Biological and Chemical Physics Commons^™

1-D And 2-D Hadamard Transformations For Protein Sequence Analysis, Esraa A. Ahmed, Abed M. Nasr, Marwa A. Abd Elwahaab

Mansoura Engineering Journal

Similarity/dissimilarity studies follow alignment-based or alignment-free methods. Many alignment-free methods involve selecting physicochemical properties. Most previous articles don’t explain their criteria for choosing the properties used. These heuristic approaches have, by definition, undeterministic and unreliable performance. Hence, there is a need for a powerful proxy for similarity/dissimilarity by a deterministic, reliable approach.

In this study, a physicochemical property is selected by a multi-criteria sequential selection process. The amino acids composing any protein sequence are replaced with their values of the chosen property to produce a discrete signal in the time domain.  The one-dimensional discrete Hadamard transforms our signal from the …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk, Yasir A. Alshehry, Matthew S. Halquist Phd, Sandro R.P. Da Rocha Phd

Graduate Research Posters

Background

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance …

Intersecting Physics And Medicine Through Computed Tomography, Christopher Wengert, Madouna Barsoum, Dominick Dingus

Student Scholar Symposium

Computed Tomography (CT) imaging is a cornerstone of modern medicine. Enabling detailed internal imaging for diagnostic and therapeutic applications. This project explores the physics underlying CT imaging, highlighting how fundamental principles of physics integrate seamlessly with medical advancements. We will examine X-Ray generation, attenuation, and image reconstruction, demonstrating how varying tissue densities influence scan results. The role of mathematical algorithms, such as filtered back protection and iterative reconstruction, will be discussed in relation to image clarity and radiation does optimization.

Additionally, we will address the balance between image resolution and patient safety, emphasizing the importance of minimizing radiation exposure while …

Modeling Mineral Redistribution In Biological Tissue Using Apple As An In Vitro Analogue, Daler Djuraev, Ali Algemsh, Halima Alazeb, Zeenia Ahmed

Publications and Research

This project aims to model mineral (ion) redistribution that occurs in human soft tissue after injury or mechanical/thermal stress. Because direct, repeatable in vivo measurements are difficult, we use apples as an in vitro analogue: their mineral content is relatively uniform and the tissue can be cut, dried, and repeatedly imaged under controlled conditions. Using X-ray imaging, we tracked how minerals in apple tissue move toward damaged regions immediately after cutting, and how subsequent drying at room temperature drives a redistribution toward the central core. We also observed that biological degradation (decay) alters mineral density over time, indicating that even …

Single-Molecule Orientation And Localization Microscopy, Sophie Brasselet, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Single-molecule localization microscopy (SMLM) offers enhanced spatial resolution in optical microscopy, providing detailed insights into the spatial organization of proteins in cells at the nanoscale. Over the past decade, SMLM has progressively incorporated the capability to retrieve the orientations of single molecules using their polarized dipolar emission pattern. Here we explore recent advancements in single-molecule orientation and localization microscopy (SMOLM), which yields super-resolved images of molecular three-dimensional (3D) orientations, wobble and 3D positions. This advancement opens possibilities to explore the nanoscale organization and conformation of biological molecules as well as to monitor and design local 3D optical fields in nanophotonics. …

Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel

Graduate Masters Theses

Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …

Quantum Dot Light Emitting Diodes As A Light Source For Photodynamic Therapy, Hamid El Hamidi

Graduate Doctoral Dissertations

ABSTRACT:

QUANTUM DOT LIGHT EMITTING DIODES AS A LIGHT SOURCE FOR PHOTODYNAMIC THERAPY

Photodynamic therapy is a cancer treatment modality that involves the accumulation of a photosensitizer, exposure to visible light, and the presence of oxygen, resulting in the formation of highly reactive and cytotoxic singlet oxygen. PDT has been shown to be more effective as the fluence rate decreases due to oxygen availability and the absence of photobleaching. On the other hand, Quantum Dot Light Emitting Diodes QLEDs- a new form of light source based on nanoparticles (quantum dots)- emerge as a potentially advantageous light source for certain types …

Facilitating The Clinical Translation Of Flash Radiotherapy Through Dosimetry Development And Beam Parameter Optimization, Kevin Liu

Dissertations and Theses (Open Access)

Advisory Professor: Emil Schüler, PhD

Radiation therapy (RT) is a crucial component of curative cancer therapy, with a majority of cancer patients in the United States receiving RT as part of treatment. The goal of RT is to maximize the therapeutic index in curing disease while minimizing any associated normal-tissue complications¹. Recently, ultra-high dose-rate (UHDR) RT (mean dose rates ≥40 Gy/s for a total duration of ≤200 ms) has been reported to selectively spare normal tissues and organs while maintaining an isoeffective tumoricidal effect compared to conventional (CONV) dose rate RT in a variety of in vivo preclinical …

2d Cuo/Rgo Nanocomposite: A Novel Architecture For Enhanced Cr(Vi) Photo-Reduction, Islam Gomaa, Nasser M. Hosny, Medhat A. Ibrahim

Nanotechnology Research Centre

he urgent need for efficient detoxification of carcinogenic hexavalent chromium (Cr(VI)) in aquatic environments has driven the development of advanced photocatalytic materials. This study presents the synthesis of 2D CuO/reduced graphene oxide (rGO) nanocomposite via probe sonication, designed to synergistically enhance the photocatalytic reduction of Cr(VI) to less toxic Cr(III). The nanocomposite was meticulously characterized using XRD, HRTEM, FESEM, XPS, and UV-Vis diffuse reflectance spectroscopy. Structural analysis confirmed the formation of CuO nanosheets (average size: 396 nm, thickness: 6 nm) integrated with rGO, where the rGO acted as an electron acceptor, mitigating charge recombination. XPS revealed Cu²⁺ in CuO and …

Nuclear Magnetic Resonance Dynamics Of Pyrazole-Litfsi Eutectic Solvents As Promising Electrolytes, Emilia Pelegano-Titmuss, Giselle De Araujo Lima E Souza, Muhammad Zulqarnain, Ramez Elgammal, Thomas Zawodzinski, Steven Greenbaum

Undergraduate Research

Deep Eutectic Solvents (DESs) have emerged as promising candidates to replace conventional organic solvents in various technological applications due to their low vapor pressure, non-flammability, and ease of preparation at low costs. In particular, Type IV DESs, which are composed of metal salts and hydrogen bond donors, are possible replacements for lithium-ion battery electrolytes due to their potential of having high lithium transference numbers. In this study, we investigated solvents of Pyrazole and LiTFSI at varying molar ratios using Fast Field Cycling (FFC) NMR Relaxometry. Notably, the 1:2 LiTFSI: Pyrazole sample shows distinct behavior, exhibiting enhanced relaxation rates for ^{1 …}

A Catalytic Pathway For The Formation Of Cyanobenzene In Nitrogen-Rich Environments And The Spectroscopy Of The Reactive Intermediates, Vincent J. Esposito, Silvia Alessandrini, David Dubois, Ryan Fortenberry

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The catalytic reaction of isocyanobenzene (C₆H₅NC) with NCN⁻ produces cyanobenzene (C₆H₅NC) through various highly stable reactive intermediate species. Nitrogen-rich environments such as Titan’s atmosphere serve as favorable locations to study reaction pathways involving nitrogenated species contributing to organic growth. Formation pathways of cyanobenzene have been characterized, but none with the contribution of anions or phenyl groups. In regions with a high abundance of nitrogen anions, such as Titan’s atmosphere, reactions with species such as NCN⁻ may play a role in the formation of cyanobenzene. Highly accurate computational methods are used …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Creasing In Thick Hemispherical Shells As A Model For Foveal Formation, Indigo Skye Peppard

Undergraduate Honors Theses

This research experimentally investigates creasing behavior on the inner surface of hemispherical shells with the ultimate goal of modelling the formation of the foveal pit, a sharp surface deformation present in the retina of the eye of many animals. Creasing is a phenomenon observed in hyperelastic materials and is characterized by sharply localized surface deformations that appear at ~35% compressive strain. The foveal pits of anoles (small iguanian lizards) are funnel-shaped and resemble creases when cut along the central axis. Furthermore, during foveal pit formation the anole eye contracts around 35% along this same axis. Given these similarities we believe …

Direct Computations Of Spatially Resolved Viscoelastic Moduli Of Biomolecular Condensates, Liwen Gu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biomolecular condensates are viscoelastic materials formed by liquid-liquid phase separations (LLPS) of biopolymers. In this study, we develop a modified graph Laplacian-based collective model to characterize viscoelastic heterogeneity within condensates based on results of lattice-based Metropolis Monte Carlo (MMC) simulations. By integrating random graph models and simulations of A1-LCD, a type of intrinsically disordered protein, we examine how network topology influences storage modulus, loss modulus, crossover frequency, and relaxation time spectra. Our results reveal a strong correlation between topological features and mechanical response, with the condensate interior exhibiting higher stiffness and faster relaxation than the interface. The relaxation spectra provide …

Experimental Evaluation Of Resource Allocation To Organelles In Eukaryotic Cells, Ronan Hanley

Senior Honors Papers / Undergraduate Theses

Among the hallmarks of the eukaryotic cell is its organization into spatially defined sub-compartments known as organelles. Organelles provide optimized environments for otherwise incompatible biochemical reactions within the cell. It has been shown that there is significant variation in the properties of organelles in a cell, and that cells have access to a limited pool of resources that they can allocate to organelles. This begs the question: by what principles do cells dictate how resources are allocated? To begin to explore this question, we look at resource allocation in S. cerevisiaefrom two perspectives. First, we use a combination of …

Unpaired Virtual Histological Staining Of Tissue From Autofluorescence Using Regularized Cycle-Consistent Adversarial Networks, Zhesi Wen

Theses and Dissertations

We present a regularized CycleGAN with a Dense Residual U-Net to virtually stain autofluorescence images of tissue into H&E-like images. Our method outperforms standard architectures, reduces artifacts, and achieves superior FID scores, enabling efficient, label-free, and accurate digital pathology for unpaired datasets using multi-channel fluorescence inputs.

Intercellular Stress Generation During 1d Collective Migration Of Cancer Cells, Logan Waddle

Physics Undergraduate Honors Theses

Physical forces drive many cellular processes such as migration and proliferation. A metastatic tumor will have invasive strands/chains that extend from the main tumor. These chains of cells collectively migrate away from the main tumor to establish new colonies elsewhere in the body. However, how physical forces drive this collective invasion and the required energy for this process is not well understood. Invasion of a metastatic tumor to surrounding tissues leads to a majority of cancer-associated death and is often a collective effort among cells, it is therefore important to fully understand the process behind collective cancer invasion.

The goal …

Developing An Unfolding-Incorporated Coarse-Grained Polymer Model For Fibrinogen To Study The Mechanical Behaviour, Vivek Sharma, Poulomi Sadhukhan

Northeast Journal of Complex Systems (NEJCS)

Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties. The fibrin monomer, Fibrinogen, has a very complex structure which is responsible for its unusual elastic behaviour. In this work, we focus on mechanism of unfolding of D-domain of Fibrinogen, and study its effect in the mechanical behaviour. We develop a coarse-grained (CG) bead-spring model for Fibrinogen which captures the unfolding of folded D-domains along with other necessary structural …

Microcanonical Analysis Of Semiflexible Homopolymers With Variable Bending Potential Width, Michael Gray

Scholars Week

I have developed an algorithm for finding phase transition in microcanonical data of simulations of homopolymers. These simulations model the behavior of homopolymers in an array of different conditions. This algorithm is generalized and can be applied to a variety of different systems. It works by taking repeated derivatives of the microcanonical entropy of the system and applying several filters, whose parameters are tuned algorithmically as well. Identification of phase transitions allows for the construction of a phase diagram.