Bulletin of the American Physical Society
Four Corners Section 2022 Meeting
Volume 67, Number 14
Friday–Saturday, October 14–15, 2022; Albuquerque, New Mexico
Session B05: Biophysics and Soft Condensed Matter I |
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Chair: Tonmoy Chakraborty, UNM Room: UNM PAIS 2540 |
Friday, October 14, 2022 10:00AM - 10:12AM |
B05.00001: Monte Carlo Simulation for Raman Spectroscopy System Analysis Eliza Ballantyne, Jordyn Hales, Haidy Rivera, Priscilla Lagunas, Jessica Jones, Dustin Shipp Raman hyperspectral imaging is limited by its time-consuming nature. Accelerating acquisition time without sacrificing image integrity often includes collecting fewer spectra and accounting for missing data with interpolation. The unique parameters of each experiment make it challenging to generalize the measurements required to accurately represent a sample. A tool predicting the limits of resolution in hyperspectral imaging would save time and make Raman results more accessible to those without expertise in hyperspectral imaging techniques. |
Friday, October 14, 2022 10:12AM - 10:24AM |
B05.00002: Microtubule rigidity and associated stability phenomena Tanner Hoole, Michael Vershinin Microtubules (MTs) are polymers of alpha-beta tubulin dimers and are the most rigid part of the cytoskeleton in eukaryotic cells. Extreme cold and heat are known to cause MT depolymerization. Several published reports showed that MTs stabilized with slow- or non-hydrolizable GTP analogs or aldehyde-type cross-linking declined with increasing temperature in a small range of temperatures (20-35°C). Taxol-stabilized microtubule rigidity was reportedly temperature independent. Our lab expanded on this by (1) expanding the temperature range from 0°C to as high as 50°C and (2) by testing single MTs polymerized using three different nucleotides: GTP with Taxol, GMPPCP with Taxol, and GMPCPP. Both GMPPCP and GMPCPP are non-hydrolizable analogs of GTP, and GMPCPP is an established promoter of MT nucleation and growth which enables MT stabilization without taxol. We observed systematic differences between persistence lengths in these three backgrounds but only statistically insignificant variation with temperature for each background. Specifically, we find that MT persistence length is log-normally distributed which not only obscures temperature variability of rigidity in our assays but also likely makes any such variability insignificant for cell function. |
Friday, October 14, 2022 10:24AM - 10:36AM |
B05.00003: Quantifying Protein-Protein Interactions using Confined Photoconversion and Single-Particle Tracking Sajjad A Khan, David Schodt, Diane S. Lidke, Keith Lidke Single particle tracking (SPT) has become a powerful tool to investigate the dynamics of single molecules in live cells. Typical SPT measurement require sparsely labeled molecules in order to identify and localize the individual molecules. This low density limits the rate at which diffusion-limited reactions can be observed. We are developing a novel technique that increases the rate of observable interactions by two orders of magnitude. We call this method SPT-REversible Saturable OpticaL Fluorescence Transitions (SPT-RESOLFT) because it uses a concept from the RESOLFT super-resolution method. The concept relies on saturated labeling and selectively imaging proteins of interest within roughly 100 nm spot. Fluorophores are activated using diffraction-limited Gaussian beam and deactivated outside of 100 nm by a Laguerre-Gauss donut beam. We experimentally demonstrate the concept using EGFR-mEos4b, which form dimers with ~ 1 s lifetimes, and with the gamma subunit of FceR1, gamma-mEos4b, which forms stable dimers. |
Friday, October 14, 2022 10:36AM - 10:48AM |
B05.00004: Bacterial navigation of narrow channels Nuris Figueroa Morales, Aramis Rivera, Ernesto Altshuler, Rodrigo B Soto, Anke Lindner, Eric Clement Advancements in medicine and environmental remediation require investigation into bacterial transport and accumulation in confined geometries with the presence of flow. By looking at the dynamics of Escherichia coli bacteria in narrow microfluidic channels, we identify a phenomenon of upstream “super-contamination” of bacteria that depends on the flow. Bacteria navigate upstream over macroscopic distances at an average speed of 1millimiter per minute. We believe the evolution of the concentration results from the downstream and upstream distances covered by bacteria as they swim along the solid boundaries of the microchannel. To prove our hypothesis, we develop unique experiments for long-distance scanning of the channel over macroscopic distances of a few millimeters. Our experimental findings can be rationalized through stochastic simulations incorporating the long tail of individual bacterial run time, as appose to the classically assumed Poisson distribution of average 1second runs. Our research provides insight into macroscopic transport processes in biological or soil networks and demonstrates that the run-and-tumble statistics determine macroscopic bacterial transport properties. |
Friday, October 14, 2022 10:48AM - 11:00AM |
B05.00005: Ultrafast Probe of Cell and Organelle Physiology by Intracavity Micro/Nano Laser Spectroscopy Paul L Gourley Healthy cells and organelles rely on a complex of trans-membrane processes to regulate internal molecular composition and function for normal cellular respiration. A key to cell health is the maintenance of a stable osmotic equilibrium. In the diseased cell state, this equilibrium is altered by changes in the membrane potential and alteration of the internal biomolecular composition. These changes in equilibrium in individual cells can be rapidly probed by novel intracavity micro/nanolaser spectroscopy and microscopy techniques that exploit intrinsic optical polarizability of biomolecules. This talk reports studies of the transformation of intra-cellular and isolated mitochondria from the normal to disease state in normal and transformed (to cancer) mouse liver cells. Intracavity laser spectroscopy reveals dramatic changes in the cell and organelle osmotic equilibrium. Mitochondrial correlation microscopy details a transition from aerobic to anerobic respiration. Changes in molecular composition are confirmed by UV absorption and luminescence excitation spectroscopy. The results confirm the unique ability of intracavity micro/nano spectroscopy to rapidly assess changes arising from altered biomolecular states of cells and organelles. |
Friday, October 14, 2022 11:00AM - 11:12AM |
B05.00006: Exciton Hamiltonian of Polymer Chlorosome Nanocomposites Alexander W Hardin, Jaime A Diaz, Gregory Uyeda, Gabriel Montaño, Inès Montaño Light harvesting in photosynthesis is a highly efficient process that can be adapted to a wide range of light conditions. Artificial photosynthesis has the potential to eclipse the efficiency of current solar technology by several times. Computational models have been used for years to predict the behavior of natural systems, but the complicated protein environment has made them difficult to analyse. Advances have been made in making synthetic versions of light harvesting organelles, known as polymer chlorosome nanocomposites. These simplified systems allow for easy comparison to computational models. The challenge at hand is to generate and understand them. Known chemical structures were input into Ab Initio computational chemistry software to gather data in the form of excited state energies and transition densities. We will present how we used this data to predict the time evolution of corresponding systems. |
Friday, October 14, 2022 11:12AM - 11:24AM |
B05.00007: Writhe, Twist and Radius of Gyration Analysis on Course-Grained Supercoiled DNA Models Jack Hawk DNA replication, translation, and storage are essential to the functions of life. DNA storage and packing impact gene expression in both prokaryotic and eukaryotic cells. Chromosomal DNA is an exotic and poorly understood phase of soft matter. From experiment, we know that the density of DNA packing reached, requires the help of proteins referred to as nucleoid-associated proteins (NAPS). We simulated simple circular bacterial chromosomes with varying amounts of NAPS. Using a course-grained DNA model, we have performed molecular dynamics methods using the LAMMPS software. We have analyzed our simulations to determine the writhe, twist, and radius of gyration of DNA for varying NAPs concentrations. These techniques allow us to see details which no microscope or experimental method can uncover. This is a first step towards our ultimate goal of producing a physically, chemically, and biology accurate simulation of the entire DNA condensing and division process of a prokaryotic cell. |
Friday, October 14, 2022 11:24AM - 11:36AM |
B05.00008: A Line-Scanning Hyperspectral Raman Microscope based on Bessel Beam Illumination Ellyse Taylor, Keith Lidke, Sheng Liu Current techniques for live imaging of metabolic processes in plants are often destructive or lack spatially explicit information. Raman spectroscopy is a nondestructive, label-free imaging technique which, in combination with Bessel beam light sheet microscopy, offers a way to rapidly measure the abundance and flux of molecules as they travel through the three dimensions of living plants. We will describe the development of a Hyperspectral Raman Light Sheet Microscope as an alternative to traditional confocal point-scanning imaging systems. The presentation will cover methods for creating a self-reconstructing Bessel beam to excite scattering in the sample, as well as modifications made to the conventional slit-spectrometer setup for capturing low intensity Raman scattered infrared light. We demonstrate the system with various test samples including Fluorinated Ethylene Propylene and Acetaminophen, and then discus future applications in biological materials. |
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