Varsha Appaji (U): Consumption Heterogeneity Across Space

The purpose of our research project would be to categorically and spatially analyze the consumption patterns of US families in a way that can account for heterogeneity. Currently, there are a number of policy conclusions that are made based on observations of aggregate consumption. However, when looking at aggregate data, a significant amount of variation across the different categories of consumption is masked. Our project would serve to reveal this heterogeneity, such that one can see how consumption patterns vary by family characteristics, economic cycles, consumption shocks, and more. Essentially, our project consists of microeconomic data analysis, with the ultimate goal of making the basis of macroeconomic policies more robust and holistic.

Varsha Appaji
Majors: Statistical science, economics, public policy
Faculty mentor: Rocio Madera

Autumn Beck (U): A Content Analysis of College-student-proposed Sense of Belonging to a Residential Community Definitions

Co-authors: Matthew Nadler and Dustin Grabsch

We sought to answer the question, "how do students define sense of belonging to their residential community?" To answer this question, we distributed a survey to 2,400 on-campus residents at a 4-year university win the southern United States and received a 38% (n = 920) response rate. 581 respondents supplied a definition. We followed an interpretive research paradigm, which views a phenomenon (sense of belonging to their residential community) through the meanings that people (residential students) attribute to it in a specific sociocultural context (residential community on a specific university campus). The responses produced three emergent themes: space and place, strengthening connections, and outcomes of belonging. We posit a student-grounded definition of residential sense of belonging. Our proposed definition and findings are written with university housing and residence life professionals, campus planners, facilities, and student affairs professionals in mind. This definition further defines what it means to belong to a residential community from the student's perspective, which may inform them on how to best enhance the student experience. Additionally, the findings from this study provide insight into how students experience belonging by an unchosen affiliation. This study adds to the growing understanding of sense of belonging in higher education.

Autumn Beck
Majors: Business Management and Film and Media Studies; Minors: Chinese and Law and Legal Reasoning
Faculty mentor: Dustin Grabsch

Daniel Chavez and Eli Laird (U): An ODE-Based Model for the Spread of COVID-19 at Southern Methodist University

Co-authors: Eli Laird

In early 2020, the SARS-CoV-2 outbreak made its way into the United States and began to rapidly breach all existing protocols for dealing with an infectious disease spreading within communities both locally and at large. As a result all academic institutions within the United States disbanded their campus and school communities so as to slow the spread of the novel virus. We modified a standard Susceptible-Exposed-Infected-Recovered (SEIR) compartmental model to examine the intertwined behaviors of both residential and community populations within university and college campuses, with a focus on Dallas' Southern Methodist University. The modified model contains a new quarantined/isolation category and an equilibrium between the susceptible and exposed categories, with a novel exposure function linking the two. Exposure rates for relevant spaces where students frequently flow through were predicted and calculated from official SMU databases and floor plans. These predictions may be used to propose disease-prevention strategies specific for college campuses.

Daniel Chavez
BS Biochemistry & BBA General Business
Faculty Mentor: Brandilyn Stigler


Dedeepya Chinnam (U): A Sequential Exploratory Mixed-Methods Study: Motivations of Undergraduate Students To Pursue Multiple Majors

Co-authors: Dustin Grabsch, Sheri Kunovich, Laura Bell, Hannah Webb, Ryan Leibowitz

This project seeks to understand the motivations of undergraduate students to pursue multiple majors. Utilizing a sequential, exploratory mixed-methods design, in phase one we will interview students who are currently pursuing multiple majors to determine themes in their expressed motivations. Following the development of themes, we will issue a brief survey instrument to undergraduate students with multiple majors to determine the prevalence of each motivation theme within the student body. Findings will aid undergraduate general education curriculum committees, academic departments, and higher education institution administrators.

Dedeepya Chinnam
Majors: Business Analytics and Supply Chain Management
Faculty mentor: Dustin Grabsch

Cole Fontenot (U): #BlackAt​: How Social Media Content Analysis Illuminates Experiences of Black Students

Co-authors: Kennedy Coleman, Tara Greig, Kish Parikh

Increasingly, BIPOC college students have utilized social media to share their experiences of racialized trauma while attending higher education institutions. Presenters outline a social media content analysis study of posts from #BlackAtSMU, highlighting themes that arose. Implications at the institutional level and future directions for this assessment methodology are discussed.

Student Affairs Undergraduate Research Team
Mentor: Allison Kanny

Tara Greig (U): Centering Black Student Voices in a Nested Model of Racial Battle Fatigue

Winner: Student Affairs (Undergraduate)

Co-authors: Kish Parikh, Cole Fontenot, Kennedy Coleman

Racial Battle Fatigue (RBF) among college students at predominantly white institutions (PWIs) is an issue of high concern. While higher education research has examined RBF concerning its prevalence, manifestations, and impact on various affective and academic outcomes, relatively few studies have sought to conceptualize this construct within an ecological systems model. This presentation presents findings that examine contributors to racial battle fatigue among Black undergraduate students in a nested environmental model. The study also sought to uncover how these relationships relate to student-level outcomes and how students utilize coping strategies to navigate these systems.

Student Affairs Undergraduate Research Team
Mentor: Allison Kanny

Sara Hatcher (U): Gait Mechanics with Single Leg Elongation

Winner: Simmons (Undergraduate)

It is common thought that structural asymmetries result in a running disadvantage, and that anatomical and mechanical symmetry is the preferred condition. Our opposition to this stance began in observation of Usain Bolt, who exhibits a 13% force difference in striking with his right versus left leg due to a leg length difference. But there are few studies on gait asymmetries to explain this phenomenon: how can the fastest man in history be asymmetrical? To investigate this, we have created a study in which we lengthen the right leg of athletes and observe the response of both legs. We propose that the body compensates by altering vertical force and contact time in the opposing limb, resulting in an adjustment to both legs. Our subjects ran a control and experimental condition where an 27mm insert was attached to the right shoe at 3, 4, 5, and 6m/s. We hypothesized that the lengthened leg would have a decreased vertical ground reaction force and increased contact time and the unlengthened leg would have an increased vertical ground reaction force and decreased contact time. We further hypothesized that the two-leg average would not change between conditions. We determined both hypotheses to be correct. These findings show that asymmetries are not an inherent disability, but rather, functional asymmetries can increase the body's effectiveness in motion.

Sara Hatcher
Major: Applied Physiology and Health Management
Faculty mentor: Peter Weyand

Matthew Heaney (U): Are azo pigments really azo pigments? Structural and spectroscopic characterization of β-naphthol reds

Naphthol reds are a group of widely used pigments with prominent historical, commercial, and cultural significance and are frequently characterized as part of a wider group called azo pigments. Azo pigments have two fundamental properties, they have the vibrant colors and low solubilities characteristic of pigments, and the presence of an azo group within their structure. The latter property, however, as other studies have found is oftentimes completely unfounded. Some of these pigments do not even possess azo groups at all, rather they possess a similar, but fundamentally different group known as a hydrazone group. In other cases these pigments can possess both the azo and hydrazone forms at the same time or undergo an enol/keto tautomeric shift under certain conditions. There are however still many common pigments which are still marketed and referred to as azo pigments with frequently little to no evidence. In this study by using the capabilities afforded to us by X-ray diffraction techniques as well as Rietveld refinement it was possible to determine not only the presence of the hydrazone group but also to elucidate the crystal structures of two pigments. Ultimately these results can fundamentally change both how we refer to these pigments from now on and how these pigments may be better used and applied in the future.

Matthew Heaney
Major: Chemistry; Minor: Geology
Faculty mentor: ‪Tomče Runčevski‬

Sydney Holder (U): Descriptive Statistics for the Explanatory Factor Analysis of the MMaRS Home Use Survey

An analysis of the explanatory factor analysis for MMaRS Home Use Survey. The research was rooted in finding whether the Home Use Survey was a reliable way of measuring at home spacial reasoning.

Sydney Holder
Majors: Applied Mathematics, Statistics, Data Science
Faculty mentor: Leanne Ketterlin Geller

Matthew Hutnyan (U): Alexithymia and Self-Referential Processing in a Healthy Population

Co-authors: Cecile S. Sunahara, Benjamin A. Tabak

Success in the social world is said to be contingent on how effectively one can decipher the mental and emotional states of others. A growing body of evidence links this ability, known as social cognition, with two psychological constructs: alexithymia – difficulty identifying and describing one’s own emotions – and self-referential processing (SRP) – the process through which we use knowledge of the self to interpret information. This study (n = 396) set out to directly examine the relationship between alexithymia and SRP in a sample of non-clinical individuals. Multilevel modeling was utilized to examine differences in accuracy between words presented in the “self” condition versus the “physical” condition, and then to examine whether alexithymia moderated the effect of referent condition when controlling for age, gender, and depressive symptoms. Results indicated that participants were more accurate at recognizing words that were presented originally with a “self” referent than words presented with a “physical” referent (b = -.39, 95% CI [-.41, -.37], p < .001) and that levels of alexithymia were linked with SRP task accuracy, such that as levels of alexithymia increased, accuracy in the “self” condition decreased. These findings establish a link between alexithymia and SRP at the behavioral level for the first time.

Matthew Hutnyan
Majors: Psychology, Health and Society; Minors: Neuroscience and Cognitive Science
Faculty mentor: Ben Tabak


Lisa Kim (U): Measuring Nitric Oxide Metabolites as a Biomarker of Concussion

A concussion is a traumatic injury that affects brain function. Although sports-related concussions are so common, the physiology of concussions is still not yet fully understood. Nonetheless, several types of research are focusing on this study to explain the physiology of concussion and identify possible biological markers. Since blood vessels in the brain behave similarly to those in the other parts of the body, one can further study the brain and the concussion by measuring the blood pressure and flow. With this idea, a research study has found nitric oxide (NO) as an important biological marker for concussion, indicating either possible inhibition or stimulation of nitric oxide synthase (NOS) in our body. By incorporating this information into my project, I have performed Griess assay to measure nitrate and nitrite in blood samples extracted from SMU athletes who have experienced concussions.

Yujin Lisa Kim
Major: Biochemistry; Minor: Chinese
Faculty mentor: Alex Lippert

Wren Lee (U): Gay & Greek: Designing for LGBTQ Fraternity and Sorority Members

College is a time of exploration and growth for many individuals. It is especially important for LGBTQ folxs; for some LGBTQ folxs, college is the first time they can explore their LGBTQ identities free of judgment. Others seek community and find it within fraternities and sororities. Yet, traditional fraternities and sororities are notoriously not LGBTQ friendly. These organizations promote a hypermasculine, heteronormative, homophobic, and transphobic environment. For LGBTQ Greeks, the situation can be emotionally taxing. Through this project, the investigators aim to deepen their learning about these experiences to build solutions to help LGBTQ Greeks feel confident in their LGBTQ identities in Greek spaces. In the long term, the investigators aim to learn more about how to develop systems to protect and empower LGBTQ individuals in anti-LGBTQ spaces. They will learn about the Greek experience for LGBTQ members at Southern Methodist University and co-create a solution for their intersectional needs. They will employ human-centered design methods to help the LGBTQ Greek community feel comfortable in spaces they might not typically occupy.

Wren Lee
Major: Creative Computation; Minors: Human Rights and Women and Gender Studies
Faculty mentor: Dustin Grabsch

Jonathan Lindbloom (U): A Bayesian Gaussian Process Model for COVID-19

Winner: Undergraduate Top 3
Winner: Dedman III (Undergraduate)

We present the Bayesian approach to parameter inference for SIR ODE models using Markov Chain Monte Carlo (MCMC) methods, along with its computational implementation using the PyMC3 probabilistic programming library. We show how changes in the transmission rate over time can be captured by change-point models. However, these change-point models fail to learn the underlying dynamics of the time-dependent transmission rate. To overcome this pitfall, we demonstrate how using Gaussian processes to place a functional prior over the time-dependent transmission rate does a better job at characterizing uncertainty in forecasts. Our approach removes the need to specify priors over change-points, captures uncertainty in the dynamics of the effective reproduction number, and flexibly fits county or state-level data without modification. To validate our model, we evaluate the accuracy of our model’s forecasts using scoring rules and compare its performance with that of other competing models submitted to the Center for Disease Control (CDC).

Jonathan Lindbloom
Mathematics, Finance
Faculty Mentor: Alejandro Aceves

Avery Mercurio (U): Mustangs For Hope: A Community Based Nonprofit Bringing Virtual Learning to Dallas Children

Mustangs For Hope is a new nonprofit organization that provides free, virtual, one-on-one tutoring for underprivileged Dallas children whose families have been affected by COVID-19 after-school program closures. Mustangs For Hope works in conjunction with Voice of Hope Ministries to match K-12th grade students with a college-aged mentor in order to foster community between young learners and college-aged students. Mustangs For Hope believes that virtual learning will remain a cornerstone in education for years to come. For this reason, Mustangs For Hope stands committed to creating an environment where academically at-risk children are never afraid to seek the help they need, to be intellectually curious and to excel in their academic journey.

Avery Mercurio
Majors: EMIS and Mathematics
Mentors: Gheorghe Spiride and Lindsay Davis

Robert Mirr (U): #BlackAtSMU

Winner: Meadows (Undergraduate)

This documentary is important because it will serve as an exploration into the issue of systemic racism and white supremacy that is deeply ingrained in our SMU community which so necessarily needs to be talked about. Our documentary will also serve as a mode of education and a dialogue starter to promote better understanding of these issues and create meaningful change in the actions of those on campus. The community being served by this project is vast, but one highlighted community is that of the black students, faculty, and alumni of SMU. Our goal with this project is to create a pedagogical tool to be used to spark conversation around all areas of SMU, from the residential commons to PRW I classes, to administration meetings. We aim to create dialogue around how people of color are treated in all areas at SMU and spark change to create a more inclusive, diverse, and accountable community. I personally hope to create a change and a dialogue within the SMU community. These issues have gone both unnoticed by the administration and student body for too long. By sparking this dialogue I hope to ensure a change so students can no longer feel this white supremacy. I hope to see a change that benefits the greater SMU community for good and forever.

Robert Mirr
Major: Film production; Minor: Graphic Design and Advertising
Faculty mentor: Amber Bemak

Fidelia Nawar (U): Covid-19 Open Research Dataset (CORD-19) Extractor

Winner: Undergraduate Top 3
Winner: Lyle (Undergraduate)

The Covid-19 Open Research Dataset is a growing resource of coronavirus research and scientific papers on Covid-19. CORD-19 is designed to facilitate the development of information retrieval systems through its collection of structured full-text papers. This study aims to contribute to the SMU AI Club's efforts to develop a search engine that parses through CORD-19 articles in order to extract relevant data about protein, compound, chemical information, and more. In the study, we describe the mechanics of dependency parsing, highlighting challenges and key design decisions, and discuss tools and upcoming shared tasks related to the search engine project. We hope this resource will introduce a new way to search for desired data related to Covid-19 and further bring together the computing and biomedical community on campus.

Fidelia Nawar
Major: Computer Science
Faculty Mentor: David (King Ip) Lin

Savannah Ostner (U): Distinguishing hypo- vs. hyper- mentalizing in social anxiety and traits related to autism spectrum disorders

Social anxiety symptoms and traits related to autism spectrum disorders have both been linked to deficits in social cognition, particularly impaired Theory of Mind (ToM) or mentalizing ability. Traits associated with autism and social anxiety symptoms will be assessed in an undergraduate population using the Autism Spectrum Quotient (AQ), the Social Phobia Scale (SPS), the Social Interaction Anxiety Scale (SIAS), and the Leibowitz Social Anxiety Scale (LSAS). This study will assess the impact of social anxiety symptoms and traits related to autism on mentalizing ability in subclinical populations. Further, the type of mentalizing errors made will be examined using the ecologically valid Movie for the Assessment of Social Cognition (MASC). The study will also explore whether the type of stimuli, either emotional or cognitive, has an effect on the type of mentalizing errors that are made.

Savannah Ostner
Major: Psychology; Minors: Neuroscience, Biology, Cognitive Science
Faculty mentor: Ben Tabak

Mushfequr Rahman (U): Cultural Competence in Sexual and Mental Health Programs across South Asian and Arab American Communities

The COVID-19 pandemic has exacerbated existing disparities across demographic lines such as race, gender, and religion among others. For example, domestic violence cases against women, mental health services, and the need for interpreters in healthcare have increased after the onset of the pandemic. Mitigating these disparities require culturally competent programs to properly care for diverse communities. In my research, I examine how organizations serving South Asian American and Arab American communities incorporate cultural competency in their sexual and mental health programs, especially in light of the pandemic. There is scarce literature on mental and sexual health about these communities, emphasizing the need for such research. This research is conducted with the help of Arab Community Center for Economic & Social Services (ACCESS) in Dearborn, Michigan and the South Asian Sexual & Mental Health Alliance (SASMHA) in Washington, D.C.

Mushfequr Rahman
Majors: International Studies, Health & Society; Minors: Biological Sciences, Spanish
Faculty mentor: Rachel Ball-Phillips

Bibiana Schindler (U): Hegemony over Human Rights: The Politics of U.S. Genocide Recognition in the al-Anfal Campaign

Winner: Dedman I (Undergraduate)

The United States is often perceived as the moral authority of the world, defending human rights and supporting fundamental American values abroad through its foreign policy. However, despite this elevated status in the political arena, the United States often distances itself from issues pertaining to human rights such as genocide, taking decades to sign the United Nations Genocide Declaration and consistently failing to recognize crimes against humanity and genocides as they occur. The rationale behind this moral failure can be understood through the lens of the 1980s Kurdish genocide in Iraq known as the al-Anfal Campaign. The United States provided Iraq with supplies and support during the Iran-Iraq War, failing to fully acknowledge Iraq's crimes until after their relationship deteriorated in the early 1990s. The United States' awareness and evaluation of Iraq's bombing campaigns can be analyzed through numerous recently declassified documents. The findings of this research suggest that the United States weighs its interests against its values in its foreign policy decisions. It appears that the U.S. often chooses its strategic interests over its moral obligations, using genocide recognition as a political tool to maintain its hegemony.

Bibiana Schindler
Majors: History and Psychology; Minors: Public Policy & International Affairs, Russian Area Studies
Faculty mentor: Sabri Ates

Bhesta Shahim (U): COVID-19 Tracking in Indigenous Communities

Indigenous Peoples experience alarming rates of inequities and systemic discrimination and also experience disproportionate rates of malnutrition and lack of access to quality healthcare, housing, and clean water. These realities make Indigenous Peoples especially vulnerable to COVID-19 and its effects; however, as COVID-19 continues to spread, Indigenous Peoples are largely being left out of the conversation. Due to the need for data and information disaggregated by Indigenous Peoples, Cultural Survival (CS) is producing a map, using Google Maps technology, to show the situations Indigenous communities are facing as a result of COVID-19, including documenting COVID-19 cases and related human rights violations. Through my research work with Dr. Smith-Morris and Cultural Survival, I have contributed to collecting this important data as well as supervising other students on this work.

Bhesta Shahim
Human Rights, Health & Society
Faculty Mentor: Carolyn Smith-Morris

Megan Sham (U): Immigrant Identity Through Food Culture

Winner: Dedman II (Undergraduate)

The main goal of this research study is to look at integration of Chinese-American immigrant families through the specific lens of their domestic culinary practices (cooking at home) as a lens of understand the food practices of immigrants in the United States. The participants in this study will include SMU students and their families, as well as other members of the Chinese-American immigrant community in the Dallas/Fort Worth Area and Houston.The study aims to understand how immigrant communities in the United States adapt to and resist mainstream American culture, starting with food and cooking in the home. Interviews will be conducted to gather qualitative information concerning attitudes towards cooking certain cuisines and the effects on the family unit. The research will be funded partially by the John G. Tower Center's Henry S. Miller Undergraduate Research Fellowship, as well as the Fry Undergraduate Research Award from the SMU Anthropology Department.

Megan Sham
Faculty Mentor: Nicolas Sternsdorff Cisterna

Trisha Punamiya (U): Evaluating the Socioeconomic Impact of COVID-19 in internal migrant workers in Mumbai and its surrounding areas

According to statistical research, Indian industries have had a large number of internal migrant workers having a sizeable impact on the economics of India. Rural to urban migrant workers mostly engage in unskilled work, characterized by low wages, job insecurity and economic vulnerability, which are peculiar characteristics of informal work environments. The Covid-19 pandemic has severely impacted the internal migrant workers in India, displacing and leaving them stranded. With factories and workplaces shutting down due to the 68 day lockdown imposed by the Indian government, the migrant worker community dealt with great uncertainty about job security, loss of income, displacement of homes and health. While this impact was greatly monitored by the Indian government and local media outlets, poor policy implications left the workers under great distress. Many were left with no of access to any form of transportation enabling them to return back to their homes, forcing them to cover the distance on foot. Most available research surrounding the migrant workers focuses on the impact of migration from villages to cities and other socio-political and economic implications of the move on their families and lives. However, there is little study of the impact of this pandemic on their lives and into exploring and comparing differences within the migrant worker community.

Trisha Punamiya
Majors: Economics and Statistics
Faculty mentor: Thomas Osang

Thomas Truong (U): VVD and ENV Equivalent Mutant Characterization

Co-authors: Nischal Karki, Brian Zoltowski

Light-Oxygen-Voltage (LOV) domains, present in all kingdoms of life, facilitate regulation of light dependent events in organisms by transducing light input into physiological signals. Examination of plant and fungal circadian networks has revealed that signaling mechanisms differ even within homologs of closely related species. Structural and computational studies of LOV-allostery have identified key signaling “hot-spots” that allow modification of the direction and amplitude of signal output. One key regulatory site was identified in Plant LOV domain proteins ZTL and FKF1, in which the amino acid residue at position 46 differentiates ZTL and FKF1 signaling mechanisms. Notably, the residue at this position differentiates FKF1-based signaling in monocots and dicots (Ala and Ser, respectively). An analogous residue substitution is observed in the LOV domain photoreceptors of two closely related filamentous fungi, Neurospora crassa VIVID and Trichoderma reesei ENVOY, where divergent signaling mechanisms gate adaptation to oxidative stress. Herein, we sought to test whether residue identity at the position equivalent to ZTL G46 (VIVID A72 and ENVOY S99) alters signal transduction in VIVID and ENVOY. To propagate signal transduction of blue-light, wildtype VVD forms a rapidly dissociating dimer whereas wildtype ENV requires oxidative conditions to form an irreversible disulfide dimer. Size exclusion chromatography (SEC) characterization revealed VVD A72S exhibits reduced dimerization capability and dimerizes at high concentrations only. Furthermore, ENV S99A dimerized under reducing conditions with a similar concentration-dependent increase in dimeric fraction. This altered dimerization capacity demonstrates evolutionary selection of G46 equivalent residues in differentiating LOV-domain photoreceptors and their signal transduction mechanisms.

Thomas Truong
Biology, Management
Faculty Mentor: Brian Zoltowski

Hannah Webb (U): A Thematic Analysis of Conference Programs for Residential College Professional Associations

Co-authors: Laura Bell, Nikita Kulkarni, Grant Stoehr

Many professional associations in higher education hold conferences and conventions on an annual or biannual basis, often with residential college stakeholders taking part. Using a qualitative historical research perspective, we derived themes from conference program schedules (e.g., program session titles, presenters, presenter affiliations) for two prominent associations related to residential colleges—The Collegiate Way International and the Residential College Society. Data were collected from 2014 to 2020, examined, analyzed by thematic content analysis, and then organized by association, year, and location. Findings revealed professional development topics relevant to residential college stakeholders: specifically, what constitutes a residential college model, the resident experience, and leadership experiences. Findings are compared between the associations, and recommendations are made for practice, including consistency in presentation count and insights into professional development topics that can advance the field. Finally, we identified key institutions within the residential college movement and discuss how to diversify the field.

Hannah Webb
Majors: Marketing and Public Policy; Minors: Law & Legal Reasoning and Economics
Faculty mentor: Dustin Grabsch

Peter Wetherbee (U): Big Reputation: An Examination of Perception in Art Museum Development

The study explores the prominent conception of New York's reputation as the reigning hub of fundraising and community engagement for art museums. However do those museums truly exhibit practices that maximize effectiveness of resources and strengthen holistic community relationships, or does their success stem primarily from their high reputation? A comparative analysis between prominent art museums' fundraising methods and engagement of their local communities is important because it allows museums to understand how effective their efforts are and how to possibly capitalize on their reputations. The following looks at the effect of reputation on fundraising and engagement practices, focusing on efficiency and impact.

Peter Wetherbee
Majors: Human Rights and International Studies; Minor: History
Faculty mentor: Alicia Schortgen

Anderson Wey (U): Synthesis and Characterization of biodegradable plastics

Co-author: Jamie Hall

A cross-linked degradable plastic network will be created by mixing and curing varying ratios of monomers derived from silicon. Properties that will be tested include biodegradability, thermal, and mechanical strength.

Anderson Wey
Major: Biochemistry
Faculty mentor: David Son

Yongjia Xu (U): Computational Mathematics in Calculating Protein pKas

A common approach to computing protein pKas uses a continuum dielectric model in which the protein is a low dielectric medium with embedded atomic point charges, the solvent is a high dielectric medium with a Boltzmann distribution of ionic charges, and the pKa is related to the electrostatic free energy which is obtained by solving the Poisson-Boltzmann equation. Starting from the model pKa for a titrating residue, the method obtains the intrinsic pKa and then computes the protonation probability for a given pH including site-site interactions. This approach assumes that acid dissociation does not affect protein conformation aside from adding or deleting charges at titratable sites. In this work we demonstrate our treecode-accelerated boundary integral (TABI) solver for the relevant electrostatic calculations. Our next step is to use machine learning to help use find patterns and better predict the pKa. We aim to make our algorithm efficient in that our protein data bank is usually very large. Careful data processing can help us filter irrelevant or less relevant features and focus more on what could potentially affect pKa values.

Yongjia Xu
Major: Mathematics
Faculty mentor: Weihua Geng

Student Presentations – Research Days 2021

Student presentations appear below.

These are listed in alphabetical order by last name of the lead student author (click “Older posts” to keep scrolling). You can use the search function to find a particular person, or look under “Project categories” to browse by discipline.

Comments are allowed and encouraged!