Biological and Chemical Physics Commons^™

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, …

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 …

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 …

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 …

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 …

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 …

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) …

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.

Understanding The Growth Mechanism Of Thiol-Conjugated Au25 Cluster, Chunhui Liu, Haiying He, Ravindra Pandey, Shashi P. Karna

Michigan Tech Publications

The synthesis of ligand-conjugated gold nanoclusters has attracted significant attention due to its ability to achieve precise control over cluster size selectivity. Among these, Au₂₅(SR)₁₈-, where R represents an alkyl group, is one of the earliest being synthesized with a very high yield, although its growth mechanism is yet to be fully understood. Using density functional theory, we present the results of a theoretical investigation on the growth process of Au₂₅(SR)₁₈-, beginning from Au₁₃(SR)₁₂-. Our findings indicate that the sulfur atoms in the core structure of Au_{13 …}

How Does Honey Make Gold Nanoparticles? Optical Analysis Of The Effects Of Temperature And Composition, Lydia Alvarnaz, Davon Ferrara Phd

SPARK Symposium Presentations

In recent years, with an increasing interest in green chemistry, there has been an effort to find and understand synthesis methods using biologically-produced reducing and capping agents to produce stable gold nanoparticles (GNPs). Previous research using honey has shown this substance is a viable reducing agent in the formation of nanoparticles but have not looked at the stability of the colloidal gold nanoparticles. In this work, gold nanoparticles were reduced from an aqueous solution of gold chloroauric acid and a solution of varying concentrations of honey and water. The formation of NPs was analyzed using UV-Visible transmission spectroscopy to confirm …

Influence Of Oil Density On Self-Propelled Motion Of Belousov-Zhabotinsky Reaction Droplet, Vivek Bharat Meshram, Anupama Sebastian, Puthiyapurayil Sibeesh, T K Shajahan

Northeast Journal of Complex Systems (NEJCS)

Belousov-Zhabotinsky reaction serves as an example of the nonlinear chemical oscillator in which the reacting substance undergoes sequential oxidation and reduction. A droplet containing the BZ reaction, when placed within the oily environment, can self-propel. In this experimental work, we explore the effect of oil medium density on the BZ reaction droplet dynamics. In an oil medium with lower density, the BZ droplet exhibits higher speed and effective diffusivity but a shorter lifetime. Both the distance and speed of the droplet initially increase with droplet volume. However, beyond a critical volume, the distance decreases while the speed stays constant. Interestingly, …

Infrared Cooling In An Anharmonic Cascade Framework: 2-Cyanoindene, The Smallest Cyano-Pah Identified In Tmc-1, Mark H. Stockett, Vincent J. Esposito, Eleanor K. Ashworth, Ugo Jacovella, James N. Bull

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Infrared (IR) cooling of polycyclic aromatic hydrocarbon (PAH) molecules is a major radiative stabilization mechanism of PAHs present in space and is the origin of the aromatic infrared bands (AIBs). Here, we report an anharmonic cascade model in a master equation framework to model IR emission rates and emission spectra of energized PAHs as a function of internal energy. The underlying (simple harmonic cascade) framework for fundamental vibrations has been developed through the modeling of cooling rates of PAH cations and other carboneaous ions measured in electrostatic ion storage ring experiments performed under “molecular cloud in a box” conditions. The …

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 …