Digital Commons Network^™

A Preliminary Comparative Study Of Molecular Visualization Software For Education, Ruoming Shen

Modeling, Simulation and Visualization Student Capstone Conference

Chemistry and biology are sciences vital for understanding metabolic processes, developing disease treatments, and improving environmental conditions. With extensive knowledge of biochemistry, we can take advantage of a material’s unique chemical composition and properties in various applications. Visualization software is essential for analyzing complex chemical and biological structures and predicting their interactions with each other. This paper presents a preliminary study of three open source molecular visualization software tools - Visual Molecular Dynamics (VMD), Jmol, and Mol*, and evaluates their strengths and deficiencies. This paper utilizes the March Molecule of the Month, Vascular Endothelial Growth Factor (VEGF), from the Protein …

Understanding The Natural History Of Juvenile Amblyomma Maculatum In Southeastern Virginia, Christina Espada, Holly Gaff

College of Sciences Posters

Amblyomma maculatum, the Gulf Coast tick, is a species of increasing public health concern. Adult A. maculatum is a known vector of several pathogens including Rickettsia parkeri, the causative agent of Rickettsia parkeri rickettsiosis. Amblyomma maculatum has expanded northward from its historic range along the Gulf Coast, with populations reportedly establishing in southeastern Virginia in 2010. Recently established populations of A. maculatum tend to have higher R. parkeri infection prevalence compared to longer established populations. This pattern holds for all populations found so far in southeastern Virginia, with a prevalence of R. parkeri in about 60% of A. …

Site Selection For Norfolk Day Services Facility, Faith N. Witkowski, Hua Liu

College of Arts and Letters Posters

In October 2021, The Center: A Temporary Shelter transitioned from its downtown location to a residential area a few blocks away. After the move, a pressing, geographic-based question has surfaced: what makes the best location for the houseless population to be able to utilize resources? Using two methods, this study endeavored to answer this question in multiple ways, through different lenses. Method one's objectives are to find an optimal location(s) for a potential Norfolk day service facility based on 1) proximity to social and health services, 2) proximity to a neighborhood that would most benefit from a day center, and …

Lattice Optics Optimization For Recirculatory Energy Recovery Linacs With Multi-Objective Optimization, Isurumali Neththikumara, Todd Satogata, Alex Bogacz, Ryan Bodenstein, Arthur Vandenhoeke

College of Sciences Posters

Beamline optics design for recirculatory linear accelerators requires special attention to suppress beam instabilities arising due to collective effects. The impact of these collective effects becomes more pronounced with the addition of energy recovery (ER) capability. Jefferson Lab’s multi-pass, multi-GeV ER proposal for the CEBAF accelerator, ER@CEBAF, is a 10- pass ER demonstration with low beam current. Tighter control of the beam parameters at lower energies is necessary to avoid beam break-up (BBU) instabilities, even with a small beam current. Optics optimizations require balancing both beta excursions at high-energy passes and overfocusing at low-energy passes. Here, we discuss an optics …

A Pathway To Solving The Structure Of Cl-Par-4 Tumor Suppressor Protein: Challenges & Findings, Krishna Raut, Samjhana Pandey, Andrea M. Clark, Komala Ponniah, Steven M. Pascal

College of Sciences Posters

Prostate apoptosis response-4 (Par-4) is a pro-apoptotic tumor suppressor protein. Down-regulation of this protein has been reported in a myriad of cancers. Conversely, up-regulation of Par-4 is found to be associated with several neurodegenerative disorders. Par-4 is unique in the sense it can selectively induce apoptosis in cancer cells. For this, caspase-dependent intracellular cleavage of Par-4 is essential to produce the functionally active fragment, cl-Par-4 (caspase-cleaved Par-4). The cl-Par-4 protein inhibits the NF-κB-mediated cell survival pathway and causes selective apoptosis in various tumor cells.

Our laboratory is interested in determining the structure of cl-Par-4 and understanding it’s interaction with various …

Investigation Of Magnesium Cation-Proton Exchange With Transmembrane Electrostatically Localized Protons (Telp) At A Liquid-Membrane Interface: Fundamental To Bioenergetics, Gyanendra Kharel, Andrew J. Evans, Christopher M. Russo, Michael Eason, James W. Lee

College of Sciences Posters

The Lee transmembrane electrostatic proton localization (TELP) theory is a revolutionary scientific theory that has successfully explained decades long-standing quandary in the field of bioenergetics in regards to ATP synthesis in biological systems, specifically alkalophilic bacteria. This study provides experimental support for the TELP theory by further demonstrating evidence of a localized proton layer existing at the liquid-membrane interface in a simulated biological membrane apparatus. Whilst monovalent cations have been studied extensively, divalent cation exchange has not been studied experimentally.

A previous study determined equilibrium constant for Na⁺ and K⁺ to exchange with localized H⁺ layer to …

A Spatially And Temporally Second Order Method For Solving Parabolic Interface Problems, Kumudu Gamage, Yan Peng

College of Sciences Posters

Parabolic interface problems have many applications in physics and biology, such as hyperthermia treatment of cancer, underground water flow, and food engineering. Here we present an algorithm for solving two-dimensional parabolic interface problems where the coefficient and the forcing term have a discontinuity across the interface. The Crank-Nicolson scheme is used for time discretization, and the direct immersed interface method is used for spatial discretization. The proposed method is second order in both space and time for both solution and gradients in maximum norm.

Examining A Neural Measure Of Attentional Bias To Emotional Faces In Social Anxiety And Depression, Nathan M. Hager, Matt R. Judah, Alicia L. Milam, Hannah C. Hamrick, Catherine R. Glenn

College of Sciences Posters

Cognitive theories suggest that attentional biases may contribute to both social anxiety and depression, such that attention may be biased to focus on or away from certain information (e.g., rejecting or sad images; Clark & McManus, 2002; Lemoult & Gotlib, 2019). Although research is mixed, recent studies using a neural measure called the N2pc (an event-related potential) has indicated attentional biases in social anxiety. However, little N2pc research has examined depression or co-occurring depression and social anxiety.

The current study used electroencephalography to measure the N2pc during a dot-probe task in which images of faces with emotional or neutral expressions …

Empirically Adjusted Weighted Ordered P-Values Method, Wimarsha Jayanetti, Sinjini Sikdar, N. Rao Chaganty

College of Sciences Posters

Recent advancements in high-throughput technologies have enabled simultaneous inference of thousands of genes. With the abundance of public databases, it is now possible to rapidly access the results of several genomic studies, each of which includes the significance testing results of a large number of genes. Researchers frequently aggregate genomic data from multiple studies in the form of a meta-analysis. Most traditional meta-analysis methods aim at combining summary results to find signals in at least one of the studies. However, often the goal is to identify genes that are differentially expressed in a consistent pattern across multiple studies. Recently, a …

Analysis Of An Existing Method In Refinement Of Protein Structure Predictions Using Cryo-Em Images, Maytha Alshammari, Jing He, Willy Wriggers, Jiangwen Sun

College of Sciences Posters

Protein structure prediction produces atomic models from its amino acid sequence. Three-dimensional structures are important for understanding the function mechanism of proteins. Knowing the structure of a given protein is crucial in drug development design of novel enzymes. AlphaFold2 is a protein structure prediction tool with good performance in recent CASP competitions. Phenix is a tool for determination of a protein structure from a high-resolution 3D molecular image. Recent development of Phenix shows that it is capable to refine predicted models from AlphaFold2, specifically the poorly predicted regions, by incorporating information from the 3D image of the protein. The goal …

Circulation, Volume 27, No. 2, Center For Coastal Physical Oceanography, Old Dominion University

CCPO Circulation

Spring 2022 issue of CCPO Circulation featuring the article "Looking Back While Moving Forward," by Sönke Dangendorf.

Summer Food Habits Of Myotis Leibii In The Central Appalachians Ecoregion And Comparison To Similar Studies, John O. Whitaker Jr., Virgil Brack Jr., James D. Kiser Jr.

Virginia Journal of Science

Food habits of Myotis leibii, Eastern Small-footed Myotis, were studied during summer in the Central Appalachians Ecoregion. Moths were 70.0% of the diet by volume and were in 97.7% of samples (percent frequency). Beetles, flies, and spiders comprised much of the remaining diet. Percent volume and percent frequency metrics produce similar results. These data and past studies indicate this bat eats a relatively low-diversity diet centered on terrestrial-based arthropod prey across a broad geographical area, irrespective of season, sex, or age. The presence of spiders in the diet may indicate gleaning.

The Influence Of Particle Concentration And Bulk Characteristics On Polarized Oceanographic Lidar Measurements, Brian L. Collister, Richard C. Zimmerman, Charles I. Sukenik, William M. Balch, Victoria J. Hill

OES Faculty Publications

Oceanographic lidar measurements of the linear depolarization ratio, δ, contain information on the bulk characteristics of marine particles that could improve our ability to study ocean biogeochemistry. However, a scarcity of information on the polarized light-scattering properties of marine particles and the lack of a framework for separating single and multiple scattering effects on δ have hindered the development of polarization-based retrievals of bulk particle properties. To address these knowledge gaps, we made single scattering measurements of δ for several compositionally and morphologically distinct marine particle assemblages. We then used a bio-optical model to explore the influence of multiple …

Empirically Derived Thermal Thresholds Of Four Coral Species Along The Red Sea Using A Portable And Standardized Experimental Approach, Nicolas R. Evensen, Christian R. Voolstra, Maoz Fine, Gabriela Perna, Carol Buitrago-López, Anny Cárdenas, Guilhem Banc-Prandi, Katherine Rowe, Daniel J. Barshis

Biological Sciences Faculty Publications

Global warming is causing an unprecedented loss of species and habitats worldwide. This is particularly apparent for tropical coral reefs, with an increasing number of reefs experiencing mass bleaching and mortality on an annual basis. As such, there is a growing need for a standardized experimental approach to rapidly assess the thermal limits of corals and predict the survival of coral species across reefs and regions. Using a portable experimental system, the Coral Bleaching Automated Stress System (CBASS), we conducted standardized 18 h acute thermal stress assays to quantitively determine the upper thermal limits of four coral species across the …

Wittgenstein And Hume On Miracles, Samuel Wheeler

Undergraduate Research Symposium

In this paper, I intend to contrast the positions of Ludwig Wittgenstein and David Hume on miracles. While Hume holds that miracles are violations of laws of nature which can never be probable, Wittgenstein would reject this definition. Instead, he takes a broader stance on miracles and holds that many events which are not transgressions of laws of nature can be seen as miraculous. And the point of this is to highlight the vastly different events we call miracles. Contra Hume, Wittgenstein thinks that even some of our greatest certainties can call up in us a sense of absolute wonder …

Dignity Norfolk: How One Tidewater Group Enabled Gay And Lesbian Catholics To Form Long Lasting Friendships And Chosen Families, Chelsea Lembert

Undergraduate Research Symposium

In the past decade, research has been conducted to look into the history of the Queer Community of the Tidewater Region. Students and community volunteers have conducted interviews and gathered documents connected to the queer community to grow the study and breadth of available information for future researchers. However, more in-depth knowledge of community connections and familial ties within the queer community in the Tidewater Region was needed. Through research into Our Own Newspaper, local historical background information, and in-person interviews, I pieced together first-hand accounts of life through the eyes of a gay man or lesbian woman living in …

Access To Nitrogen Heterocycles Via Borrowing Hydrogen Catalysis, Robert P. Reynolds, Kellen P. Mcguire, Conor T. Mccormick, Kyle M. Lambert

Undergraduate Research Symposium

Nitrogen heterocycles are ubiquitous motifs which occur as the core structure of several alkaloid natural products exhibiting inherent biological activity against an array of bacteria, fungi, viruses, and cancer cell lines. These azacycles serve as key synthetic building blocks for medicinal chemists to access more structurally complex and diverse compounds with tunable biological properties. A synthetic approach to these valuable motifs employing intramolecular borrowing hydrogen catalysis has been developed. The utility of the developed chemistry will be applied to synthetic efforts towards the recently isolated Cylicomorphins A-E.

Oxidation Of Thiols To Disulfides Using An Environmentally “Green” Organocatalyst And New Mechanistic Insights, Kosta V. Vlasakakis, Olivia M. White, Robert P. Reynolds, Shayne M. Weierbach, Shannon M. Weaver, Ramsey T. Ritter, Nishi H. Patel, Eric C. Hayes, Sydney Dunmire, Kyle M. Lambert

Undergraduate Research Symposium

The selective oxidation of thiols to disulfides is an area of great importance in the areas of materials and medicinal chemistry research. The production of polymers, rubber, pharmaceuticals, and the folding of proteins in biological systems all rely on the formation of disulfide bonds. Herein, we introduce a stoichiometric and electrocatalytic method for the oxidation of various pharmaceutically and biologically relevant thiols into their respective disulfides in more environmentally benign solvents such as water and alcohol solvents. The scope of the transformation was evaluated and a detailed mechanistic study involving control experiments, experimental kinetic studies, and computational investigations led to …

Hsp90 Inhibitors Modulate Sars-Cov-2 Spike Protein Subunit 1-Induced Human Pulmonary Microvascular Endothelial Activation And Barrier Dysfunction, Ruben Manuel Luciano Colunga Biancatelli, Pavel Solopov, Betsy W. Gregory, Yara Khodour, John D. Catravas

Bioelectrics Publications

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 5 million deaths worldwide. Multiple reports indicate that the endothelium is involved during SARS-Cov-2-related disease (COVID-19). Indeed, COVID-19 patients display increased thrombophilia with arterial and venous embolism and lung microcapillary thrombotic disease as major determinants of deaths. The pathophysiology of endothelial dysfunction in COVID-19 is not completely understood. We have investigated the role of subunit 1 of the SARS-CoV-2 spike protein (S1SP) in eliciting endothelial barrier dysfunction, characterized dose and time relationships, and tested the hypothesis that heat shock protein 90 (HSP90) inhibitors would prevent and repair such injury. S1SP …

Habitat Restoration Restores Underwater Soundscapes And Larval Recruitment, Jack Butler, Emily R. Anderson, Mark J. Butler

Biological Sciences Faculty Publications

Habitat degradation alters many ecosystem processes, and the potential for the reestablishment of ecosystem function through restoration is an area of active research. Among marine systems, coastal habitats are particularly vulnerable to anthropogenic degradation and, in response, are the focus of marine ecological restoration. One of the crucial functions of structurally complex coastal habitats (e.g., saltmarshes, seagrass meadows, kelp forests, coral reefs) are as nurseries to coastal and offshore species, many of whose larvae utilize sound to locate suitable nursery habitat. However, the effect of habitat degradation and subsequent restoration on underwater soundscapes and their function as navigational cues for …

Natural Phaeosphaeride A Derivatives Overcome Drug Resistance Of Tumor Cells And Modulate Signaling Pathways, Victoria Abzianidze, Natalia Moiseeva, Diana Suponina, Sofya Zakharenkova, Nadezhda Rogovskaya, Lidia Laletina, Alvin A. Holder, Denis Krivorotov, Alexander Bogachenkov, Alexander Garabadzhiu, Anton Ukolov, Vyacheslav Kosorukov

Chemistry & Biochemistry Faculty Publications

n the present study, natural phaeosphaeride A (PPA) derivatives are synthesized. Anti-tumor studies are carried out on the PC3, K562, HCT-116, THP-1, MCF-7, A549, NCI-H929, Jurkat, and RPMI8226 tumor cell lines, and on the human embryonic kidney (HEK293) cell line. All the compounds synthesized turned out to have better efficacy than PPA towards the tumor cell lines listed. Among them, three compounds exhibited an ability to overcome the drug resistance of tumor cells associated with the overexpression of the P-glycoprotein by modulating the work of this transporter. Luminex xMAP technology was used to assess the effect of five synthesized compounds …

Monarch Science Observer, Volume 13, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2022, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

Monitoring Extinction Risk And Threats Of The World's Fishes Based On The Sampled Red List Index, Rafael Miranda, Imanol Miqueleiz, William Darwall, Catherine Sayer, Nicholas K. Dulvy, Kent E. Carpenter, Beth Polidoro, Nadia Dewhurst-Richman, Caroline Pollock, Craig Hilton-Taylor, Robin Freeman, Ben Collen, Monika Böhm

Biological Sciences Faculty Publications

Global biodiversitytargets require us to identify species at risk of extinction and quantify status and trends of biodiversity. The Red List Index (RLI) tracks trends in the conservation status of entire species groups over time by monitoring changes in categories assigned to species. Here, we calculate this index for the world’s fishes in 2010, using a sampled approach to the RLI based on a randomly selected sample of 1,500 species, and also present RLI splits for freshwater and marine systems separately. We further compare specific traits of a worldwide fish list to our sample to assess its representativeness. Overall, 15.1% …

Sex Differences In The Association Of Sibship Size And Position In Sibship With Lipid Profile During Adolescence: A Cross-Sectional Study, Ali H. Ziyab, Mohammad Almari, Anwar Mohammad, Abdullah Al-Taiar, Wilfried Karmaus

Community & Environmental Health Faculty Publications

Background. Epidemiologic studies have reported associations of sibship size and position of the child in the sibship with multiple health outcomes, including adiposity and diabetes. However, little is known about sibling effects on lipids. Hence, this study sought to evaluate associations of the number of total, older, and younger siblings with lipid profile among adolescents. Methods. In a cross-sectional study among high school students aged 14 to 19 years, lipid levels were measured in capillary blood. Parents reported the number of siblings (total, older, and younger). Geometric means of lipids were calculated, and linear regression was used to estimate the …

Monarch, Philip Walzer (Editor)

Monarch Magazine

Winter 2022 issue of Monarch, the Old Dominion University Magazine.

Subtitled: President Brian O. Hemphill, Ph.D., First Lady Marisela Rosas Hemphill, Ph.D. - Moving ODU forward

Blockchain-Based Digital Trust Mechanism: A Use Case Of Cloud Manufacturing Of Lds Syringes For Covid-19 Vaccination, Trupti Rane, Jingwei Huang

Engineering Management & Systems Engineering Faculty Publications

Trust is essential in the digital world. It is a critical task to build digital trust for the ongoing digital engineering transformation. Aiming at developing a blockchain-based digital trust mechanism for Cloud Manufacturing or Manufacturing-as-a-Service (MaaS), in this paper, we use the manufacturing of low dead space (LDS) medical syringes through Cloud Manufacturing as a motivating scenario to develop a basic framework. To meet the need of optimally saving COVID-19 vaccine doses to save more lives, the medical device manufacturing community needs to make a swift move to meet the surged need for LDS syringes. Cloud Manufacturing is a form …

Improving The Heat Tolerance Of Vulnerable Corals Through Their Algal Symbionts, Cathryn M. Bowling

OUR Journal: ODU Undergraduate Research Journal

Tropical coral reefs are one of the most impressive and diverse ecosystems on the face of the earth. Found in warm, tropical waters around the globe, these reefs are major supporters of the immense biodiversity of the area. The health of coral reefs is highly influential on the overall health of the entire ecosystem. In recent years, intensifying climate change has resulted in an accelerated rise in seawater temperatures and the frequency and severity of coral bleaching. Coral bleaching occurs in response to harsh environmental conditions that cause corals to enter a period of extreme stress. During this time, corals …

Author Biographies

OUR Journal: ODU Undergraduate Research Journal

No abstract provided.

Coral Reef Restoration Methods In The Caribbean And Florida Keys, Melissa Wagner

OUR Journal: ODU Undergraduate Research Journal

There has been a massive decline in coral population worldwide, but the Caribbean Sea has been particularly impacted. The Caribbean was once the home to millions of branching coral, Acropora, but has seen severe degradation in the past few decades due to climate change, pollution, coral disease, bleaching events, overfishing, coastal development and other disturbances. Coral reef restoration has since expanded rapidly with thousands of coral nurseries in the Caribbean alone and has become an important process in maintaining coral reefs in our oceans today. Corals help protect our shorelines, maintain biodiversity in our oceans, provide jobs for fisheries …

The State Of The Art Of Information Integration In Space Applications, Zhuming Bi, K. L. Yung, Andrew W.H. Ip., Yuk Ming Tang, Chris W.J. Zhang, Li Da Xu

Information Technology & Decision Sciences Faculty Publications

This paper aims to present a comprehensive survey on information integration (II) in space informatics. With an ever-increasing scale and dynamics of complex space systems, II has become essential in dealing with the complexity, changes, dynamics, and uncertainties of space systems. The applications of space II (SII) require addressing some distinctive functional requirements (FRs) of heterogeneity, networking, communication, security, latency, and resilience; while limited works are available to examine recent advances of SII thoroughly. This survey helps to gain the understanding of the state of the art of SII in sense that (1) technical drivers for SII are discussed and …