Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session F46: Undergraduate Research VUndergrad Friendly
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Sponsoring Units: SPS Chair: Brad Conrad, AIP Room: Room 314 |
Tuesday, March 7, 2023 8:00AM - 8:12AM |
F46.00001: Mechanical Properties of Fish Shoals Gabriel Kuntz, Mitchell Rask, Pasha A Tabatabai Schooling fish stay as a cohesive unit despite each individual consuming energy and moving on its own. This collective can be considered an amorphous soft material that both influences and is influenced by its individual components, but still retains quantifiable physical properties. We investigate these properties of soft active materials by finding the mechanics and structure of fish shoals in an experimental laboratory setting. We use imaging and image analysis techniques to extract the positions and trajectories of individual fish within groups confined to a quasi 2D volume of water. In order to find how individuals take up space within a shoal and interact with their neighbors we apply a Voronoi tessellation to the fish positions, which defines an effective unit cell for our amorphous material. This allows us to measure how changing the shoal's confinement geometry and population affect individual fish and the shoal as a whole. |
Tuesday, March 7, 2023 8:12AM - 8:24AM |
F46.00002: The Effects of Changing Geometry on Fish Motion in Shoals Mitchell Rask, Gabriel Kuntz, Pasha A Tabatabai Fish within schools exhibit intriguing collective behaviors. These collectives can be considered assemblies of active interacting constituents within an amorphous material. The fish propel themselves while simultaneously processing information about their environment. We view shoals as assemblies of active particles-- This perspective allows us to categorize the movement of individual fish and see in what ways they differ from assemblies of passive particles. We investigate the dynamics of individual fish moving by recording videos of fish swimming within the lab in quasi-2D volumes of water. We identify and track fish positions, trajectories, and velocities over time for each fish within the collective. We observe that by controlling the group size and system density, we can control fish motion and speed. |
Tuesday, March 7, 2023 8:24AM - 8:36AM |
F46.00003: Studying Turing patterns in vegetation Brendan D'Aquino Reaction-diffusion equations are a widely studied class of mathematical models that describe systems in which the rate of change of each state variable is determined by local interactions between the variables and their diffusion in space. In 1952, Alan Turing discovered a mechanism by which small random perturbations from an initially homogeneous equilibrium state could cause the development of complex spatial patterns in certain reaction-diffusion systems. This provides an explanation for patterns observed in many areas of ecology, physics, and developmental biology. In this work we show experimental measurements of Turing patterns in vegetation obtained in space using chia seeds growing in four different substrates with varying levels of diffusion, daily irrigation, and evaporation. We developed interactive GPU simulations of a 2D reaction-diffusion model of vegetation growth (Rietkerk) with model parameters fitted to the experiments. We demonstrate that the model is able to reproduce the experimental patterns for the different levels of diffusion, irrigation, and evaporation. We believe this is the first time a vegetation model has been validated directly with experiments. |
Tuesday, March 7, 2023 8:36AM - 8:48AM |
F46.00004: Energetic Models of Artificial Chlorosome Light Harvesting Systems Alexander W Hardin, Jaime A Diaz, Ysaris A Sosa, Gregory Uyeda, Gabriel Montaño, Inès Montaño It is well known that light harvesting in photosynthesis is a highly efficient process that functions under a wide range of light conditions. This is accomplished through varying chromophore composition and system size. Computational models have been used for years to predict the behavior of natural systems, but the complicated protein environment has made them difficult to analyze. Synthetic light harvesting complexes, known as polymer chlorosome nanocomposites (PCN), consist of a large array of diverse chlorophyll chromophores. PCN look and function like native cholorosomes but with several advantages, most importantly, their composition can be systematically varied. In this work, we discuss how the properties of known chemical structures, determined through Ab Initio computational chemistry methods, can be used to simulate the time evolution of corresponding PCN. |
Tuesday, March 7, 2023 8:48AM - 9:00AM |
F46.00005: Exploring Membrane-Damaging Effects of Amyloid Aggregates on the Clustering Behaviors of Lipid Molecules in Simulated Neuronal Membranes Using Unsupervised Machine Learning (NMFk) Algorithm Ngoc Nguyen Recent experimental studies have indicated that neuronal membranes contain dynamic, phase-separated nanodomains distributed on both leaflets of the lipid bilayers. Using microsecond MD simulations, we have created many phase-separated lipid bilayers containing ordered (Lo), disordered (Ld), mixed Lo and Ld (Lod), and ganglioside-cluster (GM1) domains that mimic the neuronal membranes. We have further demonstrated Lod and GM1 domains represent major membrane damage targets of several cytotoxic amyloid protein oligomers associated with Alzheimer’s disease (AZ). At present, a robust computational tool to characterize the membrane disruptive effects of these oligomers based on the clustering behaviors of nanodomains is not available. By implementing the Non-Negative Matrix Factorization (NMFk), an unsupervised Machine Learning (ML) algorithm, we have decomposed the time-dependent lipid-lipid proximity matrix into two latent signatures and activities matrices, sorted all the constituent lipids into domains, and assessed the clustering disruption behaviors of nanodomains through the transient change in the signatures assignment of each lipid. The results of this ML study will provide new insights into the membrane-damaging mechanisms of cytotoxic amyloid oligomers linked to the early pathogenesis of AZ. |
Tuesday, March 7, 2023 9:00AM - 9:12AM |
F46.00006: Measuring the Motility of Pseudomonas aeruginosa Near Surfaces Victoria Torres, Orrin Shindell, Hoa Nguyen, Frank Healy, Bruce E Rodenborn Many motile bacteria, including Pseudomonas aeruginosa, achieve motility by using their flagellar motor to generate a torque that rotates a helical filament and propels their body forward. When swimming near a surface, P. aeruginosa follows relatively curved trajectories, spontaneously retreating by switching the direction of the flagellar motor’s rotation. With its simple body structure, P. aeruginosa is a prime model organism for performing numerical simulations of bacterial motility near a surface. The aim of this work is to experimentally measure the motion of P. aeruginosa near a surface and input those measurements to a numerical model to compute the torque required to rotate the flagellum. |
Tuesday, March 7, 2023 9:12AM - 9:24AM |
F46.00007: Moving Towards Crystallizing Rev1 Mutans to Investigate the Structure Daniel A Nordquist ISLAND CURE is a new research collaboration that focuses on using physics techniques and apparatuses to perform biochemical measurements. One of the projects of the ISLAND CURE is to investigate X-ray crystal structures of Rev1, a Y family DNA polymerase. In order to understand the unique mechanism by which it replicates DNA, we investigated the structures of Rev1 with specific amino acid mutations. I have taken a leadership role in this group where I served as a research assistant using a post-doctoral model of lab management. The responsibilities of this role include performing not just biochemical tasks, but physics based projects, ranging from transforming bacteria to constructing an inverted microscope stage. The post-doctoral model is a potential model for professors with heavy teaching loads to overcome the time constraints for implementing CUREs in their classes. |
Tuesday, March 7, 2023 9:24AM - 9:36AM |
F46.00008: Time-Fractional Radial Diffusion in a Sphere with Non-Constant Surface Concentration Ted Clarke, Rachel Stephens The standard integral equation describing the inward radial diffusion from the surface of a sphere of radius R has been generalized to a time-fractional integral equation describing fractional radial diffusion. Using Laplace transform techniques and Mittag-Leffler functions, the solution has been obtained for the case when the concentration at the surface of the sphere is non-constant. |
Tuesday, March 7, 2023 9:36AM - 9:48AM |
F46.00009: Non-linear Computational Analysis of the Azeotropic Behavior of a Ternary Refrigerant Mixture Ahmad Mardini Finding an optimum refrigerant mixture while considering cost and keeping an eye on the effect it has on the environment has been a major topic in physical environmental studies. In this project an in-depth computational analysis on a system of ternary mixture of refrigerants was performed. The purpose was to find the best-fit constants to a system of nonlinear equations that model the vapor-liquid equilibrium of a ternary mixture of refrigerants that exhibit an azeotrope. The algorithms proposed in this study could be extended to other mixtures and the number of elements can be expanded on for future work. The computational results were compared to experimental data from published research articles, and the agreement with a binary mixture was excellent and very good for a ternary mixture. The approximation was performed numerically with MATLAB along with experimental data at the azeotropic point as an input. This method can be a valuable tool to predict the vapor-liquid phase behavior of azeotropic mixtures. |
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