Bulletin of the American Physical Society
2020 Annual Meeting of the APS Four Corners Section (Virtual)
Volume 65, Number 16
Friday–Saturday, October 23–24, 2020; Albuquerque, NM (Virtual)
Session J03: Biophysics and Soft Condensed Matter IILive
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Chair: Ann Junghans, LANL |
Saturday, October 24, 2020 8:00AM - 8:12AM Live |
J03.00001: Computational Enzyme Design with Molecular Dynamics Talmage Coates Enzymes catalyze reactions with lower environmental impact and often with greater efficiency than traditional chemical methods. Effective enzyme design is of industrial and academic relevance because many reactions are not catalyzed by known natural enzymes at appreciable rates. Computational enzyme design studies attempt to reduce the difference in Gibbs free energy between the transition state of the rate limiting reaction and the unactivated substrate. This energy difference is often calculated for a single state of the enzyme, even though enzymes exist in a thermodynamic ensemble of states. We use molecular dynamics simulations to account for dynamic effects in ranking designed sequences for the cyclization of ethyl-4,5,6-trihydroxy hept-2-enoate into ethyl 2-(2,3,4-trihydroxycyclopentyl) acetate using a radical S-adenosyl methionine enzyme. [Preview Abstract] |
Saturday, October 24, 2020 8:12AM - 8:24AM Live |
J03.00002: Ion Binding to a Mammalian Sodium/proton Exchanger Membrane Protein from Molecular Dynamics Simulations Chenou Zhang The Na+/H+ exchangers (NHE) are a family of proteins that contribute to the control of the cell functions. However, despite their physiological importance, detailed molecular-level structural information for the NHE has been lacking. Although a number of prokaryotic structures of sodium/proton antiporters are known, it is not clear in how far the insights from these structures are applicable to the medically important mammalian homologs. Here we report molecular dynamics (MD) simulations at both atomic and coarse-grained (CG) level of detail based on the first atomic-resolution structure of a mammalian NHE9. We focus on the transporter-Na+ ion and transporter-lipid interactions. Multiple protonation states of the model were identified through heuristic pKa calculations. The atomic equilibrium MD simulations tested different combinations of those protonation states and identified a conserved aspartic acid residue as the likely ion-biding site. Based on the simulations we developed a detailed microscopic picture of events necessary for sodium. Because previous work suggested the membrane composition is critical for NHE activation and cell-volume regulation, we also investigated the interaction of the transporter with membrane lipids and cholesterol. [Preview Abstract] |
Saturday, October 24, 2020 8:24AM - 8:36AM Live |
J03.00003: Rapid Solidification of Micro-L Blood Drops Into Homogeneous Thin Solid Films: A New Device, InnovaStrip, for Fast, Accurate, Comprehensive Small Volume Blood Diagnostics via Ion Beam Analysis and X-Ray Fluorescence Wesley Peng, Thilina Balasooriya, Nikhil Suresh, Aashi Gurijala, Mohammed Sahal, Amber Chow, Shaurya Khanna, Lauren Puglisi, Srivatsan Swaminathan, Abbie Elison, Eric Culbertson, Robert Culbertson, Nicole Herbots Blood Diagnostics (BD) analyzes 1-10 mL of liquid blood in hrs to days. BD leads to greater than 80{\%} rates of Hospital-Acquired Anemia - a serious illness for cancer patients and premature infants. In this work, a new, Small Volume BD device, InnovaStrip$^{\mathrm{1}}$, rapidly solidifies blood drops into flat, Homogeneous Thin Solid Films (HTSF). Hyper-hydrophilic HemaDrop$^{\mathrm{1}}$ coatings on InnovaStrip$^{\mathrm{1}}$ are optimized via micro-fluidics to yield HTSFs fit for solid state analysis.~HTSFs undergo Ion Beam Analysis and X-ray Photoelectron Spectroscopy in vacuo and X-ray Fluorescence (XRF) in air without significant radiation damage. They yield electrolytes and metals levels in min. with accuracy and reproducibility to $+$/-10{\%}. Hand-held XRF can be used at Point-of-Care.~Built-in HTSFs from calibration solutions on InnovaStrip$^{\mathrm{1}}$ benchmark HTSF and conversion of atomic {\%} into mg/dL, a key unit for BD.~InnovaStrip$^{\mathrm{1}}$ yields comprehensive BD using micro-Ls instead of mLs of blood. [1] Herbots, Suresh, Peng \textit{et al}. Int. US. Pat. Pend (2020). [Preview Abstract] |
Saturday, October 24, 2020 8:36AM - 8:48AM Live |
J03.00004: Kinetic Diagram Analysis: A Python Library for Algebraic Solutions for Steady-State Observables of Kinetic Networks Nikolaus Awtrey, Oliver Beckstein T.L. Hill's development of biochemical cycle kinetics can be used to calculate steady-state observables and construct analytic solutions [Terrell L. Hill. Free Energy Transduction and Biochemical Cycle Kinetics. en. New York: Springer-Verlag, 1989.doi:10.1007/978-1-4612-3558-3.1]. His theory focuses on constructing diagram representations of distinct-state systems with coupled chemical reactions. Hill shows how these diagrams yield rational algebraic expressions for steady-state cycle fluxes and state probabilities. Despite the benefits of his method, these problems are typically solved using ODE solvers or matrix methods due to their simplicity. Kinetic Diagram Analysis (https://github.com/Becksteinlab/kda) is a Python library that takes aim at this issue, bringing Hill's methods forward without the learning curve of his diagrammatic method. KDA leverages the NetworkX library to create diagrams and generate related directional and flux diagrams. It uses the SymPy library to simplify functions, make algebraic and calculus manipulations, and convert the output into Python lambda functions for rapid calculation. This is demonstrated using examples from Hill's book. [Preview Abstract] |
Saturday, October 24, 2020 8:48AM - 9:00AM Live |
J03.00005: Exploring a Reduced Model of Neuronal Activity Joshua Rasband Mathematical models of neuronal activity are critical to understanding the brain. Two such models are the Hodgkin-Huxley (HH) and Fitzhugh-Nagumo (FN) models. The HH model is a mechanistic model. It uses underlying physical relationships to make predictions. In contrast, the FN model is a phenomenological model. It describes mathematically the behavior of the system, but is not derived from physical theory. These two types of models have complementary advantages and disadvantages. The FN model is phenomenological and has few parameters, making it easy to develop intuition about and computationally less expensive. The HH model is mechanistic and has a large number of parameters, making it difficult to develop intuition about or fit to data. We consider the problem of constructing a model that lends itself to human intuition while preserving the physical theory present in the HH model. We use model reduction techniques to remove irrelevant parameters from the HH model, i.e., parameters whose variation are unnecessary to explain a specific behavior. We then ask whether the reduced HH model can accurately mimic behavior exhibited by the FN model. In this way, we preserve the physical nature of the HH model while reducing its complexity to something more like the FN model. [Preview Abstract] |
Saturday, October 24, 2020 9:00AM - 9:12AM Live |
J03.00006: Prospects for Incoherent Diffractive Imaging at a Compact XFEL Andrew Shevchuk, John Spence, Richard Kirian, Kevin Schmidt The first generation of compact X-ray free-electron lasers (XFELs) is currently under construction and will have the capability to produce much shorter X-ray pulses than large XFELs, albeit also with much lower intensity. This presents a challenging question: What techniques are well-suited to imaging biomolecules with shorter yet weaker X-ray pulses? We analyze the viability of a new technique known as incoherent diffractive imaging (IDI) under these conditions. IDI applies the principles of intensity interferometry (famously known in quantum optics via the Hanbury Brown and Twiss effect) to image biomolecules using their coherent X-ray fluorescence and has some advantages over the standard technique of coherent diffractive imaging, including elemental specificity and 3D structural information in a single diffraction pattern. We study IDI through theory and simulations with a model of inner-shell fluorescence generated by semiclassical dipole radiators (i.e., excited high-Z atoms). Our results suggest that IDI will benefit substantially from the sub-femtosecond pulse duration possible at compact XFELs despite a pulse fluence orders of magnitude smaller than that currently achievable at large XFELs. [Preview Abstract] |
Saturday, October 24, 2020 9:12AM - 9:24AM Live |
J03.00007: Instrumentation for Simulation of Simultaneous Reduced Gravity and Ionizing Radiation Space Environment Effects on Biological System. Achal Duhoon, Lori Caldwell, JR Dennison, Elizabeth Vargis A novel and versatile experimental apparatus has been developed to simulate the effects of simultaneous exposure to reduced gravity and ionizing radiation in cellular biological systems. The design, system capabilities, and limitations are discussed. The mini rotary cell culture system (mRCCS) is compatible with the Space Survivability Test (SST) chamber at Utah State University that has a \textasciitilde 100 mCi Sr$^{\mathrm{90}}$ source emitting 0.2 to 2.5 MeV $\beta $ radiation. The mRCCS has 5 cylindrical vessels that are synchronously rotated by a motor-driven chain. The cell clusters are suspended inside the vessels in a viscous neutral-buoyant fluid, reaching terminal velocity as they fall with near zero net forces from gravity, buoyancy, viscous drag, and vessel rotation thereby approximating a reduced gravity environment from \textasciitilde 10 \textmu g to \textasciitilde 20 mg as determined by the vessel rotational speed. The combined mRCCS and SST chamber system can provide average effective dose rates for the cells controlled over a broad range (\textgreater 900X) from \textasciitilde 3.7 mGy/day to 3.4 Gy/day. This apparatus demonstrate that it can reliably simulate ionizing radiation and \textmu g hazards of the space environment. [Preview Abstract] |
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