Bulletin of the American Physical Society
2016 Annual Meeting of the APS Mid-Atlantic Section
Volume 61, Number 16
Saturday–Sunday, October 15–16, 2016; Newark, Delaware
Session D3: Biophysics and Medical Physics II |
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Chair: Cesar Caro, University of Delaware Room: Sharp Laboratory 131 |
Saturday, October 15, 2016 4:00PM - 4:36PM |
D3.00001: You are what you eat: the biological consequences of lipidomic complexity Invited Speaker: Ed Lyman Your cell membranes are made mostly of lipids, the class of biological macromolecule that includes fat, oil, and wax. This "lipidome" is a complex mixture of some 800 different types of lipid, which changes with your diet and with the administration of lipid synthesis drugs like statins. Altering the lipid composition of a membrane changes its biophysical properties, such as thermodynamic phase, fluidity, viscosity, and curvature stress. Changes in biophysical properties may in turn affect cellular functions like signaling, which often relies on the diffusive encounter of membrane-bound receptors. I will give an overview of the state of membrane biophysics, with a particular focus on recent experimental breakthroughs which admit measurements of lipid diffusion with unprecedented spatiotemporal precision. I will then discuss our own efforts to use modeling approaches in collaboration with experimental colleagues to rationalize lipid and protein spatiotemporal organization in model membranes, and our plans to extend these approaches to interpret recent measurements on live cell membranes [Preview Abstract] |
Saturday, October 15, 2016 4:36PM - 4:48PM |
D3.00002: Simulation and Theory of Antibiotic Resistant Bacteria Populations JD Russo, JJ Dong Bacteria developing antibiotic resistance is a ubiquitous threat to medical treatment. Main mechanisms for the emergence of resistance include conjugation and transformation. We focus on the effect of transformation. Plasmids are small, independently replicating genetic materials, often including DNA segments that encode antibiotic resistance. A cell can absorb a plasmid and its associated trait through transformation. However, this comes with a small fitness cost, which manifests as a slower doubling time. We used a combined approach of Kinetic Monte Carlo simulation and mathematical modeling methods to explore the interplay among growth, death, transformation, and plasmid availability. We focused on the effects of differential growth and transformation, finding that whether the susceptible or resistant population dominates is heavily dependent on transformation rate. [Preview Abstract] |
Saturday, October 15, 2016 4:48PM - 5:00PM |
D3.00003: Nanoscale Structure of Lipid Bilayers Revealed by In-Silico and Experimental Small Angle Neutron Scattering Mitchell Dorrell, Fred Heberle, John Katsaras, Edward Lyman Through the combination of simulations and numerical analysis with small angle neutron scattering, we probe the lateral organization of lipid bilayer mixtures. Small Angle Neutron Scattering (SANS) is an excellent complement to optical techniques, as it reveals molecular scale structural details without fluorescent probes. On its own, however, SANS is not sufficient to determine the organization of the membrane. We therefore take a two-pronged approach, comparing molecular dynamics simulations of ternary mixtures to experimental data obtained for the same mixtures. In-silico neutron scattering experiment intensities on simulated membranes are fitted to the experimental data, simultaneously validating the simulation data and providing a molecular scale model of the experimental system. In this way, the transverse variation in scattering length density across the bilayer — which, under fully deuterated solvent, is much more significant than lateral contributions — is used to infer lateral structure. [Preview Abstract] |
Saturday, October 15, 2016 5:00PM - 5:12PM |
D3.00004: Multiscale Model for Optical Response of SWCNT-based bio-sensor materials Wenxin Huang, Slava Rotkin Single-wall Carbon Nanotube (SWCNT) hybrids have raised considerable interest as biological sensors, in cancer detecting and other fields. We developed a multiscale Multiphysics model for the electronic structure and response of Single-wall Carbon Nanotube hybrids in complex solutions via combined quantum mechanics and electrodynamics approach. The model allows to investigate the response of SWCNT-hybrids to different environments. In particular, it has been reported that single-stranded DNA (ssDNA) interacts strongly with SWCNTs and forms a stable ssDNA-SWCNT hybrid that effectively disperses SWCNTs in aqueous solution. Here, the electrostatic potential and charge density of ssDNA-SWCNT hybrids in aqueous solution has been modeled. We discuss various level of model approximations that can be used (along with the full solution). One can describe the local SWCNT response function in terms of quantum capacitance and geometric capacitance. Such an approach can be further advanced by using full Green’s function, solved here by numerical resolvent method. Example patterns of charge density distributions for external point-like and chain-like potentials are presented. [Preview Abstract] |
Saturday, October 15, 2016 5:12PM - 5:24PM |
D3.00005: Numerical investigation of ultrasound attenuation through trabecular bone Philippe Guyenne, Robert Gilbert A composite viscoelastic model for ultrasound propagation through trabecular bone in the time domain is proposed. The trabecular matrix of cancellous bone is described as an isotropic viscoelastic material, while the interstitial fluid is modeled by Stokes flow. Realistic 2D bone samples with complicated microstructure are reconstructed from CT-scanned images of real human calcaneus and from random distributions of fluid-solid particles generated by the turning bands method. Direct numerical simulations of the acoustic propagation equations are performed based on an accurate staggered-grid finite-difference scheme. Motivated by laboratory experiments, ultrasound attenuation through trabecular bone is examined as a function of excitation frequency and bone porosity. Comparison is made with homogenization results on various elastic properties. This model allows us to assess in detail the role of bone microstructure in ultrasound attenuation. In view are medical applications to the recovery of bone parameters for the assessment of bone quality and for the early detection of such diseases as osteoporosis by quantitative ultrasound techniques. [Preview Abstract] |
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