Matching Items (18)
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- Creators: Armbruster, Dieter
- Resource Type: Text
Description
Signaling cascades transduce signals received on the cell membrane to the nucleus. While noise filtering, ultra-sensitive switches, and signal amplification have all been shown to be features of such signaling cascades, it is not understood why cascades typically show three or four layers. Using singular perturbation theory, Michaelis-Menten type equations are derived for open enzymatic systems. When these equations are organized into a cascade, it is demonstrated that the output signal as a function of time becomes sigmoidal with the addition of more layers. Furthermore, it is shown that the activation time will speed up to a point, after which more layers become superfluous. It is shown that three layers create a reliable sigmoidal response progress curve from a wide variety of time-dependent signaling inputs arriving at the cell membrane, suggesting that natural selection may have favored signaling cascades as a parsimonious solution to the problem of generating switch-like behavior in a noisy environment.
ContributorsYoung, Jonathan Trinity (Author) / Armbruster, Dieter (Thesis advisor) / Platte, Rodrigo (Committee member) / Nagy, John (Committee member) / Baer, Steven (Committee member) / Taylor, Jesse (Committee member) / Arizona State University (Publisher)
Created2013
Description
Bacteriophage (phage) are viruses that infect bacteria. Typical laboratory experiments show that in a chemostat containing phage and susceptible bacteria species, a mutant bacteria species will evolve. This mutant species is usually resistant to the phage infection and less competitive compared to the susceptible bacteria species. In some experiments, both susceptible and resistant bacteria species, as well as phage, can coexist at an equilibrium for hundreds of hours. The current research is inspired by these observations, and the goal is to establish a mathematical model and explore sufficient and necessary conditions for the coexistence. In this dissertation a model with infinite distributed delay terms based on some existing work is established. A rigorous analysis of the well-posedness of this model is provided, and it is proved that the susceptible bacteria persist. To study the persistence of phage species, a "Phage Reproduction Number" (PRN) is defined. The mathematical analysis shows phage persist if PRN > 1 and vanish if PRN < 1. A sufficient condition and a necessary condition for persistence of resistant bacteria are given. The persistence of the phage is essential for the persistence of resistant bacteria. Also, the resistant bacteria persist if its fitness is the same as the susceptible bacteria and if PRN > 1. A special case of the general model leads to a system of ordinary differential equations, for which numerical simulation results are presented.
ContributorsHan, Zhun (Author) / Smith, Hal (Thesis advisor) / Armbruster, Dieter (Committee member) / Kawski, Matthias (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Arizona State University (Publisher)
Created2012
Description
This paper intends to analyze the Phoenix Suns' shooting patterns in real NBA games, and compare them to the "NBA 2k16" Suns' shooting patterns. Data was collected from the first five Suns' games of the 2015-2016 season and the same games played in "NBA 2k16". The findings of this paper indicate that "NBA 2k16" utilizes statistical findings to model their gameplay. It was also determined that "NBA 2k16" modeled the shooting patterns of the Suns in the first five games of the 2015-2016 season very closely. Both, the real Suns' games and the "NBA 2k16" Suns' games, showed a higher probability of success for shots taken in the first eight seconds of the shot clock than the last eight seconds of the shot clock. Similarly, both game types illustrated a trend that the probability of success for a shot increases as a player holds onto a ball longer. This result was not expected for either game type, however, "NBA 2k16" modeled the findings consistent with real Suns' games. The video game modeled the Suns with significantly more passes per possession than the real Suns' games, while they also showed a trend that more passes per possession has a significant effect on the outcome of the shot. This trend was not present in the real Suns' games, however literature supports this finding. Also, "NBA 2k16" did not correctly model the allocation of team shots for each player, however, the differences were found only in bench players. Lastly, "NBA 2k16" did not correctly allocate shots across the seven regions for Eric Bledsoe, however, there was no evidence indicating that the game did not correctly model the allocation of shots for the other starters, as well as the probability of success across the regions.
ContributorsHarrington, John P. (Author) / Armbruster, Dieter (Thesis director) / Kamarianakis, Ioannis (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Dividing the plane in half leaves every border point of one region a border point of both regions. Can we divide up the plane into three or more regions such that any point on the boundary of at least one region is on the border of all the regions? In fact, it is possible to design a dynamical system for which the basins of attractions have this Wada property. In certain circumstances, both the Hénon map, a simple system, and the forced damped pendulum, a physical model, produce Wada basins.
ContributorsWhitehurst, Ryan David (Author) / Kostelich, Eric (Thesis director) / Jones, Donald (Committee member) / Armbruster, Dieter (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2013-05
Description
Analytic research on basketball games is growing quickly, specifically in the National Basketball Association. This paper explored the development of this analytic research and discovered that there has been a focus on individual player metrics and a dearth of quantitative team characterizations and evaluations. Consequently, this paper continued the exploratory research of Fewell and Armbruster's "Basketball teams as strategic networks" (2012), which modeled basketball teams as networks and used metrics to characterize team strategy in the NBA's 2010 playoffs. Individual players and outcomes were nodes and passes and actions were the links. This paper used data that was recorded from playoff games of the two 2012 NBA finalists: the Miami Heat and the Oklahoma City Thunder. The same metrics that Fewell and Armbruster used were explained, then calculated using this data. The offensive networks of these two teams during the playoffs were analyzed and interpreted by using other data and qualitative characterization of the teams' strategies; the paper found that the calculated metrics largely matched with our qualitative characterizations of the teams. The validity of the metrics in this paper and Fewell and Armbruster's paper was then discussed, and modeling basketball teams as multiple-order Markov chains rather than as networks was explored.
ContributorsMohanraj, Hariharan (Co-author) / Choi, David (Co-author) / Armbruster, Dieter (Thesis director) / Fewell, Jennifer (Committee member) / Brooks, Daniel (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2013-05
Description
We attempt to analyze the effect of fatigue on free throw efficiency in the National Basketball Association (NBA) using play-by-play data from regular-season, regulation-length games in the 2016-2017, 2017-2018, and 2018-2019 seasons. Using both regression and tree-based statistical methods, we analyze the relationship between minutes played total and minutes played continuously at the time of free throw attempts on players' odds of making an attempt, while controlling for prior free throw shooting ability, longer-term fatigue, and other game factors. Our results offer strong evidence that short-term activity after periods of inactivity positively affects free throw efficiency, while longer-term fatigue has no effect.
ContributorsRisch, Oliver (Author) / Armbruster, Dieter (Thesis director) / Hahn, P. Richard (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Balancing temporal shortages of renewable energy with natural gas for the generation of electricity is a challenge for dispatchers. This is compounded by the recent proposal of blending cleanly-produced hydrogen into natural gas networks. To introduce the concepts of gas flow, this thesis begins by linearizing the partial differential equations (PDEs) that govern the flow of natural gas in a single pipe. The solution of the linearized PDEs is used to investigate wave attenuation and characterize critical operating regions where linearization is applicable. The nonlinear PDEs for a single gas are extended to mixtures of gases with the addition of a PDE that governs the conservation of composition. The gas mixture formulation is developed for general gas networks that can inject or withdraw arbitrary time-varying mixtures of gases into or from the network at arbitrarily specified nodes, while being influenced by time-varying control actions of compressor units. The PDE formulation is discretized in space to form a nonlinear control system of ordinary differential equations (ODEs), which is used to prove that homogeneous mixtures are well-behaved and heterogeneous mixtures may be ill-behaved in the sense of monotone-ordering of solutions. Numerical simulations are performed to compute interfaces that delimit monotone and periodic system responses. The ODE system is used as the constraints of an optimal control problem (OCP) to minimize the expended energy of compressors. Moreover, the ODE system for the natural gas network is linearized and used as the constraints of a linear OCP. The OCPs are digitally implemented as optimization problems following the discretization of the time domain. The optimization problems are applied to pipelines and small test networks. Some qualitative and computational applications, including linearization error analysis and transient responses, are also investigated.
ContributorsBaker, Luke Silas (Author) / Armbruster, Dieter (Thesis advisor) / Zlotnik, Anatoly (Committee member) / Herty, Michael (Committee member) / Platte, Rodrigo (Committee member) / Milner, Fabio (Committee member) / Arizona State University (Publisher)
Created2023
DescriptionUnderstanding the evolution of opinions is a delicate task as the dynamics of how one changes their opinion based on their interactions with others are unclear.
ContributorsWeber, Dylan (Author) / Motsch, Sebastien (Thesis advisor) / Lanchier, Nicolas (Committee member) / Platte, Rodrigo (Committee member) / Armbruster, Dieter (Committee member) / Fricks, John (Committee member) / Arizona State University (Publisher)
Created2021
Description
Gene expression models are key to understanding and predicting transcriptional dynamics. This thesis devises a computational method which can efficiently explore a large, highly correlated parameter space, ultimately allowing the author to accurately deduce the underlying gene network model using discrete, stochastic mRNA counts derived through the non-invasive imaging method of single molecule fluorescence in situ hybridization (smFISH). An underlying gene network model consists of the number of gene states (distinguished by distinct production rates) and all associated kinetic rate parameters. In this thesis, the author constructs an algorithm based on Bayesian parametric and nonparametric theory, expanding the traditional single gene network inference tools. This expansion starts by increasing the efficiency of classic Markov-Chain Monte Carlo (MCMC) sampling by combining three schemes known in the Bayesian statistical computing community: 1) Adaptive Metropolis-Hastings (AMH), 2) Hamiltonian Monte Carlo (HMC), and 3) Parallel Tempering (PT). The aggregation of these three methods decreases the autocorrelation between sequential MCMC samples, reducing the number of samples required to gain an accurate representation of the posterior probability distribution. Second, by employing Bayesian nonparametric methods, the author is able to simultaneously evaluate discrete and continuous parameters, enabling the method to devise the structure of the gene network and all kinetic parameters, respectively. Due to the nature of Bayesian theory, uncertainty is evaluated for the gene network model in combination with the kinetic parameters. Tools brought from Bayesian nonparametric theory equip the method with an ability to sample from the posterior distribution of all possible gene network models without pre-defining the gene network structure, i.e. the number of gene states. The author verifies the method’s robustness through the use of synthetic snapshot data, designed to closely represent experimental smFISH data sets, across a range of gene network model structures, parameters and experimental settings (number of probed cells and timepoints).
ContributorsMoyer, Camille (Author) / Armbruster, Dieter (Thesis advisor) / Fricks, John (Committee member) / Hahn, Richard (Committee member) / Renaut, Rosemary (Committee member) / Crook, Sharon (Committee member) / Kilic, Zeliha (Committee member) / Arizona State University (Publisher)
Created2024
Description
This dissertation investigates the classification of systemic lupus erythematosus (SLE) in the presence of non-SLE alternatives, while developing novel curve classification methodologies with wide ranging applications. Functional data representations of plasma thermogram measurements and the corresponding derivative curves provide predictors yet to be investigated for SLE identification. Functional nonparametric classifiers form a methodological basis, which is used herein to develop a) the family of ESFuNC segment-wise curve classification algorithms and b) per-pixel ensembles based on logistic regression and fused-LASSO. The proposed methods achieve test set accuracy rates as high as 94.3%, while returning information about regions of the temperature domain that are critical for population discrimination. The undertaken analyses suggest that derivate-based information contributes significantly in improved classification performance relative to recently published studies on SLE plasma thermograms.
ContributorsBuscaglia, Robert, Ph.D (Author) / Kamarianakis, Yiannis (Thesis advisor) / Armbruster, Dieter (Committee member) / Lanchier, Nicholas (Committee member) / McCulloch, Robert (Committee member) / Reiser, Mark R. (Committee member) / Arizona State University (Publisher)
Created2018