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Molecular dynamics simulation of DNA translocation through solid-state nanopores
Get PDFThis thesis explores the use of molecular dynamics (MD) simulations to model double-stranded DNA (dsDNA) translocation through nanopores, aiming to optimize nanopore-based DNA sequencing technologies. Using both LAMMPS and NAMD, the study investigates the potential for MD simulations to provide insights into nanopore sequencing mechanisms and system behaviors. Insights gained from LAMMPS tutorials by Simon Gravelle informed the understanding of force fields, system minimization, heating, and equilibrating processes necessary for accurate MD simulations. The atom pull method presented in these tutorials was foundational in understanding force application within molecular systems, analogous to grid-steered molecular dynamics (G-SMD) techniques later applied to DNA sequencing.Following these foundational steps, NAMD simulations based on protocols by Jeffrey R. Comer were performed to simulate dsDNA translocation through two types of nanopores: an alpha-hemolysin biological nanopore and a Silicon Nitride (Si₃N₄) solid-state nanopore. The alpha-hemolysin simulation allowed for an initial examination of DNA behavior in a biological nanopore, while the Si₃N₄ nanopore simulation provided detailed ionic current signatures critical for sequencing analysis. Protocols from Comer’s nanopore modeling guide were closely followed to accurately construct these systems, and no structural modifications were made. Results indicate that nanopore geometry, such as the hourglass shape in Si₃N₄, provides a stable pathway for DNA translocation and yields consistent current signals. The simulations utilized a higher-than-normal voltage to accelerate translocation, which provided faster insights but deviated from experimental conditions, suggesting areas for methodological refinement. The high than normal voltage is due to this work following steps described 15 years ago before GPU-computing which led to simplifications in the system. These findings were compared with both another Si₃N₄ simulation and real-world experimental data using Si₃N₄. The findings suggest that MD simulations can offer valuable insights into nanopore design and sequencing efficiency, providing a foundation for further optimization of real-world DNA sequencing applications. Future work could focus on refining computational methods to simulate translocation under more realistic voltages, ultimately bridging the gap between simulation and experimental results. This study contributes to the evolving field of nanopore sequencing, suggesting avenues for improvements in nanopore structure and operational conditions to enhance sequencing accuracy and reliability
INFLUENCE OF UNSTEADY BOUNDARY LAYER GROWTH BEHIND A NORMAL SHOCK WAVE ON THE DYNAMICS OF SPHERICAL WATER DROPLETS ON A SHOCK TUBE WALL
No full textThe discrete increase of local pressure and temperature caused by a shock wave passing over a certain location in a shock tube allows for many potential investigations of the process of combustion. One of these investigations is the aero breakup of a liquid droplet, which could be a fuel droplet, and the instantaneous temperature rise results in potential combustion of the broken up fuel droplet. A specific study in how a wall-laden droplet breaks up in different freestream unit Reynolds number, diameter, and droplet attachment angle was conducted in order to characterize the different potential breakup modes seen by the aerobreakup of a droplet. Pointwise pressure data was employed to obtain freestream conditions, and shadowgraphs capturing the temporal evolution of the aerobreakup of a droplet on a shock tube wall in region 2 of a shock tube was observed. Edge detection was employed to quantify the droplet’s deformation over time. It was observed that lower freestream Reynolds number and larger droplet diameters delayed the breakup of the droplet, despite being at comparable Weber numbers. The attachment angle also impacted the rate of deformation. Instabilities on the upstream side of the droplet were observed to generally decrease with an increase of diameter. These trends were observed for all possible conditions
Music Performance and ADHD: A Qualitative Study on the Experiences of Graduate Music Performance Students with ADHD
No full textAttention Deficit Hyperactive Disorder (ADHD) is a neuropsychological disorder that may cause learning difficulties and a variety of comorbid issues. College-aged students with ADHD are at greater risk of low academic performance, issues with time management, disorganization, likelihood of academic probation, and withdrawal from classes. At the time of this writing, there was a large quantity of research related to music learning in children with ADHD. Additionally, researchers have explored issues with ADHD in professional classical musicians. As of now, research concerning ADHD in graduate music performance students is limited. In this document, I employed a phenomenological case study approach to explore the experiences of two graduate music performance students with ADHD from major universities in the United States. In doing so, I uncovered insight into three themes: practice and teaching strategies, anxiety and musician performance anxiety (MPA), and loss of motor control. These themes were determined to have been affected by ADHD symptoms that participants encountered in studio lessons, practice sessions, rehearsals, and performances. Both participants consented to a 45 minute to 1-hour semi-structured interview. Interview responses were first organized into narratives for each participant. Second, the data was summarized into three main themes reflective of each research question topic. Of the discovered strategies, I found the most insight into how the participants utilized interest for motivation. Additional information was ascertained regarding the relationship between ADHD and MPA and in the experiences of hyperfocus suggesting the need for further research. Implications include practice and teaching strategies for graduate music performance students with ADHD along with future research concerning ADHD and MPA, hyperfocus, and motor control
STRATIGRAPHIC AND PETROPHYSICAL CONTROLS ON RESERVOIR PAY AND ITS SPATIAL VARIABILITY, WILLIAMS FORK FORMATION, MAMM CREEK FIELD, COLORADO
No full textThe Upper Cretaceous Williams Fork Formation of the Mesaverde Group within the Piceance Basin of northwestern Colorado is a significant producer of natural gas from low permeability reservoirs (tight-gas sandstones). The Williams Fork Formation consists of six stratigraphic intervals. From base to top, these zones include the Lower Williams Fork Formation including 1) Cameo-Wheeler Coal Zone, 2) Middle Sandstone/South Canyon Coal Zone, 3) Upper Sandstone, and 4) Paonia Shale Member, and the 5) Middle Williams Fork, and 6) Upper Williams Fork. The two lowermost zones of the Lower Williams Fork Formation consist of fluvial sandstones, shales, and laterally extensive coal zones. The upper two zones of the Lower Williams Fork Formation record a transition from lower coastal plain and swamp to coastal plain deposits represented by fewer coals and a higher proportion of fluvial sandstones. From the upper two zones of the Lower Williams Fork Formation to the Middle and Upper Williams Fork, a transition from coastal plain to an alluvial plain setting is reflected by a greater proportion of sandstones.This study combines well-log and 3D seismic data to yield 3D lithology, porosity, permeability, water saturation, bulk volume water, and reservoir pay models to explore the stratigraphic and petrophysical controls on reservoir pay within the Williams Fork Formation in Mamm Creek Field. The data set includes approximately 48 mi2 (125 km2) of 3D seismic data in time and depth domains, core porosity and permeability data from the Last Dance 43C-3-792 well, and 234 wells with digital well-logs including gamma ray, neutron porosity, density porosity, and resistivity logs. Three-dimensional petrophysical property models reveal that Williams Fork Formation sandstones exhibit total and effective porosity ranges of ~5-15% and ~1-8%, respectively, absolute permeability of ~0.7- 10 µD, and bulk volume water of ~0.03-0.06. Core data suggest that matrix permeability is positively correlated with total and effective porosity. Within the study area, 40% of the Williams Fork Formation is composed of thick, laterally extensive reservoir pay sandstones that on average, reflect total porosity ~9-11%, effective porosity ~3-4%, slightly higher permeability ~7-20 µD, water saturation ~50-85% (avg. ~80%), and bulk volume water ~0.01-0.05 (avg. 0.03). While the range and mean values of petrophysical properties do not vary significantly stratigraphically, lithology, reservoir pay, and pore volume are highly variable stratigraphically. The majority of reservoir pay is confined within the lower two-thirds of the Williams Fork Formation (Lower Williams Fork Formation and Middle Williams Fork). Of the two major reservoir pay contributors, the Lower Williams Fork Formation contains the thickest pay sandstones that range in thickness from ~350-550 ft (106-167 m). 3D reservoir models of lithology, effective porosity, and other petrophysical properties illustrate the stratigraphic and petrophysical controls on high reservoir quality sandstones that form natural gas reservoirs. This work demonstrates that the most prospective reservoir intervals occur within the lower two-thirds of the Williams Fork Formation, with optimal reservoir properties concentrated in thick, laterally extensive sandstone bodies in the central-southeast portion of the study area
Choosing Repertoire for the Percussion Methods Course
Get PDFThis document serves as a guide to finding band literature that is relevant and pedagogically beneficial for beginning percussion students. It can be an essential tool for the collegiate percussion methods instructor. In the context of percussion methods classes, covering such a large amount of information in a relatively small timeframe is challenging, and having a supply of relevant repertoire for classroom exercises is essential to success.
The first section of this document defines in detail the most important skills for beginning percussionists to master on snare drum, timpani, and keyboard percussion. The second section then supplies an organized catalog of band literature that contains the fundamental skills for these instruments, with in-context examples included. Pieces are organized by each fundamental skill, with each skill subsequently being listed in order of difficulty. The third section of the document then discusses strategies for incorporating this information and relevant activities into a one-semester collegiate percussion methods curriculum.
Percussion methods courses are one of the primary pathways to reaching future educators. The versatile nature of this document enables it to be used by instructors with any level of experience. The end goal for this research is provide a comprehensive resource for music educators about teaching beginning percussionists that is approachable, and can therefore have an impact on the current state of beginning percussion education
Deception in Wireless Communications: Benefits and Perils
Get PDFWireless signals, ubiquitous and capable of penetrating obstacles, are increasingly exploited to infer personal information such as vital signs, human activities, and crowd counts. This surge in wireless sensing techniques benefits society but also poses significant security threats. Adversaries could potentially use these signals for wireless inference attacks, determining a target's activities with little regard for privacy or security. This dissertation mainly includes two studies on deception in existing wireless networks and systems. On one hand, it proposes proactive measures to send deceptive signals to mislead eavesdroppers, thus convincing them their attempts are successful when, in fact, they are failing. On the other hand, it identifies vulnerabilities in wireless liveness detection systems, where an attacker can use such wireless deceptive techniques to compromise these systems.
The first study proposes proactive defenses against all existing Channel State Information (CSI)-based vital signs and crowd counting inference attacks by establishing ambush locations and then transmitting deceptive signals designed to mimic vital signs or person count, albeit falsely, thereby protecting the user's true vital signs or person count data. Experimental results on software-defined radio (SDR) platforms demonstrate that these defensive strategies can effectively mislead eavesdroppers, who then receive falsified breathing rates or person counts.
Conversely, the second study demonstrates how attackers exploit these wireless deceptive techniques to compromise wireless liveness detection systems. Malicious attackers are capable of crafting fake wireless signals synchronized with spoofed video or audio streams to deceive systems into accepting fraudulent activities as legitimate. We refer to such attacks as phantom-CSI attacks. Experimental results on SDR platforms verify that these phantom-CSI attacks can significantly reduce the accuracy of spoof detection in wireless liveness systems
Characterizing the Effects of Land Cover Changes on the Spatiotemporal and Microphysical Properties of Convective Cells in Houston, Texas
Get PDFThis study examines the behavior and microphysical properties of convective cells across different environments in the Houston metropolitan area during summer 2022. Using KHGX NEXRAD radar observations of 22,372 cell tracks, convective properties
were analyzed across upwind, urban, and downwind regions. The upwind region, dominated by coastal processes, exhibited peak cell initiation during early morning hours (80% of total cells) with smaller (42.5 km²), less intense (36 dBZ) cells. The urban region showed approximately double the number of initiated cells per unit land area compared to upwind and 4–5 times more than downwind regions. Urban-influenced cells displayed greater variability in hydrometeor characteristics, larger mean raindrop sizes (ZDR ∼ 1.8 dB), and higher liquid water content (KDP ∼ 1.4 deg/km). Despite more frequent initiation, urban cells had lower precipitation efficiency. The downwind region demonstrated the highest precipitation efficiency (30 mm/cell) despite lower cell density.
Analysis of cell lifecycles revealed distinct patterns across regions. Urban impacts persisted downstream, with cells maintaining higher intensities through mature and dissipating stages. Upwind cells showed more uniform microphysical characteristics throughout their lifecycle, while downwind cells exhibited extended vertical development of ice particles during the developing and mature stages. This research advances understanding of how urban environments alter precipitation formation mechanisms and how the combined effects of sea breeze and urban heat island influence the spatiotemporal evolution of convective storms. It also highlights the need for further investigation into the combined effects of sea breeze and urban heat island on convective storm evolution
Reality Television Viewing and Peer-Directed Relational Aggression in Emerging Adulthood
Get PDFRelational aggression is a form of aggression characterized by harming or attempting to harm an individual’s social relationships. Previous research has identified a link between the consumption of relationally aggressive media and the perpetuation and endorsement of relational aggression. Previous studies have also identified reality television programs as significantly more relationally aggressive compared to their scripted counterparts. This study investigated the association between reality television consumption and peer-directed relational aggression and normative beliefs about relational aggression, as well as the moderating role of perceived realism in these associations. Follow-up analyses were conducted to further understand whether these associations differed depending on the specific type of reality television that was viewed. Participants were 336 college students (83% female) who completed an online survey. Though perceived realism was not a moderator of these associations, it did emerge as a significant predictor of peer-directed relational aggression. Additionally, male participants held stronger normative beliefs about relational aggression
THE HEDGE FUND NEWSPAPER OWNERSHIP ERA: FACTORS THAT MAKE THE INDUSTRY VULNERABLE, AND THE NEGATIVE IMPACTS ON MEDIA MANAGEMENT AND THE ROLE OF JOURNALISM IN DEMOCRACY
Get PDFThis dissertation sheds light on the relationship between ownership and media management, particularly focusing on the impacts of hedge fund ownership in journalism. While the effects of hedge fund ownership have been studied across various industries, they have not been systematically examined in the field of journalism.
Some research has looked at the concurrent effects of ownership by activist hedge funds in general or in other target industries such as real estate and nursing homes (Morgenson & Rosner, 2023; Stulz, 2007), but none of it has focused on the U.S. daily newspaper industry. This issue only recently caught the attention of the industry when Tribune Publishing was acquired by Alden Global Capital in 2021 (Coppins, 2021). While a few studies have investigated the financial impacts of profit margin requirements in the newspaper industry from the stock market (Beam, 2002; Demers, 1996), or the effects of private investors on media management decisions (Picard, 2006; Lacy, Shaver, & Cyr, 1996; Soloski, 2013), none of them have specifically addressed the influence of hedge fund ownership.
Two studies were conducted in this dissertation, together providing a comprehensive picture. Study One examined financial issues, while Study Two explored human issues, offering insights not only into why the newspaper industry became vulnerable to hedge fund attacks but also into the concurrent management struggles under full hedge fund governance, thus extending the threats to the role of journalism in democracy. Specifically, Study One was a longitudinal study spanning from 2007 to 2022, analyzing 55 annual reports from four newspaper companies over 16 years, including Gannett, Lee Enterprises, Tribune Publishing, and McClatchy. Study Two conducted in-depth interviews, targeting individuals in management positions at newspapers acquired by hedge funds, namely Tribune Publishing (acquired by Alden in 2021) and McClatchy (acquired by Chatham in 2019). A total of 21 participants were successfully recruited, and the data showed saturation, indicating that no more new viewpoints emerged.
This study also contributes to the research on media firm ownership. The digital age eroded the financial security of news media firms, which have for two decades failed to achieve a sustainable business model in the public ownership era (Hollifield, 2012; Picard, 2010; Chyi & Ng, 2020), leaving them open to a new kind of ownership that no longer values the journalism product and professional values—the hedge fund ownership era
Exploring ParE Toxin Dynamics: from Impact to Quantification in Bacterial Cells
Get PDFThe increasing prevalence of antimicrobial resistance (AMR) in pathogenic bacteria has brought significant challenges to global public health. However, it has been decades since the discovery of the last antibiotic, making it essential to explore novel therapeutic targets and mechanisms to combat bacterial infections. Bacterial toxin-antitoxin (TA) systems, which exist widely among bacterial species, have been attracting attention in the field for their potential to be co-opted for health purposes. These non-secreted TA systems typically consist of a stable toxin that inhibits essential cellular processes, leading to cell growth inhibition or cell death, and a labile antitoxin (RNA or protein) that neutralizes the cognate toxin under normal growth conditions. In the case of Type-II ParDE TA system, the ParE toxin protein is neutralized by the ParD antitoxin protein through direct protein-protein interactions. Under stress conditions, degradation of the ParD antitoxin releases the ParE toxin. Similar to quinolone antibiotics, this liberated ParE toxin interacts with and inhibits DNA gyrase, causing the accumulation of double-strand breaks (DSBs) in DNA in the bacterial cell, which could lead to cell death. The detrimental DNA gyrase inhibition mediated by ParE toxins and their widespread presence in Gram-negative bacteria of concern make them a potential, potent agent for antibacterial drug development.
The idea of co-opting TA systems as a strategic tool to control bacterial growth is still in its early stage due to the lack of knowledge on how to artificially activate the toxins in vivo. This dissertation focuses on ParE subfamily members from Pseudomonas aeruginosa and Mycobacterium tuberculosis and aims to provide new insights for the proof of concept of co-opting the ParE toxins as a novel therapeutic agent. By exploring the effects of ParE toxin-mediated DNA damage on bacterial growth, genetic resistance, and antibiotic susceptibility, this work addresses a key gap in our understanding of the role of the ParE toxin in bacterial physiology and therapeutic development. This dissertation comprises three key research chapters:
The work in Chapter II investigated the phenotypic impacts of induced ParE toxin expression on bacterial growth, genetic mutation, and antibiotic susceptibility. The expression of ParE toxins—originating from P. aeruginosa and M. tuberculosis—was induced in P. aeruginosa cells and Escherichia coli surrogate cells. Differential toxicity profiles were noted, with the PaParE1 toxin exhibiting essentially no toxicity and the other ParE toxins exhibiting dose-dependent toxicity. ParE toxin-mediated DSBs in DNA trigger error-prone DNA repair pathways, such as the SOS response, which could lead to the accumulation of genetic mutations potentially contributing to the emergence of antibiotic resistance. Results indicated that the expression of potent ParE toxins led to an increased mutation frequency, except for the case of the attenuated ParE toxin. However, this increase in mutation frequency did not translate into significant resistance against a broad spectrum of common clinical antibiotics within the observation period. These findings support the concept of co-opting TA systems as an antibacterial approach.
The work in Chapter III uncovered a survival mechanism that E. coli cells use to evade the lethal effects of plasmid-mediated ParE toxin expression. In the work of Chapter II, we observed an interesting phenotype where E. coli cells, after exposure to the plasmid-mediated inducible expression of the ParE1 toxin from M. tuberculosis, became “insensitive” to subsequent induction of the ParE1 toxin. Moreover, the proportion of these insensitive cells increased with continued passages in the presence of the inducer. This phenotype was not correlated with changes in the plasmid sequence and could not be rescued by increasing the inducer uptake. Instead, it was associated with a marked reduction in plasmid copy number (PCN). This reduction in PCN was reproducible across various E. coli strains and ParE toxins, indicating a generalized response mechanism. Furthermore, bacterial whole genome sequencing revealed a N845S residue substitution in DNA polymerase I, which is known to participate in the replication of the type of plasmid used in our experiments. This observed survival strategy of reducing PCN highlights the adaptability of bacterial cells to stress conditions and provides valuable insights into microbial adaptation and genetic engineering methods.
The work in Chapter IV validated the feasibility of using a novel bio-layer interferometry (BLI)-based method to quantify low-abundance ParE protein molecules in cell lysate. In the work of Chapter II, we noticed that despite sharing a conserved three-dimensional structure, the ParE toxins exhibited varying toxicity profiles. This differential potency may stem from variations in protein sequence or expression levels. Traditional detection methods like Western blot and mass spectrometry failed to detect those potent ParE toxins due to their toxic nature and resulting low abundance in cell lysate. To overcome the limitation, we employed the highly sensitive BLI technique. Using the attenuated ParE1 toxin from P. aeruginosa, which allows for robust expression and purification, we optimized the specific binding of ParE1 toxin molecules to biosensors by adjusting the number of dips and cell lysate concentration in the running buffer. We established linear relationships between the specific binding signals and ParE1 toxin concentrations using different types of biosensors, demonstrating the feasibility of using BLI-based method for the quantification of ParE protein molecules in cell lysate.
Overall, this dissertation not only provides a comprehensive view on the phenotype impacts of ParE toxins on bacterial growth, genetic mutation, DNA stability, and antibacterial response, laying the foundation for co-opting TA systems as an antibacterial strategy, but also introduces a novel methodological approach. This approach will enhance our understanding of the molecular dynamics of toxin proteins, which facilitates future studies on TA system biology