Physical Sciences and Mathematics Commons^™

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …

Beauty Of Life In Dynamical Systems: Philosophical Musings And Resources For Students, Soumya Banerjee, Joyeeta Ghose, Tarakeswar Banerjee, Kalyani Banerjee

Journal of Humanistic Mathematics

Information plays a key role in life and in complex biological systems, and dynamical systems underlie and can be used to represent many complex systems. Indeed, dynamical systems and information processing capabilities may be the hallmarks of life-like systems. In this paper we combine dynamical systems with a computational framework to generate art. The framework can be used to generate aesthetically appealing forms of life-like systems. Our work suggests that we may need an ``aesthetic sense'' to recognize life that we have not seen before. We also provide teaching resources for students in schools and undergraduate institutions.

Students Arts Participation Increases Stem Motivation Via Self-Efficacy, Stephen M. Dahlem

The STEAM Journal

This work found that there exists a correlation between student motivation in science, technology, engineering and mathematics (STEM) and student participation in the arts during high school with self-efficacy being a mediator. STEM is an important component of student success from a broad, national, perspective, as well as from a domain-specific point of view. The results of this work may provide aid to teachers, parents, administrators, and even students seeking to find ways to increase student motivation and performance in the STEM subjects. Additionally, this work may be of interest to advocates of the arts. This quantitative correlational study was …

Challenge-Based Learning & Steam Curriculum, Diana Lockwood

The STEAM Journal

STEAM education is being integrated into elementary schools as a way to engage more students in creativity, hands-on learning, and problem-based learning also referred to as Challenge-Based-Learning (CBL). This article focuses on elementary educators’ curriculum design for STEAM and presenting students with open-ended questions phrased as a challenge as a way to raise student interest and achievement (DeJarnette, 2018; Hunter-Doniger, 2018). When students received challenges to solve, they felt more open to sharing their ideas since there was more than one potential right answer (DeJarnette, 2018; Drake, 2012). When implementing CBL, teachers act as facilitators using a constructivist approach as …

Using Computational Fluid Dynamics And Optical Sensor Technology To Scale Cell Culture Platforms, Mandar Makwana

KGI Theses and Dissertations

Different cell culture vessels ranging from micro scale to laboratory scale to commercial scale play critical role in upstream process development for biologics manufacturing. Based on the mode of operation, cell culture vessels have different hydrodynamic environments, making it challenging to scale. Integrated approaches using computational tools supported by experimental studies can overcome these challenges. Computational Fluid Dynamics (CFD) is one such tool that can simulate hydrodynamics within the cell culture vessels and can provide insights at macro and micro-scale. Accuracy of a CFD model significantly depends on the fluid model and assumptions. Traditionally, simple two-equation fluid models were developed …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Quantifying The Carbon Stored And Sequestered By The Trees On Pomona College’S Campus, Paola A. Giron-Carson

Scripps Senior Theses

We are experiencing a climate crisis that must be confronted with strategic mitigation. Pomona College contributes to the climate crisis through its emissions for which there is a baseline record. However there is no baseline record of the climate mitigation currently performed by the trees on Pomona’s campus through carbon storage. This study seeks to determine a current baseline quantity of carbon stored and sequestrated by Pomona’s trees as well as possible courses of climate mitigation for Pomona College to take. Initial information gathering was conducted through interviews with several stakeholders. This study was conducted using data collected prior to …

Stem Education And Retention For Black Women Using High-Impact Practices: Historically Black Colleges And Universities Vs. Predominantly White Liberal Arts Colleges, Annette Njei

CMC Senior Theses

Black women are significantly underrepresented within the fields of science, technology, engineering, and mathematics (STEM). To address this, the Association of American Colleges & Universities crafted ten high-impact practices to increase student engagement and promote retention. This research paper examines how three specific high-impact practices (learning communities, mentoring, and undergraduate research experience) are utilized in STEM education.This research paper explores and compares the best high impact approaches that successfully teach and retain Black women within the various fields of STEM within the differing academic environments of historically Black colleges & universities ( HBCUs) and predominantly white liberal art colleges (PWLACs). …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Here, There, And Everywhere: Probing Ubiquitin-Cavitand Binding Via 15n-1h Hsqc, Julia Didziulis

Scripps Senior Theses

Ubiquitination and other post-translational modifications play a major role in the proliferation of many neurodegenerative diseases, developmental disorders, and cancers, and as such are subjects of recently increased biochemical interest. Expanding upon such research, this study confirmed a robust method of ubiquitin expression and purification, then used 15N-1H HSQC to analyze ubiquitin samples containing varying concentrations of a deep cavitand with affinity for lysine and arginine side chains. In the pure ubiquitin spectrum, arginine side chain chemical shifts were detected in the nitrogen 80-85 ppm range and lysine side chain signals were undetected. However, upon introduction of the cavitand, collection …

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

Spatial Geochemical Changes In Central And East Texas Soils Over Time Resulting From Human Decomposition, Isabela Marisol Overturf

CMC Senior Theses

Human decomposition is studied to aid forensic investigations and better understand the impact of cemeteries on urban resources like soil and groundwater. The purpose of this study was to identify changes in soil geochemistry at and around a human grave to search for lateral nutrient movement and possibly identify new patterns in elemental concentrations that could be used in estimating post-mortem intervals (PMIs). At the Forensic Anthropology Research Facility (FARF) at Texas State San Marcos, soil samples were collected from a shallow grave over the course of 54 days to conduct analysis for organic matter content, texture, pH, and bulk …

Energy As A Limiting Factor In Neuronal Seizure Control: A Mathematical Model, Sophia E. Epstein

CMC Senior Theses

The majority of seizures are self-limiting. Within a few minutes, the observed neuronal synchrony and deviant dynamics of a tonic-clonic or generalized seizure often terminate. However, a small epilesia partialis continua can occur for years. The mechanisms that regulate subcortical activity of neuronal firing and seizure control are poorly understood. Published studies, however, through PET scans, ketogenic treatments, and in vivo mouse experiments, observe hypermetabolism followed by metabolic suppression. These observations indicate that energy can play a key role in mediating seizure dynamics. In this research, I seek to explore this hypothesis and propose a mathematical framework to model how …

Qualitative Analysis Of A Resource Management Model And Its Application To The Past And Future Of Endangered Whale Populations, Glenn Ledder

CODEE Journal

Observed whale dynamics show drastic historical population declines, some of which have not been reversed in spite of restrictions on harvesting. This phenomenon is not explained by traditional predator prey models, but we can do better by using models that incorporate more sophisticated assumptions about consumer-resource interaction. To that end, we derive the Holling type 3 consumption rate model and use it in a one-variable differential equation obtained by treating the predator population in a predator-prey model as a parameter rather than a dynamic variable. The resulting model produces dynamics in which low and high consumption levels lead to single …

Environmental Controls On The Spatial Distribution Of Greenfin Darters And Biodiversity In The Blue Ridge Mountains, Dri Tattersfield

CMC Senior Theses

Disproportionate concentrations of biodiversity in mountains worldwide suggest linkages between geologic processes and biodiversity that are not yet well understood. The Tennessee River Basin in the Blue Ridge Mountains of the southeastern U.S. is a global hotspot for freshwater fish biodiversity. To investigate drivers of biodiversity in the Tennessee River Basin, and explore links to geologic processes, I study the Greenfin Darter (Nothonotus chlorobranchius), a small fish endemic to the upper Tennessee River Basin. I use generalized linear models (GLMs) to evaluate the influence of topography, lithology, climate and land use on the distribution of the Greenfin Darter, …

Using Nmr Spectroscopy And Computational Chemistry To Confirm The Structure Of Novel Antibiotic Nocamycin O, Stephanie Lewis

CMC Senior Theses

In recent years, many medically promising antibiotics have been discovered in nature, especially in insect-microbe symbioses. One of the better-studied examples of this kind of defensive relationship is that of fungus-growing ants and the antibiotic-producing Actinobacteria. These bacteria produce several defensive chemicals with myriad uses, including one antibiotic that inhibits the growth of several bacterial strains, including other Actinobacteria. This antibiotic (known as nocamycin O) is a promising candidate for medicinal use due to its similarities to bacterial RNA polymerase inhibitors tirandamycin and streptolydigin, which inhibit several human pathogens. The determination of the structure of nocamycin O will be an …

Heat Stress During Larval Stages On Coral Survivorship For M. Capitata, Sarah Woo

Pitzer Senior Theses

Very little is known about how heat stress during larvae stages effect larvae survivorship, early coral recruit settlement, and later stage coral survivorship. We focused on determining how heat stress during larvae stages effected Montipora capitata survivorship over time. After thermally stressing larvae, we asked how many larvae survived the treatment, how the treatment affected settlement, how many larvae survived the heat treatment but did not settle, and later stage coral survivorship experienced residual effects from the heat stress treatment. We exposed coral larvae to ambient seawater temperatures at 30°C and heated seawater temperatures to 34°C for an hour and …

Neither “Post-War” Nor Post-Pregnancy Paranoia: How America’S War On Drugs Continues To Perpetuate Disparate Incarceration Outcomes For Pregnant, Substance-Involved Offenders, Becca S. Zimmerman

Pitzer Senior Theses

This thesis investigates the unique interactions between pregnancy, substance involvement, and race as they relate to the War on Drugs and the hyper-incarceration of women. Using ordinary least square regression analyses and data from the Bureau of Justice Statistics’ 2016 Survey of Prison Inmates, I examine if (and how) pregnancy status, drug use, race, and their interactions influence two length of incarceration outcomes: sentence length and amount of time spent in jail between arrest and imprisonment. The results collectively indicate that pregnancy decreases length of incarceration outcomes for those offenders who are not substance-involved but not evenhandedly -- benefitting white …

Evolution Of Island, Dominique Kongsli

The STEAM Journal

Evolution of Island emerged from the depths of an ocean of blue paint. My process involves observation of nature: I remember scuba diving in Thailand in the Andaman Sea and having a spiritual experience underwater while observing Christmas-tree worms pop in and out of the coral.

Visual Arts Enhance Instruction In Observation And Analysis Of Microscopic Forms In Developmental And Cell Biology, Max Ezin, Christina Noravian, Amira Mahomed, Adam Lyle, Aveleen Gill, Tamira Elul

The STEAM Journal

Two important skills for scientists in developmental and cell biology, as well as in fields such as neurobiology, histology and pathology, are: 1) observation of features and details in microscopic images of cells, and 2) quantification of cellular features observed in microscopic images. However, current training in developmental and cell biology does not emphasize observation and quantitative analysis of microscopic images, and it is unclear how best to teach students these skills. Here, we describe our experiences applying visual artistic approaches to instruct undergraduate and graduate students in how to observe and analyze cellular forms in microscopic images. At Loyola …

Modeling Residence Time Distribution Of Chromatographic Perfusion Resin For Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study, Kevin Vehar

KGI Theses and Dissertations

The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation's physical resource demand. Specifically, …

Extending Power Series Methods For The Hodgkin-Huxley Equations, Including Sensitive Dependence, James S. Sochacki

CODEE Journal

A neural cell or neuron is the basic building block of the brain and transmits information to other neurons. This paper demonstrates the complicated dynamics of the neuron through a numerical study of the Hodgkin-Huxley differential equations that model the ionic mechanisms of the neuron: slight changes in parameter values and inputted electrical impulses can lead to very different (unexpected) results. The methods and ideas developed for the ordinary differential equations are extended to partial differential equations for Hodgkin-Huxley networks of neurons in one, two and three dimensions.

Natural By Design, Craig Steele

Journal of Humanistic Mathematics

I’m a professor in the Department of Biology and Health Sciences at Edinboro University, in Edinboro, Pennsylvania, a small, comprehensive liberal arts institution within the Pennsylvania State System of Higher Education. My major teaching duties involve environmental biology, zoology, and ichthyology. I emphasize to my students how mathematics underlies the natural world of plants and animals, pointing out to them how many of “our” most amazing engineering and constructional achievements are copied from nature (from geodesic domes to the fusiform bows of modern commercial ships), as well as how plant and animal physiology and animal behavior (of individuals and of …

Intercropping For Water Conservation: Environmental And Economic Implications Of A Sustainable Farming Practice In California's Central Valley, Sophie Baker

Scripps Senior Theses

California’s agricultural sector is the biggest water consumer in the state and faces intense pressure to reduce its overall water usage. Industrialized monoculture systems dominate the industry and often disregard long-term environmental and economic externalities for short-term profit maximization. To maintain longstanding food security and economic stability as well as protect the state’s water supply, it is critical that these systems transition to more sustainable and resilient production mechanisms. As an alternative to monoculture, intercropping affords greater potential to conserve water, protect soil quality, and increase crop yields, among other metrics of sustainability. However, there has been much controversy over …

Machine Learning Methods For The Analysis Of Metagenomes, Vito Adrian Cantu Alessio Robles

CGU Theses & Dissertations

As of October 2020, there are 18.6 × 1015 DNA base pairs publicly available in the Sequence Read Archive and this number is growing at an exponential rate. As DNA sequencing prices continue to drop, many research groups around the world have incorporated high throughput sequencing in their research, giving us access to sequences from many distinct ecosystems. This has revolutionized the field of metagenomics, which aims to fully characterize all organisms and their interactions in a particular system. Nevertheless, the plethora of available data has made its analysis difficult as traditional techniques such as genome assembly or sequence alignment …

Use Of Kalman Filtering In State And Parameter Estimation Of Diabetes Models, Cassidy Le

HMC Senior Theses

Diabetes continues to affect many lives every year, putting those affected by it at higher risk of serious health issues. Despite many efforts, there currently is no cure for diabetes. Nevertheless, researchers continue to study diabetes in hopes of understanding the disease and how it affects people, creating mathematical models to simulate the onset and progression of diabetes. Recent research by David J. Albers, Matthew E. Levine, Andrew Stuart, Lena Mamykina, Bruce Gluckman, and George Hripcsak¹ has suggested that these models can be furthered through the use of Data Assimilation, a regression method that synchronizes a model with a …

Complex Ciliary Flows Around Stentor Polymorphus In Solutions Of 2% Buttermilk And Chlamydomonas Reinhardtii, Eliana B. Smithstein

Scripps Senior Theses

Stentor are large, unicellular ciliates of the Heterotricha order. They live in both freshwater and marine habitats and are mostly found in ponds. I studied Stentor polymorphus, which is a species of Stentor only recently discovered to be lab culturable. They range from 0.5-1.5mm in length and are unusual because they live with endosymbiotic algae and are much more likely than other, more widely studied, species of Stentor to form aggregates while they are eating. There are three main components to this thesis: First, I established protocols for keeping a viable S. polymorphus culture, since no protocols had been …

Antifungal Defense Molecules From Bacterial Symbionts Of North American Trachymyrmex Ants, Georgia Scherer

CMC Senior Theses

Defensive symbioses, in which microbes provide molecular defenses for an animal host, hold great potential as untapped sources of therapeutically useful antibiotics. Fungus-growing ants use antifungal defenses from bacterial symbionts to suppress pathogenic fungi in their nests. Preliminary chemical investigations of symbiotic bacteria from this large family of ants have uncovered novel antifungal molecules with therapeutic potential, such as dentigerumycin and selvamicin.

In this study, the bacterial symbionts of North American Trachymyrmex fungus-growing ants are investigated for antifungal molecules. Plate-based bioassays using ecologically-relevant fungal pathogens confirmed that these bacteria have antifungal activity. In order to purify and identify the antifungal …

Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell

CMC Senior Theses

Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …

Third Voices Conference On Teaching Stem With Music, September 22-23, 2019, Lawrence M. Lesser

Journal of Humanistic Mathematics

The third annual VOICES (Virtual Ongoing Interdisciplinary Collaborations on Educating with Song; https://www.causeweb.org/voices/) conference will be held online September 22-23, 2019. Chaired by Tiffany Getty, this conference will explore the use of song to teach STEM (science, technology, engineering, and mathematics) at the postsecondary (or secondary) level.