Session D61: Undergrad Research III

Investigating the electromagnetic induction response of neurons on stimulus waveform shapes and coil geometries

The nervous system in humans operate based on electrical conduction through action potentials. So, when nerves are damaged, electrical pathways in the body are broken, which leads to the loss of muscle control and other bodily functions. To treat such patients, doctors at the Medical College of Georgia have carried out clinical studies that show damaged nerve function can be improved by electromagnetic induction. However, the interaction mechanism of how an induced electric field interacts with damaged nerves and its implication within a clinical setting is not fully understood. The goal of this project is to understand how optimizing the setup used to induce an electric field can affect the clinical treatment of a damaged nerve. Using a computational approach that models the nerves within the Hodgkin-Huxley paradigm and the electromagnetic interaction of the nerves with the Roth-Basser equation, we find that for the unmyelinated neurons there is a greater stimulus imparted to the nerve for long pulse durations. In addition a biphasic signal is not as effective as a monophasic signal. The geometry of the coil also affects the stimulus of the nerve with a circular coil geometry generating the largest impact. We also investigate the above effects for myelinated axons.   

Cell Size Affects Synthetic Cell-Cell Signal Output In Vivo

Cell-cell signaling and communication are integral to the existence of complex life. Cells often communicate through juxtacrine signaling mediated by a ligand presented on a cell surface binding to a specific receptor on a neighboring cell. Synthetic Notch (synNotch), based on the native Notch signaling pathway, transduces a unique input signal in the receiving cell due to contact with a neighboring ligand cell to produce a custom gene expression output. Here, our work in collaboration with the Langridge lab focuses on the synNotch output patterns in the developing fruit fly larvae, visualized with the green fluorescent protein (GFP). We extract cell size and shape parameters and the intensity of the GFP response to evaluate and quantify biophysical trends underlying synthetic cell-cell signaling. Our results support our previous computational model predictions showing an increase in synNotch response with increasing cell size. As cells undergo dramatic changes in size and morphology during development, our results show that cell size could affect cellular communication.   

Pigmentation Pattern Recreation in Reaction-Diffusion Systems using Realistic Bounds

Research into the application of reaction-diffusion models to understand natural systems has uncovered its novel capability to mechanistically recreate realistic animal pigmentation patterns. Reaction-diffusion systems, first proposed by Alan Turing in 1952, describe the rate of change of the concentrations of substances by their interactions and diffusions in space. The complex spatial periodic patterns created by the model develop autonomously through the random perturbations of an initially homogeneous equilibrium state, and have been found to correspond to numerous natural phenomena, including animal pigmentation. With the implementation of a reparameterized version of the system, we use silhouettes of various species as spatial bounds to create GPU simulations of the development of their pigmentation patterns in their natural shape. We study the relationship between the features of an animal's surface and its developed pigmentation pattern complexity. We also analyze variations in the parameters, which produce a wide range of pigmentation patterns associated with different species of animal. Our analysis allows for biological and mathematical insight into the core mechanisms of general animal pattern development.   

Collectively moving filaments in oil suspensions of the nematode T. aceti

Previous research indicates that the nematoda Turbatrix aceti, commonly known as vinegar eels, can synchronize their body oscillations under favorable conditions, such as the droplet's contact angle ( θ > 68°) to produce metachronal waves similar to the one that sports fans create on the stadiums. It is unknown whether these nematodes can still synchronize their motion in high viscosity fluids. We study the collective motion of nematodes in oils of different molecular weight and viscosity. We find that contrary to the water suspensions, nematodes in oil form collectively propagating filaments. We measure the oscillation frequency inside and outside the oil, the number of filament splits, the density of nematodes per region, and how fast the filaments are advancing. We find that the nematodes in less viscous oils were able to spread out faster and create interlocking filaments. In comparison, nematodes in more viscous oils only spread individually without creating collectively moving filaments. Their travel distance was smaller than the one of collective filaments in low viscosity oil. Further research is necessary to determine whether other factors such as oil density may have contributed to the results.   

Observing subdiffusion in artificial cytoplasm: polyethylene glycol as a crowding agent

Biological cells are crowded viscoelastic environments and cellular cytoplasm's spatial organization plays a massive role in biological systems, yet their underlying physical-chemical properties are not fully understood. The development of an artificial cellular cytoplasm is desired to contribute to the understanding of biological intracellular environments. We studied the motion of inert tracer particles in monodisperse and polydisperse aqueous solutions with varying concentrations and chain lengths of the crowding agent polyethylene glycol (PEG) to determine the circumstances that allow for a subdiffusive artificial intracellular environment. PEG is a chain molecule available in a variety of lengths specified by its molecular mass. We find that subdiffusion is observed consistently in aqueous solutions of approximately monodisperse longer PEG (20000 g/mol) at 25 mg/mL concentration as well as with lengths as low as 200 g/mol with concentrations of 40% by volume. Generally, subdiffusivity increases with the medium's PEG concentration or length. The dependence of subdiffusivity on higher concentration and longer polymer chain lengths suggests that PEG produces a caging effect within artificial environments. These findings support the use of PEG as a tunable crowding agent for an artificial cytoplasm and have exciting implications for the creation of an artificial cell.   

Fabrication and characterization of gold microdisks for cancer treatment

Gold particles have been explored as radiosensitizers in cancer treatment due to their high-mass energy absorption coefficients and biocompatibility. However, the reticuloendothelial system recognizes and rapidly clears injected gold particles via phagocytosis from the blood circulation resulting in less than 1% of the gold particles reaching the tumor sites. Recent work has shown that disk-shaped particles are more resistant to phagocytosis in comparison to spherical particles resulting in prolonged circulation time. Here we report the fabrication and characterization of gold microdisks with varying geometries to investigate their ability to evade phagocytosis by macrophages. Gold disks of 2µm or 10µm in diameter and 20 nm or 100 nm in thickness were fabricated using photolithography, sputtering deposition, and the lift-off process and characterized by small-angle X-ray reflectivity and atomic force microscopy. The fabricated gold disks were incubated with macrophages, which enabled the study of the gold disk phagocytosis using confocal microscopy.   

Rev1 DNA Polymerase Repair Mechanism and Optical Tweezer Measurements on Damaged DNA

Replication of damaged DNA leads to cancer. The nucleotide arrangement of DNA contributes to its strength, which can be altered by damage. One mechanism by which the body repairs damage is DNA polymerases, specifically Rev1. Rev1 is an enzyme that facilitates the replication or repair of specific damaged or absent nucleotides in DNA and is a component of the body's ability to prevent mutated DNA from replication and cancer. We hypothesize two amino acids in the active site of Rev1 facilitate its unique Y-family polymerase repair mechanisms using protein purification and x-ray crystallography.



In conjunction with understanding Rev1's ability to repair damaged DNA, we are also investigating the inherent structural properties of DNA and how damage alters those properties. A comparison between healthy DNA and unrepaired DNA is crucial. Force measurements necessary to break healthy and unhealthy DNA can be acquired using optical tweezers. The force measurements will provide numerical data for a previously unquantifiable event. Our group built a custom optical tweezer setup for undergraduate institutions lacking sufficient funds to buy optics equipment. These force measurements will help us better comprehend the importance of Rev1's DNA repair mechanism.

  

Construction of Optical Tweezers and Inverted Microscope

PLAIDX is a research collaboration working across high school and undergraduate institutions to create opportunities for students to engage in original multi-disciplinary research. One of our research objectives is to construct cost-effective optical tweezers to study forces on non-damaged and damaged DNA. Part of achieving this goal is to build a visible light prototype that will be used to test concepts before developing an IR tweezing system (required for biomolecule research). This presentation will focus on how that objective was achieved. Building this prototype involved constructing and aligning a custom inverted microscope and optimizing a beam path using a HeNe laser to facilitate trapping molecules. This will lead to the project's next phase, which includes constructing a homemade current driver for a 1064 nm laser diode. This is happening in parallel with projects relating to biophysical applications.   

Development Of An Automated Steerable Radio Telescope.

The paper presents an innovative approach towards the design and construction of a steerable radio telescope with an automated control system. The telescope uses a combination of motors and sensors to steer towards celestial objects of interest, with the ability to track moving targets such as satellites. The authors detail the technical specifications of the telescope, including its radio frequency range, sensitivity, and accuracy, and discuss the challenges encountered during its development. This research paper is highly relevant to the field of astrophysics as radio telescopes play a critical role in studying the properties of the universe. The development of an automated steerable radio telescope presents new opportunities for data collection and analysis, allowing astronomers to observe the universe more efficiently and effectively. The paper demonstrates the application of physics principles, such as mechanics and electromagnetism, in the design and operation of the telescope. The findings of this study can contribute to further research in astrophysics, including studies of the cosmic microwave background, radio galaxies, and other extragalactic sources. Overall, the development of an automated steerable radio telescope represents a significant advancement in the field of astrophysics and presents new avenues for research and discovery in the coming years.   

Progress of Development and Design of DUCK (Detector of Unusual Cosmic-ray casKades)

A large mystery that is currently being investigated by the High Energy Physics (HEP) field is the origin and the nature of the Ultra-high energy Cosmic Rays (UHECR). Coming from deep within the Universe, they bring information from afar as well as on possible new physics. This talk reports on progress of the development and design of DUCK (Detector system of Unusual Cosmic-ray casKades) at the Clayton State University campus. The main scientific importance for the DUCK project will be to contribute to the general EAS event analysis methodology novel approach using the full waveform and detector response width, and to an independent verification of the detection of the ‘unusual’ cosmic ray events by the Horizon-T detector system that may be indicating direction towards the novel physics possibilities.   

Characterizing the Structure of Magnetic Fields in Spiral Galaxies with Radio and Far-Infrared Polarimetric Observations

​​Large-scale spiral magnetic field structures are commonly observed in spiral galaxies. These fields contribute to the total pressure that balances the interstellar medium against gravity as well as influence the flow of gas within a galaxy. The structure of these B-fields can be estimated through polarimetric observations and quantified as a pitch angle. Previous analyses that have characterized these pitch angles were model-dependent, e.g. assume a logarithmic spiral functional form. We propose a new method to quantify the morphology of the large-scale magnetic fields in galaxies which is more flexible and model-independent than current approaches. This method was adapted from the analysis of Event Horizon Telescope polarization data. We compute a linear decomposition of the azimuthal modes of the polarization field in radial galactocentric bins. We apply this approach to five low-inclination spiral galaxies with both far-infrared dust polarimetric observations (FIR: 154 μm) and radio (6 cm) synchrotron polarization observations. Using this new approach, we found that the average pitch angle of these large-scale B-fields was smaller and had greater angular dispersion in the FIR data compared to radio, meaning that the B-fields in the disk midplane traced by FIR dust polarization are more tightly wound and more disordered than the B-field structure in radio.