Bulletin of the American Physical Society
Fall 2019 Meeting of the Ohio-Region Section and the Michigan Section of the American Association of Physics Teachers
Volume 64, Number 15
Friday–Saturday, October 11–12, 2019; Flint, Michigan
Session B03: Biophysics, Chemical Physics and Medical Physics |
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Chair: Ronald Kumon, Kettering University Room: Kettering University Academic Building 4507 |
Saturday, October 12, 2019 8:00AM - 8:12AM |
B03.00001: DNA folding in a crowded environment Mark Taylor, Wolfgang Paul At the molecular level, biological systems operate in very crowded solution environments. It has long been recognized that this crowding can affect the conformational stability and phase transitions of the biopolymers comprising such systems. Similar issues must be addressed in developing biotechnology applications based of dense arrays of surface-tethered polymers. In our recent work we directly measure the entropy reduction resulting from crowding/confinement using Wang-Landau computer simulation techniques [1]. Here we will discuss the folding transition of a specific single-stranded DNA oligomer that has been studied extensively by the Plaxco group [2]. We develop a coarse-grained model for this ssDNA and use it to examine the entropic effects associated with both surface tethering and surface crowding. For the tethered ssDNA oligomer crowded by other tethered oligomers, we find, in agreement with experiment, that both stabilization and destabilization are possible depending on the conformational state of the crowders. [1] Taylor, Macromolecules 50, 6967 (2017); J. Chem. Phys. 147, 166101 (2017); [2] Watkins et al, JACS 134, 2120 (2012); JACS 136, 8923 (2014). [Preview Abstract] |
Saturday, October 12, 2019 8:12AM - 8:24AM |
B03.00002: Configurational contribution to the Soret effect of a protein ligand system Jutta Luettmer-Strathmann Many of the biological functions of proteins are closely associated with their ability to bind ligands and change conformations in response to changing conditions. Since binding state and conformation of a protein affect its response to a temperature gradient, they may be probed with thermophoresis. In recent years, thermophoretic techniques to investigate biomolecular interactions, quantify ligand binding, and probe conformational changes have become established. To develop a better understanding of the mechanisms underlying the thermophoretic behavior of proteins and ligands, we employ a simple, off-lattice model for a protein and ligand in explicit solvent. To investigate the partitioning of the particles in a temperature gradient, we perform Wang-Landau type simulations in a divided simulation box and construct the density of states over a two-dimensional state space. This method gives us access to the entropy and energy of the divided system and allows us to estimate the configurational contribution to the Soret coefficient. For dilute solutions of hydrophobic proteins, we find that a hard-sphere solvent model captures important aspects of protein-ligand interactions and allows us to relate the binding energy to the change in Soret coefficient upon ligand binding. [Preview Abstract] |
Saturday, October 12, 2019 8:24AM - 8:36AM |
B03.00003: Discotic Liquid Crystals without Tails Mitchell Powers, John Portman, Scott Bunge, Robert Twieg, Brett Ellman Discotic liquid crystals are typically rigid disc shaped molecules, surrounded by long flexible tails, which self assemble into long columns. The tails form a buffer between columns, and serve as an entropy reservoir which helps to maintain the liquid crystal mesophase. However, these tails are difficult to include in both \textit{ab-initio}and molecular dynamics modeling. Frequently the tails are omitted in calculations and simulations as a convenient approximation, but only rarely are they omitted in nature. In this talk we will discuss a novel group of tailless discotic liquid crystals and their properties, both experimentally and \textit{in silico. }Experimental measurements of these molecules, both mesogenic and non-mesogenic, are used to motivate a molecular dynamics study of these unusual materials. [Preview Abstract] |
Saturday, October 12, 2019 8:36AM - 8:48AM |
B03.00004: Chemical Diode Behavior in the Belousov-Zhabotinsky Reaction due to Inhomogeneous Diffusion Chase Fuller Excitable Reaction-Diffusion systems profuse nature, including in critical functions in the human body. It is of interest, then, to study laboratory examples to inform investigations of other systems. In this study, we numerically integrated the Tyson-Fife model of the Belousov-Zhabotinsky reaction using a finite difference method. We constructed simulations of two dimensional channels bounded by Carl Neumann no-flux boundary conditions and introduced soft obstacles in the form of activator and inhibitor diffusion coefficient inhomogeneities. We describe the mechanism by which excitation waves die due to fast inhibitor diffusion and show that, under particular configurations of soft obstacles, excitation waves exhibit unidirectional propagation behavior. [Preview Abstract] |
Saturday, October 12, 2019 8:48AM - 9:00AM |
B03.00005: Visualizing dynamical systems with fire fronts Niklas Manz, Flavio Fenton Simple nonlinear table-top experiments are great media to explore spatiotemporal properties of dynamical systems. We are using a one-dimensional oil-candle system and two-dimensional matchstick arrays to experimentally investigate the behavior of excitable reaction-diffusion systems. In these setups, propagating fire fronts can display complex spatial dynamics by varying the oil viscosity and wick material of the candle system or the match type, arrangement, and slope of the matchstick array system. [Preview Abstract] |
Saturday, October 12, 2019 9:00AM - 9:12AM |
B03.00006: Holographic Visualization for Performance of Percutaneous Ablation of Solid Liver Tumors: Translating from Bench to First-in-Human Evaluation Crew Weunski, Aydan Hanlon, B.S., Sara Al-Nimer, M.S., Amelia Chapman, B.S., Karl West, M.S., Jeffery Yanof, Ph.D, Charles Martin III, M.D. Percutaneous thermal ablation (PTA) of solid tumors is the leading, minimally-invasive treatment used in Interventional Oncology, especially in the liver. However, surgeons currently use 2D screens with image guidance for an inherently 3D task, which can lead to inaccurate ablation probe placement, tumor recurrence, and procedural complications. The objective of this study was to develop and evaluate true 3D-holographic guidance for PTA (3D-HPA) from bench to first-in-human clinical evaluation for liver tumors, leading to increased ablation accuracy and usability. 3D-HPA functions by projecting holograms of the patient’s anatomy and GPS-tracked probes directly onto the operative site with HoloLens (an untethered, head-mounted AR display) to overcome limitations of 2D screens. Probe placement accuracy and HoloLens’s ease of use were assessed on the bench. Next, feasibility was assessed in a clinical study while maintaining standard of care. HoloLens image captures were reviewed from the first-in-human evaluation. Preliminary results show significant potential to improve PTA accuracy. [Preview Abstract] |
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