Matching Items (8)
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- All Subjects: Mathematics
- All Subjects: Protein
- Creators: Department of Physics
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
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
News outlets frequently portray people with disabilities as either helpless victims or objects of motivation. Portrayal of people with disabilities has improved over the years, but there is still room to grow. News outlets tend to make disability the center of the story. A story about a disabled person is primarily about their disability, with their other accomplishments framed by it.
As one example of the victimhood narrative, ABC News used to run a special called My Extreme Affliction as part of 20/20 until 2012. As the name implies, the specials covered people with disabilities, specifically extreme versions. One 2008 episode on Tourette’s syndrome described Tourette’s like it was some sort of demonic possession. The narrator talked about children who were “prisoners in their own bodies” and a family that was at risk of being “torn apart by Tourette’s.” I have Tourette’s syndrome myself, which made ABC’s special especially uncomfortable to watch. When not wringing their metaphorical hands over the “victims” of disability, many news outlets fall into the “supercrip” narrative. They refer to people as “heroes” who “overcome” their disabilities to achieve something that ranges from impressive to utterly mundane. The main emphasis is on the disability rather than the person who has it. These articles then exploit that disability to make readers feel good. As a person with a disability, I am aware that it impacts my life, but it is not the center of my life. The tics from my Tourette’s syndrome made it difficult to speak to people when I was younger, but even then they did not rule me.
Disability coverage, however, is still incredibly important for promoting acceptance and giving people with disabilities a voice. A little over a fifth of adults in the United States have a disability (CDC: 53 million adults in the US live with a disability), so poor coverage means marginalizing or even excluding a large amount of people. Journalists should try to reach their entire audience. The news helps shape public opinion with the stories it features. Therefore, it should provide visibility for people with disabilities in order to increase acceptance. This is a matter of civil rights. People with disabilities deserve fair and accurate representation.
My personal experience with ABC’s Tourette’s special leads me to believe that the media, especially the news, needs to be more responsible in their reporting. Even the name “My Extreme Affliction” paints a poor picture of what to expect. A show that focuses on sensationalist portrayals in pursuit of views further ostracizes people with disabilities. The emphasis should be on a person and not their condition. The National Center for Disability Journalism tells reporters to “Focus on the person you are interviewing, not the disability” (Tips for interviewing people with disabilities). This people-first approach is the way to improve disability coverage: Treat people with disabilities with the same respect as any other minority group.
As one example of the victimhood narrative, ABC News used to run a special called My Extreme Affliction as part of 20/20 until 2012. As the name implies, the specials covered people with disabilities, specifically extreme versions. One 2008 episode on Tourette’s syndrome described Tourette’s like it was some sort of demonic possession. The narrator talked about children who were “prisoners in their own bodies” and a family that was at risk of being “torn apart by Tourette’s.” I have Tourette’s syndrome myself, which made ABC’s special especially uncomfortable to watch. When not wringing their metaphorical hands over the “victims” of disability, many news outlets fall into the “supercrip” narrative. They refer to people as “heroes” who “overcome” their disabilities to achieve something that ranges from impressive to utterly mundane. The main emphasis is on the disability rather than the person who has it. These articles then exploit that disability to make readers feel good. As a person with a disability, I am aware that it impacts my life, but it is not the center of my life. The tics from my Tourette’s syndrome made it difficult to speak to people when I was younger, but even then they did not rule me.
Disability coverage, however, is still incredibly important for promoting acceptance and giving people with disabilities a voice. A little over a fifth of adults in the United States have a disability (CDC: 53 million adults in the US live with a disability), so poor coverage means marginalizing or even excluding a large amount of people. Journalists should try to reach their entire audience. The news helps shape public opinion with the stories it features. Therefore, it should provide visibility for people with disabilities in order to increase acceptance. This is a matter of civil rights. People with disabilities deserve fair and accurate representation.
My personal experience with ABC’s Tourette’s special leads me to believe that the media, especially the news, needs to be more responsible in their reporting. Even the name “My Extreme Affliction” paints a poor picture of what to expect. A show that focuses on sensationalist portrayals in pursuit of views further ostracizes people with disabilities. The emphasis should be on a person and not their condition. The National Center for Disability Journalism tells reporters to “Focus on the person you are interviewing, not the disability” (Tips for interviewing people with disabilities). This people-first approach is the way to improve disability coverage: Treat people with disabilities with the same respect as any other minority group.
ContributorsMackrell, Marguerite (Author) / Gilger, Kristin (Thesis director) / Doig, Steve (Committee member) / Walter Cronkite School of Journalism & Mass Comm (Contributor) / School of Politics and Global Studies (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46 residue-long, protein interaction module composed of a WW domain and corresponding polyproline ligand (PDB id: 1k9r). The dynamic flexibility index (DFI) was computed for the binding site of the wild type and mutant WW domains to quantify the mutations effect on the rigidity of the binding pocket. DFI is used as a metric to quantify the resilience of a given position to perturbation along the chain. Using steered molecular dynamics (SMD), we also measure the effect of the point mutation on allosteric regulation by approximating the binding free energy of the system calculated using Jarzynski's Equality. Calculation of the DFI shows that the overall flexibility of the protein complex increases as a result of the distal point mutation. Total change in DFI percentile of the binding site showed a 0.067 increase suggesting an allosteric, loss of function mutation. Furthermore, we see that the change in the binding free energy is greater for that of the mutated complex supporting the idea that an increase in flexibility is correlated to a decrease in proteinlig and binding affinity. We show that sequence mutation of an allosteric site affects the mechanical stability and functionality of the binding pocket.
ContributorsMarianchuk, Tegan (Author) / Ozkan, Sefika (Thesis director) / Ros, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor)
Created2018-05
Description
A working knowledge of mathematics is a vital requirement for introductory university physics courses. However, there is mounting evidence which shows that many incoming introductory physics students do not have the necessary mathematical ability to succeed in physics. The investigation reported in this thesis used preinstruction diagnostics and interviews to examine this problem in depth. It was found that in some cases, over 75% of students could not solve the most basic mathematics problems. We asked questions involving right triangles, vector addition, vector direction, systems of equations, and arithmetic, to give a few examples. The correct response rates were typically between 25% and 75%, which is worrying, because these problems are far simpler than the typical problem encountered in an introductory quantitative physics course. This thesis uncovered a few common problem solving strategies that were not particularly effective. When solving trigonometry problems, 13% of students wrote down the mnemonic "SOH CAH TOA," but a chi-squared test revealed that this was not a statistically significant factor in getting the correct answer, and was actually detrimental in certain situations. Also, about 50% of students used a tip-to-tail method to add vectors. But there is evidence to suggest that this method is not as effective as using components. There are also a number of problem solving strategies that successful students use to solve mathematics problems. Using the components of a vector increases student success when adding vectors and examining their direction. Preliminary evidence also suggests that repetitive trigonometry practice may be the best way to improve student performance on trigonometry problems. In addition, teaching students to use a wide variety of algebraic techniques like the distributive property may help them from getting stuck when working through problems. Finally, evidence suggests that checking work could eliminate up to a third of student errors.
ContributorsJones, Matthew Isaiah (Author) / Meltzer, David (Thesis director) / Peng, Xihong (Committee member) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Optometry is an important field in medicine as it allows people a chance to have their vision corrected and it serves as a health screening opportunity for those who receive a dilated eye examination. One of the largest barriers to receiving a dilated eye exam is insurance coverage. Most health insurance policies have limited optometric coverage. By expanding health insurance plans to be more inclusive of optometric care, people who use these health insurance plans will have a better access of care.
ContributorsFurey, Colleen (Author) / Ruth, Alissa (Thesis director) / Mullen, Tyler (Committee member) / School of Life Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Lyme disease is a common tick-borne illness caused by the Gram-negative bacterium Borrelia burgdorferi. An outer membrane protein of Borrelia burgdorferi, P66, has been suggested as a possible target for Lyme disease treatments. However, a lack of structural information available for P66 has hindered attempts to design medications to target the protein. Therefore, this study attempted to find methods for expressing and purifying P66 in quantities that can be used for structural studies. It was found that by using the PelB signal sequence, His-tagged P66 could be directed to the outer membrane of Escherichia coli, as confirmed by an anti-His Western blot. Further attempts to optimize P66 expression in the outer membrane were made, pending verification via Western blotting. The ability to direct P66 to the outer membrane using the PelB signal sequence is a promising first step in determining the overall structure of P66, but further work is needed before P66 is ready for large-scale purification for structural studies.
ContributorsRamirez, Christopher Nicholas (Author) / Fromme, Petra (Thesis director) / Hansen, Debra (Committee member) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
This qualitative study sought to investigate the potential reaction between the 3,3',5,5'-tetramethylbenzidine (TMB) radical and LAF-1 RGG, the N-terminus domain of an RNA helicase which functions as a coacervating intrinsically disordered protein. The study was performed by adding horseradish peroxidase to a solution containing TMB and either LAF-1 or tyrosine in various concentrations, and monitoring the output through UV-Vis spectroscopy. The reacted species was also analyzed via MALDI-TOF mass spectrometry. UV-Vis spectroscopic monitoring showed that in the presence of LAF-1 or tyrosine, the reaction between HRP and TMB occurred more quickly than the control, as well as in the highest concentration of LAF-1, the evolution of a peak at 482 nm. The analysis through MALDI-TOF spectrometry showed the development of a second peak likely due to the reaction between LAF-1 and TMB, as the Δ between the peaks is 229 Da and the size of the TMB species is 240 Da.
ContributorsDavis, Morgan (Author) / Ghirlanda, Giovanna (Thesis director) / Heyden, Matthias (Committee member) / Mazor, Yuval (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor)
Created2022-12
Description
The Jordan curve theorem states that any homeomorphic copy of a circle into R2 divides the plane into two distinct regions. This paper reconstructs one proof of the Jordan curve theorem before turning its attention toward generalizations of the theorem and their proofs and counterexamples. We begin with an introduction to elementary topology and the different notions of the connectedness of a space before constructing the first proof of the Jordan curve theorem. We then turn our attention to algebraic topology which we utilize in our discussion of the Jordan curve theorem’s generalizations. We end with a proof of the Jordan-Brouwer theorems, extensions of the Jordan curve theorem to higher dimensions.
ContributorsClark, Kacey (Author) / Kawski, Matthias (Thesis director) / Paupert, Julien (Committee member) / Department of Physics (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05