Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session U28: Focus Session: Biological Hydrodynamics II |
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Sponsoring Units: DBP DFp Chair: Steve Quake, Stanford University Room: Baltimore Convention Center 325 |
Thursday, March 16, 2006 8:00AM - 8:36AM |
U28.00001: Fluidic control over cell proliferation and chemotaxis Invited Speaker: Microscopic flows are almost always stable and laminar that allows precise control of chemical environment in micro-channels. We describe design and operation of several microfluidic devices, in which various types of environments are created for different experimental assays with live cells. In a microfluidic chemostat, colonies of non-adherent bacterial and yeast cells are trapped in micro-chambers with walls permeable for chemicals. Fast chemical exchange between the chambers and nearby flow-through channels creates essentially chemostatic medium conditions in the chambers and leads to exponential growth of the colonies up to very high cell densities. Another microfluidic device allows creation of linear concentration profiles of a pheromone ($\alpha$-factor) across channels with non-adherent yeast cells, without exposure of the cells to flow or other mechanical perturbation. The concentration profile remains stable for hours enabling studies of chemotropic response of the cells to the pheromone gradient. A third type of the microfluidic devices is used to study chemotaxis of human neutrophils exposed to gradients of a chemoattractant (fMLP). The devices generate concentration profiles of various shapes, with adjustable steepness and mean concentration. The ``gradient'' of the chemoattractant can be imposed and reversed within less than a second, allowing repeated quantitative experiments. [Preview Abstract] |
Thursday, March 16, 2006 8:36AM - 8:48AM |
U28.00002: The Conformation of Clathrin Triskelia in Solution Matthew L. Ferguson, Kondury Prasad, Dan L. Sackett, Hacene Boukari, Eileen M. Lafer, Ralph Nossal A principal component in the protein coat of certain post-golgi and endocytic vesicles is clathrin, a three-legged heteropolymer (known as a triskelion) that assembles into polyhedral cages principally made up of pentagonal and hexagonal faces. In vitro, this assembly depends on the pH, with cages forming more readily at low pH and less readily at high pH. We have developed procedures, based on static and dynamic light scattering, to determine the radius of gyration, R$_{g}$, and hydrodynamic radius, R$_{H,}$ of isolated triskelia, under conditions where cage assembly occurs. Calculations based on rigid molecular bead models of a clathrin triskelion show that the measured values can be accounted for by bending of the legs and a puckering at the vertex. We also show that the values of R$_{g}$ and R$_{H}$ measured for clathrin triskelia in solution are qualitatively consistent with the conformation of clathrin in a ``D$_{6}$ barrel'' cage assembly measured by cryoEM tomography. [Preview Abstract] |
Thursday, March 16, 2006 8:48AM - 9:00AM |
U28.00003: A macromolecular model for the endothelial surface layer James Harden, Darina Danova-Okpetu, Gary Grest The endothelial surface layer (ESL) is a micron-scale macromolecular lining of the luminal side of blood vessels composed of proteoglycans, glycoproteins, polysaccharides and associated plasma proteins all in dynamic equilibrium. It has numerous physiological roles including the regulation of blood flow and microvascular permeability, and active participation in mechanotransduction and stress regulation, coagulation, cell adhesion, and inflammatory response. The dynamic structure and the mechanical properties of the ESL are crucial for many of its physiological properties. We present a topological model for the ESL composed of three basic macromolecular elements: branched proteoglycans, linear polysaccharide chains, and small plasma proteins. The model was studied using non-equilibrium molecular dynamics simulations and compared with scaling theories for associating tethered polymers. We discuss the observed dynamical and mechanical properties of the ESL captured by this model, and the possible physical insight it provides into the physiological behavior of the ESL. [Preview Abstract] |
Thursday, March 16, 2006 9:00AM - 9:12AM |
U28.00004: Simulation of metachronal wave in a model of pulmonary cilia Sorin Mitran A simulation of the formation of metachronal waves in carpets of pulmonary cilia is presented. The cilia move in a two-layer fluid model. The fluid layer adjacent to the cilia base is purely viscous while the tips of the cilia move through a viscoelastic fluid. An overlapping fixed-moving grid formulation is employed to capture the effect of the cilia on the surrounding fluid. The 9+2 internal microtubule structure of an individual cilium is modeled using large-deflection, curved, finite-element beams. Realistic models of the forces exerted by dynein molecules are extracted from measurements of observed cilia shapes. The possibility of formation of metachronal waves under different assumptions of boundary conditions is investigated and shown to be dependent on the surrounding geometry. [Preview Abstract] |
Thursday, March 16, 2006 9:12AM - 9:48AM |
U28.00005: On the Evolution of Voltage Gated Ion Channels Invited Speaker: This talk summarizes some ideas, calculations and data analysis/collection surrounding the structure and evolution of ion channels, in particular voltage gated sodium channels. The great advantage of ion channels is that they are individual proteins whose function has long been known and is readily inferred through voltage measurements. Their evolution can be tracked through the growing data base of sequences. Kinetic data is readily available, showing important differences between nearly identical channels. I will discuss our efforts to collate available functional data on voltage gated sodium channels into an 'ion channel property space' . We then use this dataset to infer underlying kinetic models, and to create evolutionary trees based on the function of the channels. Finally, I will discuss our endeavors to how ion channels evolved to be the way they are: Examples of questions we would like to answer include: to what extent do design principles dictate the details of the kinetic schemes of ion channels, such as (a) the symmetry of the sodium and potassium channels (or lack thereof), as reflected in their kinetic schemes ; (b) the coupling of sodium channel kinetics to potassium channel kinetics; or (c) activation/inactivation of the channels themselves. [Preview Abstract] |
Thursday, March 16, 2006 9:48AM - 10:00AM |
U28.00006: Optimization of Anguilliform Swimming Stefan Kern, Petros Koumoutsakos Anguilliform swimming is investigated by 3D computer simulations coupling the dynamics of an undulating eel-like body with the surrounding viscous fluid flow. The body is self-propelled and, in contrast to previous computational studies of swimming, the motion pattern is not prescribed a priori but obtained by an evolutionary optimization procedure. Two different objective functions are used to characterize swimming efficiency and maximum swimming velocity with limited input power. The found optimal motion patterns represent two distinct swimming modes corresponding to migration, and burst swimming, respectively. The results support the hypothesis from observations of real animals that eels can modify their motion pattern generating wakes that reflect their propulsive mode. Unsteady drag and thrust production of the swimming body are thoroughly analyzed by recording the instantaneous fluid forces acting on partitions of the body surface. [Preview Abstract] |
Thursday, March 16, 2006 10:00AM - 10:12AM |
U28.00007: Flow measurement in an in-vitro model of a single human alveolus Sudhaker Chhabra, Ajay Prasad The alveolus is the smallest and most important unit in the acinar region of the human lung. It is responsible for gas exchange between the lungs and the blood. A complete knowledge of the airflow pattern in the acinar region is necessary to predict the transport and deposition of inhaled aerosol particles. Such knowledge will benefit the pharmaceutical community in its effort to deliver therapeutic aerosols for lung-specific as well as system-wide ailments. In addition, it can also help to assess the health effects of the toxic aerosols in the environment. We have constructed an in-vitro model of a single spherical alveolus on a circular tube. The alveolus is capable of expanding and contracting in phase with the oscillatory flow through the tube. Realistic breathing conditions are reproduced by matching Reynolds and Womersley numbers. Experimental methods such as particle imaging velocimetry and laser induced fluorescence are used to study the resulting flow patterns. In particular, recirculating flow within the alveolus, and the fluid exchange between the alveolar duct and the alveolus are important for better understanding the flow in the acinar region. [Preview Abstract] |
Thursday, March 16, 2006 10:12AM - 10:24AM |
U28.00008: Transport and collective dynamics in suspensions of swimming particles Michael Graham, Juan Hernandez Direct simulations of large populations of hydrodynamically interacting swimming particles at low Reynolds number are performed. Hydrodynamic coupling between the swimmers leads to large-scale coherent vortex motions in the flow that are consistent with experimental observations. At low concentrations, swimmers propelled from behind (like spermatazoa) strongly migrate toward solid surfaces in agreement with simple theoretical considerations; at higher concentrations this localization is disrupted by the large-scale coherent motions. Correspondingly, at large concentrations the swimmers move with velocities several times larger than they could achieve in isolation. [Preview Abstract] |
Thursday, March 16, 2006 10:24AM - 10:36AM |
U28.00009: Computational Modeling of Microfluidic Rapid-Mixing Device Used in Infrared Micro-Spectroscopy Mark Dickins, Jarmila Guijarro, Aihua Xie Microfluidic rapid-mixing device is employed to chemically trigger biological functions of proteins for time-resolved Fourier transform Infrared (FTIR) micro-spectroscopic study. There are two criteria for the optimal design of such devices: (i) minimizing the mixing time (thus better time-resolution) and (ii) minimizing the consumption of protein samples. Computational modeling has been performed on the Poiseuille and diffusional flow patterns. Due to the low-Reynolds number of microfluidic flow in study, finite-difference methods for the Navier-Stokes and advection-diffusion equations are employed in our computational modeling. The viscosity of the fluids is related to the pressure gradient required to achieve maximum velocity according to Pouisulle flow. Several mixing channels are modeled in order to determine the optimal dimensions for our microchip according to the design criteria. We will report our computational modeling results and their relevance to the optimal design of rapid-mixing devices used in time-resolved infrared micro-spectroscopy. [Preview Abstract] |
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