Biological and Chemical Physics Commons^™

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Novel Alchemical Methodologies For Modeling Molecular Binding, Solmaz Azimi

Dissertations, Theses, and Capstone Projects

Molecular recognition is fundamental to all biological and biochemical processes. Understanding the interactions between molecules is the foundation for drug discovery and development, for understanding biological processes, and for the design of biosensors and nanomaterials. There is tremendous interest in the development of computer models to predict molecular association equilibria. In structure-based drug discovery enterprises, predicting the strength and selectivity of a small molecule to a biological target can advance target identification, aid ligand design, and accelerate high-throughput screening of drug compounds. This work focuses on free energy models, a class of computational methodologies grounded on the fundamental physical and …

A Sensitivity Analysis Of The Modeling Of Polycyclic Aromatic Hydrocarbon Emission In Galaxies, A. Maragkoudakis, C. Boersma, P. Temi, J. D. Bregman, L. J. Allamandola, Vincent J. Esposito, A. Ricca, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We have conducted a sensitivity analysis on the mid-infrared spectral decomposition of galaxies and the modeling of the polycyclic aromatic hydrocarbon (PAH) emission spectrum with the NASA Ames PAH Infrared Spectroscopic Database (PAHdb) to assess the variance on the average galaxy PAH population properties under a grid of different modeling parameters. We find that the short-low and short-low+long-low Spitzer-IRS decomposition with PAHFIT provides consistent modeling and recovery of the 5–15 μm PAH emission spectrum. For PAHdb modeling, application of a redshift to the calculated spectra to account for anharmonic effects introduces a 15%–20% variance on the derived parameters, while its …

Photolysis And Sublimation Chemistry Of Ammonium Cyanide With Relevance To Cometary Environments, O. H. Wilkins, K. M. Yocum, Vincent J. Esposito, E. Harel, S. N. Milam, P. A. Gerakines

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bulk nitrogen is depleted in solar system objects, including the terrestrial planets, chondritic meteorites, and comets. Recently, it was suggested that cometary nitrogen may be locked up in ammonium salts—ionic solids comprising ammonia (NH₃) and an acid such as hydrogen cyanide (HCN)—based on Rosetta/ROSINA data from comet 67P/Churyumov–Gerasimanko. Among the proposed salts to have been found in 67P were ammonium cyanide (NH₄CN) and ammonium cyanate (NH₄OCN), which were inferred from identifying HCN, cyanamide (NH₂CN), and isocyanic acid (HNCO) in the mass spectrometry data collected in the coma of 67P. However, the relationship …

Impact Of Y-Mixer Geometry And Flow Rate Modulation On Chemical Gradient Generators In Microfluidic Devices, Elizabeth Thurston Hutton

College of Graduate Studies: Theses & Dissertations

Various microfluidic structures are devised to generate tunable, stable spatiotemporal chemical gradients for single-cell studies. This work addresses the role of Y-mixer junctions in generating nonlinear gradients by increasing the width of one arm (bias), which is suspected to cause premature diffusion within the mixer. This study introduced a cinching feature to narrow the wider arm locally and redefine the junctions of these biased Y-mixers using four novel geometries defined by a 5-micrometer drawing rule. Furthermore, three flow rate factors allowed us to explore the impact on the generated gradient landscapes. The results showed that the four novel designs similarly …

Development And Application Of Gpu Based Monte Carlo Simulation Techniques In Radiation Medicine, Satzhan Sitmukhambetov

Physics Dissertations - Archive

Cancer remains a significant public health challenge, with treatments like radiation therapy forming a cornerstone of modern care. To address this challenge, advanced computer simulations can improve radiotherapy in two primary ways. From one hand, mechanistic simulations help elucidate the fundamental radiobiological working principles, which could contribute to the clinical advancements from a bottom-up framework. On the other hand, modality simulations could help design better clinical systems with better detection and therapeutic capabilities. This research enhances these critical simulation tools by introducing two significant developments.

First, this work introduces a metaphase DNA model into a microscopic Monte Carlo simulation framework …

Structural Optimization And Stability Enhancement Of Uba(2) And Ntl9 Using The Computational Tool: Emcast, Bahar Ghazi Esfahani

Graduate Student Theses, Dissertations, & Professional Papers

This study enhances protein stability prediction by refining EmCAST (Empirical C-Alpha Stability Tool), a computational tool used to identify stabilizing mutations in protein domains. We applied EmCAST to two model proteins: the α-helical ubiquitin-associated domain 2 (UBA(2)) and the α/β N-terminal domain of ribosomal protein L9 (NTL9). Protein stability is critical for proper function, and mutations can lead to misfolding and disease. To validate EmCAST’s predictions, guanidine hydrochloride-induced denaturation was monitored using circular dichroism (CD) spectroscopy for both wild-type and mutant variants. Results guided refinements to EmCAST’s algorithm, incorporating new experimental datasets to improve accuracy. Additionally, we examined the assumption …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Vibrational And Electronic Spectroscopy Of 2-Cyanoindene Cations, Thomas E. Douglas-Walker, Eleanor K. Ashworth, Mark H. Stockett, Francis C. Daly, Isabelle Chambrier, Vincent J. Esposito, Marius Gerlach, Angel Zheng, Julianna Palotás, Andrew N. Cammidge, Ewen K. Campbell, Sandra BrüNken, James N. Bull

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

2-Cyanoindene is one of the few specific aromatic or polycyclic aromatic hydrocarbon (PAH) molecules positively identified in Taurus molecular cloud-1 (TMC-1), a cold, dense molecular cloud that is considered the nearest star-forming region to Earth. We report cryogenic mid-infrared (550–3200 cm^–1) and visible (16,500–20,000 cm^–1, over the D2 ← D0 electronic transition) spectra of 2-cyanoindene radical cations (2CNI⁺), measured using messenger tagging (He and Ne) photodissociation spectroscopy. The infrared spectra reveal the prominence of anharmonic couplings, particularly over the fingerprint region. There is a strong CN-stretching mode at 2177 ± 1 cm^–1 (4.593 …

Cross-Interactions Of Amyloid Proteins: Implications For Aggregation Dynamics And Disease Pathology, Zhiyuan Song

All Dissertations

Amyloid aggregation is a pervasive form of protein misfolding implicated in the pathology of several prominent human diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and type 2 diabetes (T2D). These diseases are marked by the accumulation of amyloid fibrils and toxic oligomers, which are highly dynamic and heterogeneous, posing challenges for understanding their roles in disease progression. Despite significant advances in the diagnosis and management of these conditions, no definitive cure is available. We investigate amyloid aggregation and cross-seeding, with a focus on amyloid-beta (Aβ), tau, alpha-synuclein (αS), and human islet amyloid polypeptide (IAPP) through discrete molecular dynamics (DMD) …

Advancing Biofabrication Methodologies To Develop Biomimetic Tissue Scaffolds For Musculoskeletal Applications, Nashaita Yezdi Patrawalla

Theses and Dissertations

Musculoskeletal injuries impose a significant global burden, affecting millions and generating an economic toll exceeding $14 billion. Tissue engineering has gained traction as a promising strategy offering potential for functional restoration of damaged musculoskeletal tissues. This research aims to advance biofabrication techniques for generation of biomimetic tissue scaffolds, by optimizing scaffold design and modulating fabrication process parameters to generate scaffolds for musculoskeletal regeneration with application-specific tailored properties. In this realm, collagen-based biomaterials have been extensively investigated for tendon and ligamentous applications, and in combination with bioceramics incorporated into the collagen framework to produce composite scaffolds that better recapitulate the native …

The Impact Of Cumulative And Acute Loading On Achilles Tendon Health, Performance, And Reported Pain In Collegiate Gymnasts, Julio Serrano Samayoa

Electronic Theses and Dissertations

Gymnasts are at a high risk of Achilles tendon (AT) injuries due to intense loads during takeoffs and landings. To better understand better the relationship between impact loading and its effects on tendon adaptation and athletic performance, this study uses Inertial Measurement Units (IMUs) to track AT loading across a collegiate gymnastics season. This data were compared against physiological and athletic performance metrics, obtained through force plates and ultrasound imaging, to explore how mechanical load influences reported pain and athletic performance. Results varied, with cumulative impacts being correlated with improved jump height (Spearman 0.362, Pearson 0.348), while peak power and …

Detection Of Methane Leaks By The Use Of Mid-Range Infrared Camera, Jared Rosario, Oscar Salcido

Undergraduate Research Symposium Posters

Timely detection of methane leaks from natural gas infrastructure, like pipelines and valves, is essential for mitigating environmental and safety risks. This research focuses on using mid-wave infrared (MwIR) cameras on unmanned aerial systems (UAS) to detect leaks. By leveraging machine learning, the study aims to develop an efficient, real-time methane inspection system that operates directly on embedded processors on UAS platforms.

This project employs the FLIR G300a OGI camera for remote gas inspection, utilizing video preprocessing and optical flow to mask gas plumes in footage. The YOLOv8 deep learning model is used to detect gas pixels and segment the …

Battle Of The Ch Motions: Aliphatic Vs Aromatic Contributions To Astronomical Pah Emission And Exploration Of The Aliphatic, Aromatic, And Ethynyl Ch Stretches, Vincent J. Esposito, Salma Bejaoui, Brant E. Billinghurst, Christiaan Boersma, Ryan C. Fortenberry, Farid Salama

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Strong anharmonic coupling between vibrational states in polycyclic aromatic hydrocarbons (PAH) produces highly mixed vibrational transitions that challenge the current understanding of the nature of the astronomical mid-infrared PAH emission bands. Traditionally, PAH emission bands have been characterized as either aromatic or aliphatic, and this assignment is used to determine the fraction of aliphatic carbon in astronomical sources. In reality, each of the transitions previously utilized for such an attribution is highly mixed with contributions from both aliphatic and aromatic CH motions as well as non-CH motions such as CC stretches. High-resolution gas-phase IR absorption measurements of the spectra of …

Design And Characterization Of De Novo Photoactivated Charge Separating Proteins, Paul M. Molinaro

Dissertations, Theses, and Capstone Projects

Light activate charge separation can provide high energy electrons for a variety of chemical processes. Reaction center proteins serve as a scaffold for small molecules that serve as “hopping” sites for electrons. Previous reaction center designs are four helix bundles that bind at minimum two metalloporphyrin’s: a zinc porphyrin serves as a light activated electron donor, mimicking chlorophyl, and a heme molecule serving as the acceptor. The efficiency of these designs is hampered by the enhanced relaxation of the singlet excited state of zinc porphyrin molecules due to spin-orbit coupling with the paramagnetic heme acceptor. The optimal design would contain …

On The Formation And Detectability Of H2Cncn And Its Progenitors, Ryan C. Fortenberry, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New highly exothermic formation pathways incorporating both thermodynamic and kinetic control for the newly astronomically detected H₂CNCN molecule are paired with extremely accurate quantum chemical rovibrational spectroscopic computations. The reactions between astronomically known CH₂CN/CH₂CCH + HNCN follow effectively identical pathways and proceed through stable intermediates and over deeply submerged transition states to form H₂CNCN and HCN/HCCH coproducts. Similarly, the reaction between CHM₂CN and NCN⁻ can also form H₂CNCN, although this pathway first requires the initial formation of NCN⁻, which is currently undetected in space, via …

Experimental Determination Of The Unusual Ch Stretch Frequency Of Protonated Fullerenes, Laura Finazzi, Vincent J. Esposito, Julianna Palotás, Jonathan Martens, Els Peeters, Jan Cami, Giel Berden, Jos Oomens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report experimental values for the CH stretch frequencies of the protonated fullerenes C₆₀H⁺ and C₇₀H⁺. Anharmonic frequency calculations at the B3LYP/6-31G level of theory, which are independent of empirical scaling factors, reproduce the experimental values to within approximately 5 cm⁻¹. Scaling theoretical harmonic frequencies by applying factors derived for polycyclic aromatic hydrocarbons deviate significantly from the experimentally measured frequency. We attribute this deviation to the unusual hydrocarbon structure that affects the degree of anharmonicity of the CH stretch. This result allows us to propose an original, specific scaling factor of …

Revolutionizing Wild Silk Fibers: Ultrasound Enhances Structure, Properties, And Regenerability Of Protein Biomaterials In Ionic Liquids., Xincheng Zhuang, Haomiao Zhu, Fang Wang, Xiao Hu

College of Science & Mathematics Departmental Research

Ultrasound-assisted regulation of biomaterial properties has attracted increasing attention due to the unique reaction conditions induced by ultrasound cavitation. In this study, we explored the fabrication of wild tussah silk nanofiber membranes via ultrasound spray spinning from an ionic liquid system, characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), atomic force microscopy (AFM), water contact angle, cytocompatibility tests, and enzymatic degradation studies. We investigated the effects of ultrasound propagation in an ionic liquid on the morphology, structure, thermal and mechanical properties, surface hydrophilicity, biocompatibility, and biodegradability …

The Role Of Efflux Pump Inhibitor In Enhancing Antimicrobial Efficiency Of Silver Nanoparticles And Methylene Blue As An Effective Photodynamic Therapy Agent, Yaran Allamyradov

Masters Theses & Specialist Projects

Efflux pumps are critical active transport systems utilized by cells to expel toxic substances, including antibiotics and photosensitizer complexes, thereby contributing to antimicrobial resistance. Efflux pump inhibitors (EPIs), which are compounds that obstruct the transport of molecules through these pumps, play a pivotal role in enhancing the effectiveness of antimicrobial therapies against pathogens. This study investigates the effects of the EPI reserpine on the photodeactivation rate of pathogens when used in conjunction with silver nanoparticles (Ag NPs) and methylene blue (MB), a common photosensitizer.

Our research reveals that the application of reserpine, in combination with Ag NPs and MB, leads …