Matching Items (26)
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Description
A primary goal in computer science is to develop autonomous systems. Usually, we provide computers with tasks and rules for completing those tasks, but what if we could extend this type of system to physical technology as well? In the field of programmable matter, researchers are tasked with developing synthetic materials that can change their physical properties \u2014 such as color, density, and even shape \u2014 based on predefined rules or continuous, autonomous collection of input. In this research, we are most interested in particles that can perform computations, bond with other particles, and move. In this paper, we provide a theoretical particle model that can be used to simulate the performance of such physical particle systems, as well as an algorithm to perform expansion, wherein these particles can be used to enclose spaces or even objects.
ContributorsLaff, Miles (Author) / Richa, Andrea (Thesis director) / Bazzi, Rida (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
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
Three populations of experimentally evolved Drosophila melanogaster populations made up of high temperature (H, constant 25 ᵒC), low temperature (C, constant 16 ᵒC) and temporal homogeneity (T, environment changes between 16 ᵒC and 25 ᵒC) were prepared and assayed to determine difference in citrate synthase activity. Between the three groups, the results were inconclusive: the resulting reaction rates in units of nmol min-1mgfly-1 were 81.8 + 20.6, 101 + 15.6, and 96.9 + 25.2 for the hot (H), cold (C), and temporally homogeneous (T) groups, respectively. We conclude that the high associated variability was due to a lack of control regarding the collection time of the experimentally evolved Drosophila.
ContributorsBelohlavek, David (Author) / Angilletta, Michael (Thesis director) / Francisco, Wilson (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2015-05
Description
Bots tamper with social media networks by artificially inflating the popularity of certain topics. In this paper, we define what a bot is, we detail different motivations for bots, we describe previous work in bot detection and observation, and then we perform bot detection of our own. For our bot detection, we are interested in bots on Twitter that tweet Arabic extremist-like phrases. A testing dataset is collected using the honeypot method, and five different heuristics are measured for their effectiveness in detecting bots. The model underperformed, but we have laid the ground-work for a vastly untapped focus on bot detection: extremist ideal diffusion through bots.
ContributorsKarlsrud, Mark C. (Author) / Liu, Huan (Thesis director) / Morstatter, Fred (Committee member) / Barrett, The Honors College (Contributor) / Computing and Informatics Program (Contributor) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
Description
Honey bees (Apis mellifera) are responsible for pollinating nearly 80\% of all pollinated plants, meaning humans depend on honey bees to pollinate many staple crops. The success or failure of a colony is vital to global food production. There are various complex factors that can contribute to a colony's failure, including pesticides. Neonicotoids are a popular pesticide that have been used in recent times. In this study we concern ourselves with pesticides and its impact on honey bee colonies. Previous investigations that we draw significant inspiration from include Khoury et Al's \emph{A Quantitative Model of Honey Bee Colony Population Dynamics}, Henry et Al's \emph{A Common Pesticide Decreases Foraging Success and Survival in Honey Bees}, and Brown's \emph{ Mathematical Models of Honey Bee Populations: Rapid Population Decline}. In this project we extend a mathematical model to investigate the impact of pesticides on a honey bee colony, with birth rates and death rates being dependent on pesticides, and we see how these death rates influence the growth of a colony. Our studies have found an equilibrium point that depends on pesticides. Trace amounts of pesticide are detrimental as they not only affect death rates, but birth rates as well.
ContributorsSalinas, Armando (Author) / Vaz, Paul (Thesis director) / Jones, Donald (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Many programmable matter systems have been proposed and realized recently, each often tailored toward a particular task or physical setting. In our work on self-organizing particle systems, we abstract away from specific settings and instead describe programmable matter as a collection of simple computational elements (to be referred to as particles) with limited computational power that each perform fully distributed, local, asynchronous algorithms to solve system-wide problems of movement, configuration, and coordination. In this thesis, we focus on the compression problem, in which the particle system gathers as tightly together as possible, as in a sphere or its equivalent in the presence of some underlying geometry. While there are many ways to formalize what it means for a particle system to be compressed, we address three different notions of compression: (1) local compression, in which each individual particle utilizes local rules to create an overall convex structure containing no holes, (2) hole elimination, in which the particle system seeks to detect and eliminate any holes it contains, and (3) alpha-compression, in which the particle system seeks to shrink its perimeter to be within a constant factor of the minimum possible value. We analyze the behavior of each of these algorithms, examining correctness and convergence where appropriate. In the case of the Markov Chain Algorithm for Compression, we provide improvements to the original bounds for the bias parameter lambda which influences the system to either compress or expand. Lastly, we briefly discuss contributions to the problem of leader election--in which a particle system elects a single leader--since it acts as an important prerequisite for compression algorithms that use a predetermined seed particle.
ContributorsDaymude, Joshua Jungwoo (Author) / Richa, Andrea (Thesis director) / Kierstead, Henry (Committee member) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
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 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
Description
Polar ice masses can be valuable indicators of trends in global climate. In an effort to better understand the dynamics of Arctic ice, this project analyzes sea ice concentration anomaly data collected over gridded regions (cells) and builds graphs based upon high correlations between cells. These graphs offer the opportunity to use metrics such as clustering coefficients and connected components to isolate representative trends in ice masses. Based upon this analysis, the structure of sea ice graphs differs at a statistically significant level from random graphs, and several regions show erratically decreasing trends in sea ice concentration.
ContributorsWallace-Patterson, Chloe Rae (Author) / Syrotiuk, Violet (Thesis director) / Colbourn, Charles (Committee member) / Montgomery, Douglas (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-05
DescriptionA two-way deterministic finite pushdown automaton ("2PDA") is developed for the Lua language. This 2PDA is evaluated against both a purpose-built Lua syntax test suite and the test suite used by the reference implementation of Lua, and fully passes both.
ContributorsStevens, Kevin A (Author) / Shoshitaishvili, Yan (Thesis director) / Wang, Ruoyu (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
We consider programmable matter as a collection of simple computational elements (or particles) that self-organize to solve system-wide problems of movement, configuration, and coordination. Here, we focus on the compression problem, in which the particle system gathers as tightly together as possible, as in a sphere or its equivalent in the presence of some underlying geometry. Within this model a configuration of particles can be represented as a unique closed self-avoiding walk on the triangular lattice. In this paper we will examine the bias parameter of a Markov chain based algorithm that solves the compression problem under the geometric amoebot model, for particle systems that begin in a connected configuration with no holes. This bias parameter, $\lambda$, determines the behavior of the algorithm. It has been shown that for $\lambda > 2+\sqrt{2}$, with all but exponentially small probability, the algorithm achieves compression. Additionally the same algorithm can be used for expansion for small values of $\lambda$; in particular, for all $0 < \lambda < \sqrt{\tau}$, where $\lim_{n\to\infty} {(p_n)^{1
}}=\tau$. This research will focus on improving approximations on the lower bound of $\tau$. Toward this end we will examine algorithmic enumeration, and series analysis for self-avoiding polygons.
}}=\tau$. This research will focus on improving approximations on the lower bound of $\tau$. Toward this end we will examine algorithmic enumeration, and series analysis for self-avoiding polygons.
ContributorsLough, Kevin James (Author) / Richa, Andrea (Thesis director) / Fishel, Susanna (Committee member) / School of Mathematical and Statistical Sciences (Contributor, Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05