Bulletin of the American Physical Society
2020 Annual Meeting of the Far West Section
Volume 65, Number 17
Friday–Saturday, October 9–10, 2020; Virtual, Pacific Time
Session L02: Soft Matter Physics and BiophysicsLive
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Chair: Patricia Sparks, Harvey Mudd College |
Saturday, October 10, 2020 2:00PM - 2:12PM Live |
L02.00001: Self-Trapping Random Walks with Attractive Interactions Alexander Klotz, Wyatt Hooper Self-avoiding walks on lattices are used to model the statistics of polymer chains. Attractive interactions between adjacent occupied sites can incorporate poor-solvent or low-temperature effects. Here we consider growing self-avoiding walks (GSAWs) on a square lattice, which grow by taking their Nth step into a randomly chosen unoccupied site adjacent to the N-1th step. Chains grow until there are no more unoccupied adjacent lattice sites and the walk becomes trapped, which is known to occur after an average of 71 steps. It has been debates as to whether the GSAW has the same universal behavior as the traditional self-avoiding walk ensemble. Incorporating self-attraction into the GSAW, we find that the mean trapping length has a non-monotonic dependence on the attractive strength, with a global minimum at weak self-attraction and an exponential divergence with strong self-attraction. Examining the statistics of the GSAW ensemble, we find evidence that the theta point is at a different location in the temperature-exponent parameter space compared to the traditional self-avoiding walk ensemble. [Preview Abstract] |
Saturday, October 10, 2020 2:12PM - 2:24PM Live |
L02.00002: Solvent-induced Collapse Transition in 2D Kinetoplast DNA Dave Holling, Alexander Klotz Kinetoplasts are a complex DNA structure consisting of circles that are linked together to form a network which resembles chain-mail armor. There is theoretical interest in the behavior of 2D materials, including thermally-induced crumpling. Kinetoplasts can serve as a model 2D polymer, where their size as determined by optical fluorescence microscopy can vary depending on solvent quality, where water serves as a good solvent and ethanol as a poor solvent. We aimed to observe the 2D version of the coil-globule transition by measuring diffusivity and radius of gyration of kinetoplasts as a function of ethanol concentration. We observed a transition in the kinetoplast's shape near 60-70% ethanol in solution, below which they appear as curved membranes and above which they appear as compact globules. More quantitative measurements of duplicated kinetoplasts will allow precision measurements of the universal size scaling exponent as a function of solvent quality. [Preview Abstract] |
Saturday, October 10, 2020 2:24PM - 2:36PM Live |
L02.00003: Percolation Threshold of Kinetoplast DNA Networks Josh Ragotskie, Nathaniel Morrison, Ryan Blair, Alexander Klotz The structure, topology, and physical behavior of kinetoplasts, two-dimensional chain-mail like structures of linked DNA rings, are of great interest to the parasitology and materials physics communities. We are interested in how their connected topology affects their physical properties. Kinetoplasts have excess DNA linkages forming a loop around their edges, but previous estimates of their topology did not take the outer boundary rings into account. We intend to measure the topology of these structures by measuring their percolation threshold: a critical point at which a sufficient number of links are removed from the structure and it is destroyed. We performed numerical simulations that indicate that the presence of an edge loop leads to two percolation thresholds. We experimentally probed the percolation threshold of Crithidia fasciculata kinetoplasts by staining them with YOYO-1 dye and examining their disintegration under blue light exposure due to photo-induced double-strand breakage. We observed fragments of the outer loops surviving after the breakages in the interior of each kinetoplast had reached percolation. These findings support our simulation predictions and we plan on further quantitative measurements of the percolation threshold using restriction enzymes. [Preview Abstract] |
Saturday, October 10, 2020 2:36PM - 2:48PM Live |
L02.00004: A Novel Calibration of L-Shell X-Ray Fluorescence Bone Lead Concentration Measurements Blaz Serna, Sarah Kroeker, MIHAI GHERASE Lead (Pb) is a well-known toxic element. \textit{In vivo} human bone Pb concentration measurement can assess life-long Pb exposure unlike blood Pb that indicates short-span exposure. Pb L-shell x-ray fluorescence (LXRF) is a practical alternative to the established \textit{in vivo} K-shell XRF method. An essential step is the calibration procedure which relates the Pb peak area measurements to a bone Pb concentration. Bone and soft tissue (ST) phantoms can be used to determine such relationships. ST overlying the human bone can vary significantly in elemental composition, density, and thickness amongst individuals. An accurate calibration procedure without any additional measurements of the ST x-ray attenuation has not been identified. Pb-doped bone phantoms containing strontium (Sr) and overlying ST phantoms of varying thickness made of three materials: polyoxymethylene (POM), resin, and wax, were used to explore relationships between bone Pb concentration and ST attenuation. Data analysis of acquired x-ray spectra found that the measured beta over alpha ratio of Sr K-shell lines reliably assessed the ST x-ray attenuation across the three different materials and varying thickness. [Preview Abstract] |
Saturday, October 10, 2020 2:48PM - 3:00PM |
L02.00005: Calibration of Optically-Stimulated Luminescence Dose Measurements for X-Ray Fluorescence Bone Lead Measurements Sarah Kroeker, Mihai Gherase An experimental phantom-based method was established in our lab for lead (Pb) concentration measurements in the human tibia bone using a microbeam-based L-shell x-ray fluorescence (LXRF). \textit{In vivo} LXRF bone lead measurements, however, require knowledge of the radiation dose delivered by the microbeam to the soft tissue overlying the bone. Optically-stimulated luminescence dosimeters (OSLDs) were selected for such dose measurements due to their reduced size similar to the small irradiated tissue volumes. Available calibrations of commercial OSLDs mostly target clinical applications such as x-ray imaging modalities and radiation therapy and could not be used for LXRF bone Pb measurements due to large differences in the x-ray photon energy. OSLD calibration was performed using an ion chamber calibrated by an x-ray beam with similar quality factor to the microbeam. Calculations and exposure rate measurements were performed at six positions along the microbeam. Calculated values were larger than the measured ones by a factor in the 1.2 to 1.7 range. Differences were explained by calculations not accounting the backscattered x-rays and the varying x-ray beam size. [Preview Abstract] |
Saturday, October 10, 2020 3:00PM - 3:12PM |
L02.00006: Kinesin Motor Number Modulates the Effect of Load on Cargo Run Length John Wilson, Arturo Zaragoza, Jing Xu Kinesin-1 is a major microtubule-based motor that drives long-range transport of cargos in living cells. The distance that kinesin transports its cargos (run length) is strongly hindered by the load the motor experiences. We previously found that load arising from the thermal diffusion of the cargo can significantly shorten run length when the cargo is carried by a single kinesin. It remains uncertain how such quantitative insights into single-molecule effects gleaned \textit{in vitro }can be translated to the \textit{in vivo} scenario; crucially, cargos in cells are often carried by small teams of motors rather than by a single motor. To close this gap, here we employed Monte Carlo-based simulations to quantify cargo transport by small teams of kinesin-1 under physiological loads. Our simulations utilize experimentally determined single-molecule characteristics of kinesin-1, include loads arising from both cargo diffusion and viscous drag, and encompass a wide range of local viscosities reported for living cells. We model the number of kinesins on the cargo using a Poisson distribution, with the mean motor number approximating the physiological range of 1-2 kinesins per cargo. Strikingly, although groups of kinesin-1 are thought to function non-cooperatively, our simulations indicate that modest increases in kinesin motor number substantially enhances the cargo run length under a variety of load conditions. Our results highlight the potential of kinesin motor number as an important control for cargo transport \textit{in vivo}. [Preview Abstract] |
Saturday, October 10, 2020 3:12PM - 3:24PM |
L02.00007: Mathematical Models for Living Forms in Medical Physics Submodel 1: The Information Processing from Teeth to Nerves Christina Pospisil This talk continues the presentation at APS March Meeting 2019 and APS April Meeting 2019. In this part of the project the first submodel is presented; The information processing from teeth to the nerves. Information processing is modeled via p-waves passing through the tooth layers enamel and dentin. Odontoblasts located in the liquid in the tubules of the tooth dentin layer perform finally the transformation into electrical information (an electrical signal) that passes along nerves. The presentation was scheduled for the APS March Meeting 2020 Conference (the APS March Meeting 2020 Conference got canceled because of Covid-19), the presentation was given at the APS April Meeting 2020 Conference. [Preview Abstract] |
Saturday, October 10, 2020 3:24PM - 3:36PM |
L02.00008: Study on Antibiotics in Treating Epidemic Disease Using Physicochemical and Computational Medicines Seojin Lee, Richard Kyung As an alternative to polymers and metal based particles, physicochemical scientists are currently focusing on new classes, such as polyphenols, nanotubes and fullerenes, as aqueous dispersions for antibiotics utilized in the treatments of pandemic diseases. This research studied the ability of nano-scaled particles to reduce Reactive Oxygen Species (ROS) in cells, which stress cell structure (leading to damaged DNA and RNA), decrease membrane activity, alter metabolic activity, and cause detrimental side reactions that generate chemicals like peroxide. In this paper, physicochemical effects of commercially used synthetic drugs were analyzed using computational simulations. Also naturally produced by plants, often used in traditional oriental medicine to treat fever and inflammation, are observed and analyzed using density functional theory. Such compounds can selectively kill affected cells without being toxic to non-affected cells. Both physiological and pharmacological effects are modeled and analyzed. [Preview Abstract] |
Saturday, October 10, 2020 3:36PM - 3:48PM |
L02.00009: Stereochemical and Thermodynamic Analysis of Retinoids and Fullerenes Used in the Treatment of Acne Euna Jang, Richard Kyung Studies on the role oxidative stress plays in the pathogenesis of acne vulgaris have suggested that antioxidants may be useful in the treatment of acne vulgaris. A few nanoparticles such as fullerenes and retinoids, prized for their electron-transport capacities, small size, and antioxidant abilities, have thus been considered to be a potent therapeutic agent. Numerous studies validating nano scaled molecules’ potential to be used in the treatment of acne vulgaris have led scientists to assess the safety of retinoids and fullerene derivatives. In this study, computational biomedical simulation technology has been used in assessing the thermodynamic stability of such molecules. Computer simulations to model the complexes that can virtually attach large quantities of protons and donate electrons to ROS-affected cells. Thermodynamical and stereochemical safety of several types of water-soluble fullerene derivatives that could be used as biological agents in acne treatment were studied. We used a molecular editing program to model, optimize, and compare the resulting molecular optimization energies and other factors of the molecules. [Preview Abstract] |
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