (to preserve the per-rule traffic counts). Instead long dependency chains are ``spliced'' to cache smaller groups of rules while preserving the semantics of the network policy. The proposed hybrid switch design satisfies three criteria: (1) responsiveness, to allow rapid changes to the cache with minimal effect on traffic throughput; (2) transparency, to faithfully support native OpenFlow semantics; (3) correctness, to cache rules while preserving the semantics of the original policy. The evaluation of the hybrid switch on large rule tables suggest that it can effectively expose the benefits of both hardware and software switches to the controller and to applications running on top of it.
ContributorsAlipourfard, Omid (Author) / Syrotiuk, Violet R. (Thesis advisor) / Richa, Andréa W. (Committee member) / Xue, Guoliang (Committee member) / Arizona State University (Publisher)
Created2014
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Description
This dissertation studies routing in small-world networks such as grids plus long-range edges and real networks. Kleinberg showed that geography-based greedy routing in a grid-based network takes an expected number of steps polylogarithmic in the network size, thus justifying empirical efficiency observed beginning with Milgram. A counterpart for the grid-based

This dissertation studies routing in small-world networks such as grids plus long-range edges and real networks. Kleinberg showed that geography-based greedy routing in a grid-based network takes an expected number of steps polylogarithmic in the network size, thus justifying empirical efficiency observed beginning with Milgram. A counterpart for the grid-based model is provided; it creates all edges deterministically and shows an asymptotically matching upper bound on the route length. The main goal is to improve greedy routing through a decentralized machine learning process. Two considered methods are based on weighted majority and an algorithm of de Farias and Megiddo, both learning from feedback using ensembles of experts. Tests are run on both artificial and real networks, with decentralized spectral graph embedding supplying geometric information for real networks where it is not intrinsically available. An important measure analyzed in this work is overpayment, the difference between the cost of the method and that of the shortest path. Adaptive routing overtakes greedy after about a hundred or fewer searches per node, consistently across different network sizes and types. Learning stabilizes, typically at overpayment of a third to a half of that by greedy. The problem is made more difficult by eliminating the knowledge of neighbors' locations or by introducing uncooperative nodes. Even under these conditions, the learned routes are usually better than the greedy routes. The second part of the dissertation is related to the community structure of unannotated networks. A modularity-based algorithm of Newman is extended to work with overlapping communities (including considerably overlapping communities), where each node locally makes decisions to which potential communities it belongs. To measure quality of a cover of overlapping communities, a notion of a node contribution to modularity is introduced, and subsequently the notion of modularity is extended from partitions to covers. The final part considers a problem of network anonymization, mostly by the means of edge deletion. The point of interest is utility preservation. It is shown that a concentration on the preservation of routing abilities might damage the preservation of community structure, and vice versa.
ContributorsBakun, Oleg (Author) / Konjevod, Goran (Thesis advisor) / Richa, Andrea (Thesis advisor) / Syrotiuk, Violet R. (Committee member) / Czygrinow, Andrzej (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Performance improvements have largely followed Moore's Law due to the help from technology scaling. In order to continue improving performance, power-efficiency must be reduced. Better technology has improved power-efficiency, but this has a limit. Multi-core architectures have been shown to be an additional aid to this crusade of increased power-efficiency.

Performance improvements have largely followed Moore's Law due to the help from technology scaling. In order to continue improving performance, power-efficiency must be reduced. Better technology has improved power-efficiency, but this has a limit. Multi-core architectures have been shown to be an additional aid to this crusade of increased power-efficiency. Accelerators are growing in popularity as the next means of achieving power-efficient performance. Accelerators such as Intel SSE are ideal, but prove difficult to program. FPGAs, on the other hand, are less efficient due to their fine-grained reconfigurability. A middle ground is found in CGRAs, which are highly power-efficient, but largely programmable accelerators. Power-efficiencies of 100s of GOPs/W have been estimated, more than 2 orders of magnitude greater than current processors. Currently, CGRAs are limited in their applicability due to their ability to only accelerate a single thread at a time. This limitation becomes especially apparent as multi-core/multi-threaded processors have moved into the mainstream. This limitation is removed by enabling multi-threading on CGRAs through a software-oriented approach. The key capability in this solution is enabling quick run-time transformation of schedules to execute on targeted portions of the CGRA. This allows the CGRA to be shared among multiple threads simultaneously. Analysis shows that enabling multi-threading has very small costs but provides very large benefits (less than 1% single-threaded performance loss but nearly 300% CGRA throughput increase). By increasing dynamism of CGRA scheduling, system performance is shown to increase overall system performance of an optimized system by almost 350% over that of a single-threaded CGRA and nearly 20x faster than the same system with no CGRA in a highly threaded environment.
ContributorsPager, Jared (Author) / Shrivastava, Aviral (Thesis advisor) / Gupta, Sandeep (Committee member) / Speyer, Gil (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Epilepsy is a group of disorders that cause seizures in approximately 2.2 million people in the United States. Over 30% of these patients have epilepsies that do not respond to treatment with anti-epileptic drugs. For this population, focal resection surgery could offer long-term seizure freedom. Surgery candidates undergo a myriad

Epilepsy is a group of disorders that cause seizures in approximately 2.2 million people in the United States. Over 30% of these patients have epilepsies that do not respond to treatment with anti-epileptic drugs. For this population, focal resection surgery could offer long-term seizure freedom. Surgery candidates undergo a myriad of tests and monitoring to determine where and when seizures occur. The “gold standard” method for focus identification involves the placement of electrocorticography (ECoG) grids in the sub-dural space, followed by continual monitoring and visual inspection of the patient’s cortical activity. This process, however, is highly subjective and uses dated technology. Multiple studies were performed to investigate how the evaluation process could benefit from an algorithmic adjust using current ECoG technology, and how the use of new microECoG technology could further improve the process.

Computational algorithms can quickly and objectively find signal characteristics that may not be detectable with visual inspection, but many assume the data are stationary and/or linear, which biological data are not. An empirical mode decomposition (EMD) based algorithm was developed to detect potential seizures and tested on data collected from eight patients undergoing monitoring for focal resection surgery. EMD does not require linearity or stationarity and is data driven. The results suggest that a biological data driven algorithm could serve as a useful tool to objectively identify changes in cortical activity associated with seizures.

Next, the use of microECoG technology was investigated. Though both ECoG and microECoG grids are composed of electrodes resting on the surface of the cortex, changing the diameter of the electrodes creates non-trivial changes in the physics of the electrode-tissue interface that need to be accounted for. Experimenting with different recording configurations showed that proper grounding, referencing, and amplification are critical to obtain high quality neural signals from microECoG grids.

Finally, the relationship between data collected from the cortical surface with micro and macro electrodes was studied. Simultaneous recordings of the two electrode types showed differences in power spectra that suggest the inclusion of activity, possibly from deep structures, by macroelectrodes that is not accessible by microelectrodes.
ContributorsAshmont, Kari Rich (Author) / Greger, Bradley (Thesis advisor) / Helms Tillery, Stephen (Committee member) / Buneo, Christopher (Committee member) / Adelson, P David (Committee member) / Dudek, F Edward (Committee member) / Arizona State University (Publisher)
Created2015
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Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial

The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.

My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.

1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.

2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
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Description
In the realm of network science, many topics can be abstracted as graph problems, such as routing, connectivity enhancement, resource/frequency allocation and so on. Though most of them are NP-hard to solve, heuristics as well as approximation algorithms are proposed to achieve reasonably good results. Accordingly, this dissertation studies graph

In the realm of network science, many topics can be abstracted as graph problems, such as routing, connectivity enhancement, resource/frequency allocation and so on. Though most of them are NP-hard to solve, heuristics as well as approximation algorithms are proposed to achieve reasonably good results. Accordingly, this dissertation studies graph related problems encountered in real applications. Two problems studied in this dissertation are derived from wireless network, two more problems studied are under scenarios of FIWI and optical network, one more problem is in Radio- Frequency Identification (RFID) domain and the last problem is inspired by satellite deployment.

The objective of most of relay nodes placement problems, is to place the fewest number of relay nodes in the deployment area so that the network, formed by the sensors and the relay nodes, is connected. Under the fixed budget scenario, the expense involved in procuring the minimum number of relay nodes to make the network connected, may exceed the budget. In this dissertation, we study a family of problems whose goal is to design a network with “maximal connectedness” or “minimal disconnectedness”, subject to a fixed budget constraint. Apart from “connectivity”, we also study relay node problem in which degree constraint is considered. The balance of reducing the degree of the network while maximizing communication forms the basis of our d-degree minimum arrangement(d-MA) problem. In this dissertation, we look at several approaches to solving the generalized d-MA problem where we embed a graph onto a subgraph of a given degree.

In recent years, considerable research has been conducted on optical and FIWI networks. Utilizing a recently proposed concept “candidate trees” in optical network, this dissertation studies counting problem on complete graphs. Closed form expressions are given for certain cases and a polynomial counting algorithm for general cases is also presented. Routing plays a major role in FiWi networks. Accordingly to a novel path length metric which emphasizes on “heaviest edge”, this dissertation proposes a polynomial algorithm on single path computation. NP-completeness proof as well as approximation algorithm are presented for multi-path routing.

Radio-frequency identification (RFID) technology is extensively used at present for identification and tracking of a multitude of objects. In many configurations, simultaneous activation of two readers may cause a “reader collision” when tags are present in the intersection of the sensing ranges of both readers. This dissertation ad- dresses slotted time access for Readers and tries to provide a collision-free scheduling scheme while minimizing total reading time.

Finally, this dissertation studies a monitoring problem on the surface of the earth for significant environmental, social/political and extreme events using satellites as sensors. It is assumed that the impact of a significant event spills into neighboring regions and there will be corresponding indicators. Careful deployment of sensors, utilizing “Identifying Codes”, can ensure that even though the number of deployed sensors is fewer than the number of regions, it may be possible to uniquely identify the region where the event has taken place.
ContributorsZhou, Chenyang (Author) / Richa, Andrea (Thesis advisor) / Sen, Arunabha (Thesis advisor) / Xue, Guoliang (Committee member) / Walkowiak, Krzysztof (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Covering subsequences with sets of permutations arises in many applications, including event-sequence testing. Given a set of subsequences to cover, one is often interested in knowing the fewest number of permutations required to cover each subsequence, and in finding an explicit construction of such a set of permutations that has

Covering subsequences with sets of permutations arises in many applications, including event-sequence testing. Given a set of subsequences to cover, one is often interested in knowing the fewest number of permutations required to cover each subsequence, and in finding an explicit construction of such a set of permutations that has size close to or equal to the minimum possible. The construction of such permutation coverings has proven to be computationally difficult. While many examples for permutations of small length have been found, and strong asymptotic behavior is known, there are few explicit constructions for permutations of intermediate lengths. Most of these are generated from scratch using greedy algorithms. We explore a different approach here. Starting with a set of permutations with the desired coverage properties, we compute local changes to individual permutations that retain the total coverage of the set. By choosing these local changes so as to make one permutation less "essential" in maintaining the coverage of the set, our method attempts to make a permutation completely non-essential, so it can be removed without sacrificing total coverage. We develop a post-optimization method to do this and present results on sequence covering arrays and other types of permutation covering problems demonstrating that it is surprisingly effective.
ContributorsMurray, Patrick Charles (Author) / Colbourn, Charles (Thesis director) / Czygrinow, Andrzej (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2014-12
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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

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
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Description
In many systems, it is difficult or impossible to measure the phase of a signal. Direct recovery from magnitude is an ill-posed problem. Nevertheless, with a sufficiently large set of magnitude measurements, it is often possible to reconstruct the original signal using algorithms that implicitly impose regularization conditions on this

In many systems, it is difficult or impossible to measure the phase of a signal. Direct recovery from magnitude is an ill-posed problem. Nevertheless, with a sufficiently large set of magnitude measurements, it is often possible to reconstruct the original signal using algorithms that implicitly impose regularization conditions on this ill-posed problem. Two such algorithms were examined: alternating projections, utilizing iterative Fourier transforms with manipulations performed in each domain on every iteration, and phase lifting, converting the problem to that of trace minimization, allowing for the use of convex optimization algorithms to perform the signal recovery. These recovery algorithms were compared on a basis of robustness as a function of signal-to-noise ratio. A second problem examined was that of unimodular polyphase radar waveform design. Under a finite signal energy constraint, the maximal energy return of a scene operator is obtained by transmitting the eigenvector of the scene Gramian associated with the largest eigenvalue. It is shown that if instead the problem is considered under a power constraint, a unimodular signal can be constructed starting from such an eigenvector that will have a greater return.
ContributorsJones, Scott Robert (Author) / Cochran, Douglas (Thesis director) / Diaz, Rodolfo (Committee member) / Barrett, The Honors College (Contributor) / Electrical Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2014-05