Digital Commons Network^™

Exploring The Chemical And Biological Foundations Of Protein Lipidation Through Functional And Computational Studies, Andrea Sprague-Getsy

Dissertations - ALL

Post-translational modifications (PTMs) are essential for the diversification of the human proteome. Prenylation is a PTM defined by the addition of a 15-carbon or 20 carbon isoprenoid group by FTase and GGTase-I, respectively, onto a cysteine near the C-terminus of proteins. This modification is the first step within the prenylation pathway where proteolysis and carboxymethylation occur afterwards, aiding in proteins localization to the cellular membrane. These prenyltransferases canonically recognize a “CaaX” box motif which has been determined through biochemical and structural studies. Recently, sequences following the C(x)3X and Cxx patterns have been shown to be prenylated as well as an …

Synergistic Use Of Sentinel-1 And Sentinel-2 Data For Mapping Of Degradation In Coastal Forests And Miombo Woodlands Of Tanzania, Daria C. Kimaro

Tanzania Journal of Science

Forest degradation is one of the leading sources of carbon emission globally. In Africa, particularly in Tanzania, forest degradation is driven by selective logging and forest fires. Monitoring degradation over large areas is very challenging due to the lack of accurate and reliable methods. This study assessed degradation in miombo woodlands and coastal forests using a synergy of remotely sensed data acquired from sentinel-1 and sentinel-2 achieved by integrating their complementary strength where sentinel-1 enhanced detection of structural changes and sentinel-2 provided spectral insight into vegetation. The 3I3D, unsupervised algorithm analysing trends for three vegetation indices (3I) in a three-dimensional …

Simulation Based Model For Canine Distemper Virus In Prey-Predator Dynamics, Mussa A. Stephano

Tanzania Journal of Science

This study investigates the dynamic interactions of a prey-predator ecosystem infected with Canine Distemper Virus (CDV), focusing on predation and disease transmission. A deterministic model, coupled with Monte Carlo simulations (MCS), employed to capture both stochastic variability and environmental fluctuations. The findings indicate that classical prey-predator cycles provide the baseline for population dynamics, but the introduction of CDV and environmental noise fundamentally alters system behavior. Initially, populations exhibit oscillations that gradually stabilize into dynamic equilibria. However, the disease persists within both prey and predator populations, suggesting endemicity rather than extinction. Predation plays a dual role in disease dynamics, while it …

Mathematical Modeling Of Awareness-Driven Interventions For Gender-Based Violence Control In A Closed Population, Furaha M. Chuma, Edward K. Ngailo, Zubeda S. Mussa

Tanzania Journal of Science

Gender-based violence (GBV) remains a critical global health issue with profound social, economic, and psychological implications. Despite concerted efforts to address this challenge, traditional intervention approaches often fall short of effectively mitigating its prevalence. In recent years, there has been growing recognition of the potential impact of awareness-based interventions in addressing various social and health crises. This paper introduces a modeling framework to explore the efficacy of awareness-based interventions in influencing the dynamics of the GBV epidemic within a closed population. A detailed sensitivity analysis, utilizing a normalized sensitivity index method, reveals that the violence transfer rate between perpetrators and …

Modelling The Impact Of Multiple Control Strategies On The Spread Of Phyllody Disease In Sesame, Augustino I. Msigwa, Furaha M. Chuma

Tanzania Journal of Science

Phyllody disease, caused by phytoplasma and transmitted by insect vectors such as leafhoppers, poses a serious threat to the productivity of sesame (Sesamum indicum) as it has caused substantial yield and oil-quality losses worldwide, with documented seed-yield reductions ranging from 38% to as high as 80% in severe outbreaks, particularly in Africa and India. Understanding phyllody dynamics is therefore critical to safeguard yields and trade. While some modeling efforts exist for sesame phyllody (for example, statistical and prediction-focused approaches), mechanistic transmission models (SEIR) assessing its full impact remain scarce. This study therefore develops and analyses impact of multiple control strategies …

Variations In Physicochemical Properties, Microbiological Profiles, And Nutrient Dynamics In The Temi River, Arusha, Tanzania: Sources And Implications, Aldo J. Kitalika

Tanzania Journal of Science

This study thoroughly investigates the physicochemical properties, microbiological profiles, and nutrient dynamics of the Temi River in Tanzania. The sources and implications of fluctuations in dissolved organic carbon (DOC) and nutrients during the wet and dry seasons are carefully analysed. Water samples were collected from various geographically referenced points along the river, and analyses were performed using the APHA Standard Methods for Water and Wastewater Testing. The results show that most parameters increased downstream in both seasons, with the highest DOC levels reaching 352.11 mg/L in the wet season, followed by a significant decrease to 126.00 mg/L during the dry …

Adaptive Generation In Evolutionary Robotics: From Adversarial Objects To Guided Optimization, Unknown Akshay

Dissertations - ALL

Evolution-inspired algorithms have proven effective for complex optimization problems butsuffer from computational inefficiency due to their reliance on random variation operators. This is problematic in domains where fitness evaluation depends on expensive procedures such as training a neural network or running a robot, either in simulation or on hardware. This dissertation presents novel approaches for evolutionary robotics that replace stochastic evolutionary operations with learned, adaptive strategies using reinforcement learning (RL), significantly improving search efficiency while maintaining population diversity.The first contribution is a voxel-based evolutionary framework for generating adversarial objects that challenge robotic grasping systems. By evolving objects with controlled similarity …

Computationally Efficient Methods For Calculation Of Light-Matter Interaction In Large Semiconductor Quantum Dots, Chandler Martin

Dissertations - ALL

Quantum dots are a class of materials in the nanometer scale that have unique optical and electronic properties due to the quantum confinement effect. Traditional electronic structure computational techniques used for calculating these properties fall to scalability issues as the size of the quantum dot increases, or introduce significant errors into the final result. This makes using computational methods to predict new materials, or verify properties of existing materials, challenging to use for experimental applications of quantum dots. This gap between experiment and computation is due to large basis sets, expensive integrals, and storage and manipulation of tensors that grow …

Microplastic Degradation Using Laccase Enzyme From Trametes Hirsuta: In The Silico Study, Hanzhola Gusman Riyanto, Diana Sylvia

Makara Journal of Science

Microplastics are a serious global problem that arises worldwide because of their widespread use. Exposure to microplastics can negatively affect human and environmental health. In this study, we used molecular docking methods with MOE software (version 2014.0901) to investigate the interaction between the laccase enzyme and several microplastic compounds as a preliminary study of microplastic degradation using enzymes. The Quantitative Structure Analysis Relationship (QSAR) analysis revealed that all microplastic ligands had higher Pa values than Pi, indicating that the laccase enzyme may be biologically active. The findings of the present study show that polyamide (PA) has the lowest binding energy …

Quantitative Structure-Activity Relationship, Pharmacokinetics, Drug-Likeness, Toxicity, And Molecular Docking Studies Of 4-N-(Methyl)-4-Aminoquinoline Derivatives As Antimalarial Compounds, Muhamad Jalil Baari, Devi Hardiyanti

Makara Journal of Science

Antimalarial drug resistance has encouraged various innovations to develop novel drug compounds that are effective, feasible, and safe, adhering to health standards. One way to do that is by observing and predicting the biological activity of drug compounds using quantitative structure–activity relationship (QSAR) analysis. In this study, QSAR analysis was conducted on the 4-N-(methyl)-4-aminoquinoline derivatives, which effectively inhibit the growth of Plasmodium falciparum as a source of malaria. The research stages involved molecular structure modeling, molecular geometry optimization using the AM1 semi-empirical method, and QSAR descriptor calculations, including electronic (atomic charges (q), HOMO and LUMO energies, polarizability (α), …

Enzyme-Free Colorimetric Sensing Of Glucose Using Silver Nanoparticles With A Green Stabilizing Agent From Capsicum Chinense Jacq Extract, Boyfannie Ivan Putra, Hermin Sulistyarti, Muhammad Mashuri Utama, Aura Ananda Haryanto, Rurini Retnowati, Mohamad Rafi, Akhmad Sabarudin

Makara Journal of Science

Diabetes mellitus (DM) is a significant global health issue characterized by abnormal glucose levels in the human body. DM diagnostics are often based on invasive sampling from blood, which poses a potential risk of infection and tissue damage. Therefore, a non-enzymatic and non-invasive method for glucose monitoring is demanded as a simple alternative to glucose detection in urine samples. In this work, enzyme-free glucose determination is based on the formation of silver nanoparticles stabilized by Capsicum chinense Jacq extract (CCJ-AgNPs). Under alkaline conditions, glucose functions as a reducing agent for silver ions, and the extract acts as a stabilizer to …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Mapping Sustainability To Cybernetic-Generative Artificial Intelligence-Based Education: An Innovative Neutrosophic Orbifold-Lattice Methodology, Mona Mohamed, Ahmed A. Metwaly

Neutrosophic Systems with Applications

The lightning-fast development of artificial intelligence (AI), notably generative artificial intelligence (Gen AI) technologies, has intrigued multiple disciplines, particularly education. In this context, Large Language Models (LLMs) serve as beneficial cognitive resources that address knowledge deficits and provide tailored educational support for learners and staff. For learners, LLMs are regarded as knowledgeable educators who offer prompt, focused responses and rationales to tricky queries. Whereby LLMs for staff, Strength enhancer, automating tedious tasks, and creating intelligent resources.Gen AI’s rapid growth offers enormous obstacles for educational systems, compelling them to discover solutions for these obstacles.

Conceptually, cybernetics is leveraged for bridging the …

Salicylic Acid Heterocyclic Derivatives: Chemical Synthesis And Biological Activity, Rawaa Hefdi Zaooli, Marwa Abdulameer Mseer, Amneen Mohammed Alsayegh

Al-Bahir

Before a drug can be widely used, it must go through a long development process, starting from the discovery of the active ingredient and continuing with tests to confirm its safety and effectiveness. In this study, new olsalazine derivatives were synthesized, containing a fused morpholine-3-one ring and two five-membered heterocyclic rings (thiadiazole and oxadiazole). Common and readily available materials, such as salicylic acid (to prepare 2-hydroxy-5-nitrobenzoic acid) and inexpensive catalysts, were used to synthesize compounds from the first, 5,5'-(diazene-1,2-diyl)bis(2-hydroxy-3-nitrobenzoic acid) (A1), to the seventh, 6,6'-(diazene-1,2-diyl)bis(N-(4-(5-amino-1,3,4-oxadiazol-2-yl)phenyl)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-carboxamide) (A7).

Each compound was characterized by FT-IR and ¹H-NMR spectroscopy, along with physical properties such …

Energetics And Kinetics Of Alkali Ion Exchange In Analcime, Jinyi Liu, An T. Ta, R. Seaton Ullberg, Jean Wilfried Hounfodji, Michael Badawi, Hans Conrad Zur Loye, Simon R. Phillpot

Faculty Publications

We employ density functional theory calculations to investigate the energetics and diffusion mechanisms of alkali metal ions (Na⁺, K⁺, Rb⁺, and Cs⁺) within the analcime framework. While Na⁺preferentially adsorbs at the center of the 8-member ring, DFT calculations show that larger ions, such as Cs⁺, occupy the center of the cage due to steric constraints. The computed exchange energies indicate that exchange of Na⁺by Cs⁺is thermodynamically favorable. Migration energy barriers, determined using the climbing image nudged elastic band method, show that Na⁺is …

Chaos Engineering In Multi-Gigahertz Solid-State Lasers: A Novel Approach To Optoelectronic Control, Mikhail V. Gorbunkov, Yulia Ya. Maslova, Yulia A. Sinichkina

Karbala International Journal of Modern Science

This paper presents a comprehensive study of a multi-gigahertz chaotic generator of light pulses based on solid-state laser sources, including fiber lasers, governed by carefully designed positive and negative feedback loops. It harnesses the inherent nonlinear dynamics within a solid-state laser controlled by a combination of two inertial feedback loops, enabling the realization of complex chaotic behavior, including the logistic map scenario, under moderate amplification conditions. The laser system dynamics are rigorously investigated through theoretical modeling, employing a nonlinear map approach, and high-resolution picosecond simulations. The results of our numerical simulations highlight the efficacy of fast electro-optical feedback system with …

Unveiling The Anticancer Potential Of Syzygium Cumini: In Silico Insights Into Its Mechanistic Action Against Non-Small Cell Lung Cancer, Nur Sofiatul Aini, Win Darmanto

Karbala International Journal of Modern Science

Non-small cell lung carcinoma (NSCLC) is the most periodic type of lung cancer and the second most diagnosed cancer globally. Syzygium cumini is plant that extensively used in cuisine and traditional medicine. However, its potential for NSCLC treatment has not yet been elucidated. This study determined the potential of S. cumini as anti-NSCLC using in silico approaches. The in silico study was applied to perform active compound analysis, selection of target candidates, network pharmacology, functional annotation, molecular docking, and molecular dynamics simulation, respectively. Based on open source databases, S. cumini contained 115 compounds and 14 of them predicted to have …

Exploring Ecological Zonation Of The Yellow River Estuary Coastal Zone Based On Nitrogen And Phosphorus Criteria, Dejuan Jiang, Song Qin, Zhengyi Liu, Ruiteng Sun, Xiaoshuai Hang, Tao Zou, Xiaoguang Li, Lijuan Li, Shichao Tian, Yanfang Li, Yongming Luo, Chuanyuan Wang, Yuan Li

Bulletin of Chinese Academy of Sciences (Chinese Version)

Estuaries, as ecologically sensitive brackish water mixing zones, face a critical bottleneck in refined management because traditional zonation based on socioeconomic attributes overlooks the ecological heterogeneity driven by salinity gradients and nutrient stoichiometry, leading to a disconnect between management measures and conservation needs. This study proposes a novel approach to coastal zonation using nitrogen and phosphorus nutrient criteria as an ecological benchmark. Overall ecological criteria are established for the Yellow River estuary (dissolved inorganic nitrogen: 0.258 mg/L; phosphate: 0.015 mg/L) and a differentiated management scheme is constructed based on a salinity gradient (26.5 PSU boundary). It is recommended to integrate …

Long-Term Ecological Research Provides Theoretical And Technical Support For Ecological Restoration And High-Quality Development In Agro-Pastoral Ecotone, Wenming Bai, Cunzheng Wei, Longyu Hou, Linghao Li, Xingguo Han, Wenhao Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Since its establishment in 2001, the Duolun Restoration Ecology Station, Institute of Botany, Chinese Academy of Sciences (Duolun Station) has been dedicated to addressing severe grassland degradation and slow economic development in the agro-pastoral ecotone, north of Beijing. A series of systematic studies were conducted on the degraded grassland ecosystem in the agro-pastoral ecotone of Duolun County, Inner Mongolia. The major research findings are summarized as follows. (1) Elucidated that species-specific trait of plant roots, along with the changes in soil properties, are the primary drivers determining how plant and microbial community structure and function respond to anthropogenic disturbances and …

Duolun Restoration Ecology Station, Institute Of Botany, Chinese Academy Of Sciences, Institute Of Botany, Chinese Academy Of Sciences

Bulletin of Chinese Academy of Sciences (Chinese Version)

No abstract provided.

Ecological Barrier Of Coastal Zone In China: Concept, Functions, And Construction Theory, Guangxuan Han, Xiaoli Bi, Xiyong Hou, Xiaoli Zhang, Qianguo Xing, Yuan Li, Haiqing Ma, Ting Wang, Song Qin

Bulletin of Chinese Academy of Sciences (Chinese Version)

The ecological barrier of coastal zone serves as a critical defense line for safeguarding coastal ecological security and sustainable socio-economic development, with multifaceted functions including wave attenuation, shoreline stabilization, and climate regulation. This study systematically elaborates on the concept and essence of ecological barriers of coastal zone, highlighting their core as land-sea continuums that synergistically leverage ecosystem integrity, hydrological connectivity, and biodiversity to provide systemic deliver protective functions. Nevertheless, China’s coastal ecological barrier construction faces four major challenges, namely, (1) theoretical frameworks, often derived from inland models, inadequately represent the complex land-sea interactions and socio-economic drivers; (2) the absence of …

Enhancing Education Through Virtual Reality: A Comparative Study Of Vr And Traditional Learning Environments, Shrivardhan Atluri

The Journal of Purdue Undergraduate Research

No abstract provided.

Self-Assembling Rna Nanostructures Are Highly Sensitive To Environmental Conditions, Jordan Aposhian, Surya Pratap S. Deopa, Scott Horowitz, Joseph D. Yesselman

Chemistry and Biochemistry: Faculty Scholarship

Recent developments in RNA nanotechnology have led to an increase in the design of specific, higher-order RNA structures, which will ultimately be used in drug delivery and immunomodulation applications. As researchers create RNA nanostructures with the intention of making them a standard tool in molecular biologists' toolkits, further investigation is required into the robustness of RNA designs. Primarily, in what different molecular contexts are the designed and intended nanostructures stable? In this work, we show that RNA nanostructure self-assembly is highly sensitive to environmental conditions by using second-order right-angle light scattering. While a test RNA hexagonal grid nanostructure forms correctly …

Assessment Of Polymeric Chloroquine Formulations For Targeted Therapy Of Ulcerative Colitis And Metastatic Colorectal Cancer, Neha Kumari

Theses & Dissertations

Effective targeted drug delivery is a critical unmet need in the management of both ulcerative colitis and metastatic colorectal cancer, where conventional systemic therapies may be hindered by suboptimal efficacy and significant side effects. This thesis explores the development and preclinical assessment of polymeric chloroquine (PCQ)-based nanotherapeutics, leveraging stimuli-responsive designs for disease-specific delivery and action.

For ulcerative colitis, a reactive oxygen species (ROS)-responsive nanogel system was engineered to release PCQ, a macromolecular derivative of hydroxychloroquine, specifically in the inflamed areas within the colon. Nanogels with well-defined size and positive surface charge were synthesized via reversible fragmentation chain transfer (RAFT) polymerization …

Macroinvertebrate Community Dynamics In A Recovering, Hypersaline Estuary, Catherine M. Eckert, Claudia A. Tamez, Erin E. Easton, David Hicks

School of Earth, Environmental, & Marine Sciences Faculty Publications

The Bahia Grande is a 6,500—acre tidal basin located at the southernmost tip of Texas. Tidal flow into this coastal estuary was cut off in the 1930s, causing the basin to dry up for ~70 y. A pilot channel connecting the Bahia Grande to tidal waters was constructed in 2005, allowing flooding of the basin to occur. Throughout the period reported herein (2005–2019), the system remained characterized by persistent spatial and temporal episodes of extreme hypersalinity (>70)—a critical factor influencing estuarine community composition and driving key ecological processes. With additional rehabilitation actions forthcoming, characterization of the estuary is essential …

Analysis Of Solutions To Research Methods: Navigating The Infinite Content Of Mathematics, Jesus Navarro

Student Scholar Symposium

In the infinite realm of mathematical research, understanding and communicating complex concepts require structured and logical approaches. However, a variety of research methods are employed in mathematical studies; these may differ in approach, historical context, and other important considerations which can contribute to confusion and a lack of effective communication. The genesis of this research began with personal confusion during my research on "Counting the Uncountable: Life in a World Without Numbers", setting the stage for the central challenge: How do mathematicians explain their research? To answer this issue, we analyzed a variety of mathematical research articles to highlight their …

Quantifying Dna Groove Binding Dynamics Of Netropsin Using Optical Tweezers, Jacob Mcnally

Honors Program Theses and Projects

Netropsin is a small molecule that binds to the minor groove of DNA and serves as a model scaffold for DNA-minor groove binding anticancer drugs. Understanding how Netropsin interacts with DNA under mechanical stress is important for characterizing how similar molecules function in biological environments. In this work, we used dual-beam optical tweezers to study how Netropsin binding affects the mechanical behavior of single DNA molecules under applied force. Individual DNA molecules were held under controlled forces while Netropsin was introduced at varying concentrations. Constant-force measurements were used to probe binding dynamics; however, we found binding occurred too rapidly to …

Wild Robots: Humans, Wilderness, And Technology In Becky Chambers’ Monk And Robot Series, Melissa Moore

Honors Theses

As technology advances and the environment deteriorates, the way people view the relationships between technology, wilderness, and humans becomes essential for society to move forward. To investigate perceptions about technology’s place in an environmentally conscious society, this project examines manifestations of wilderness/wildness and technology in Becky Chambers’ Monk and Robot series through the lens of ecocriticism. Using Timothy Morton's concept of the ecological thought as a framework for analysis, the circumstances present in the novel suggest that the triangle separating humans, wilderness, and technology has actually collapsed, replaced by an enmeshment of technology, wilderness, and humanity.

The Role Of Dust Inputs And Sediment Phosphorus Diffusion Into Utah Lake, Utah, United States Of America, Kristen E. Smith

Theses and Dissertations

Human activities have led to excessive nutrient enrichment which is greater than lake systems can naturally assimilate. This process is known as eutrophication and it is driving significant algae growth resulting in the more common release of harmful toxins. Utah Lake, located in Utah County, UT is one such water body that even after major reductions in anthropogenic phosphorus influent, continues to experience frequent, harmful algal blooms. The extent to which natural processes, like atmospheric dust deposition and sediment recycling, contribute to the lake's phosphorus budget is still poorly understood.

To address this gap of knowledge, this study quantified phosphorus …