Bulletin of the American Physical Society
67th Annual Meeting of the APS Division of Fluid Dynamics
Volume 59, Number 20
Sunday–Tuesday, November 23–25, 2014; San Francisco, California
Session L5: Biofluids: Cellular and Molecular Biophysics |
Hide Abstracts |
Chair: Manu Prakash, Stanford University Room: 3008 |
Monday, November 24, 2014 3:35PM - 3:48PM |
L5.00001: Coupling a mechanosensitive channel with a vesicle under shear flow On Shun Pak, Yuan Nan Young, Shravan Veerapaneni, Howard Stone Mechanosensitive channels enable cells to respond to their local environment. Continuum mechanical models have been proposed to describe how bilayer deformation induced by the transmembrane protein and the membrane tension influence the free energy of channel gating under static conditions. The dynamics of mechanosensitive channels under flow conditions however remains largely unexplored. Cells under flow display interesting features not observed under static environments. Here we present a model coupling a mechanosensitive channel with the dynamics of a vesicle under shear flow to investigate how the channel gating responds to hydrodynamic stress. The model could be used to investigate the release of signaling molecules, transport of ions or drugs across cell membranes under flow in biological systems, as well as the design and control of channel gating in synthetic cells. [Preview Abstract] |
Monday, November 24, 2014 3:48PM - 4:01PM |
L5.00002: Formation and organization of protein domains in the immunological synapse Andreas Carlson, L. Mahadevan The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse. Here, we propose a minimal mathematical model for the dynamics of the IS that encompass membrane mechanics, hydrodynamics and protein kinetics. Simple scaling laws describe the dynamics of protein clusters as a function of membrane stiffness, rigidity of the adhesive proteins, and fluid flow in the synaptic cleft. Numerical simulations complement the scaling laws by quantifying the nucleation, growth and stabilization of proteins domains on the size of the cell. Direct comparison with experiment suggests that passive dynamics suffices to describe the short-time formation and organization of protein clusters, while the stabilization and long time dynamics of the synapse is likely determined by active cytoskeleton processes triggered by receptor binding. Our study reveals that the fluid flow generated by the interplay between membrane deformation and protein binding kinetics can assist immune cells in regulating protein sorting. [Preview Abstract] |
Monday, November 24, 2014 4:01PM - 4:14PM |
L5.00003: Could Life Originate between Mica Sheets? Helen Hansma Muscovite mica has many advantages as a site for the origins of life. Some of these advantages are: A. Spaces between mica sheets serve as cell-like compartments. B. K$^{+}$ ions bridge Muscovite mica sheets, providing a high K$^{+}$ environment, as found in all living cells. C. Mica's hexagonal 0.5-nm clay crystal lattice is comparable to the length of the amino acids, sugars, and nucleotides that polymerize to form life's major biological macromolecules. D. Mechanical energy from mica sheets, moving in response to water flows and temperature changes, provide an endless energy source for forming chemical bonds, rearranging polymers, and blebbing off protocells in a primitive form of cell division. [1-3] How might fluid dynamics in the planar nanometer- to micron-high spaces between mica sheets affect the processes involved in the origins of life? \\[4pt] [1] Hansma, H G (2009) In \textit{Probing Mechanics at Nanoscale Dimensions.} N. Tamura, A. Minor, C. Murray and L. Friedman.Warrendale, PA, Materials Research Society. \textbf{1185: }II03-15.\\[0pt] [2] Hansma, H G (2010) \textit{Journal of Theoretical Biology }\textbf{266}(1): 175.\\[0pt] [3] Hansma, H G (2013) \textit{J. Biol. Struct. Dynamics }\textbf{31}(8): 888. [Preview Abstract] |
Monday, November 24, 2014 4:14PM - 4:27PM |
L5.00004: A mathematical model of stress generation in microtubule pair interactions Fang Fang, Meredith Betterton, Michael Shelley Microtubules and motor proteins are basic ingredients in many cellular structures and of new biosynthetic ``active'' suspensions. The interaction of microtubules with their surrounding fluid medium depends fundamentally upon the force generation afforded them through cross-linking motile motor proteins. Here we develop a simple mathematical model, based on the statistical mechanics, motor proteins binding and unbinding, to study the generation of active fluid stresses. We study the role and contributions of ``polarity sorting'' and ``tether'' relaxation on the generation of intrinsic, destabilizing stresses. [Preview Abstract] |
Monday, November 24, 2014 4:27PM - 4:40PM |
L5.00005: Mechanoregulation of molecular motors in flagella Hermes Gadelha Molecular motors are nano-biological machines responsible for exerting forces that drive movement in living organisms, from cargo transport to cell division and motility. Interestingly, despite the inherent complexity of many interacting motors, order and structure may arise naturally, as exemplified by the harmonic, self-organized undulatory motion of the flagellum. The real mechanisms behind this collective spontaneous oscillation are still unknown, and it is challenging task to measure experimentally the molecular motor dynamics within the flagellar structure in real time. In this talk we will explore different competing hypotheses that are capable of generating flagellar bending waves that ``resemble'' in-vitro observations, emphasizing the need for further mathematical analysis and model validation. It also highlight that this is a fertile and challenging area of inter-disciplinary research for applied mathematicians and demonstrates the importance of future observational and theoretical studies in understanding the underlying mechanics of these motile cell appendages. [Preview Abstract] |
Monday, November 24, 2014 4:40PM - 4:53PM |
L5.00006: Hydrodynamics of pronuclear migration Ehssan Nazockdast, Daniel Needleman, Michael Shelley Microtubule (MT) filaments play a key role in many processes involved in cell devision including spindle formation, chromosome segregation, and pronuclear positioning. We present a direct numerical technique to simulate MT dynamics in such processes. Our method includes hydrodynamically mediated interactions between MTs and other cytoskeletal objects, using singularity methods for Stokes flow. Long-ranged many-body hydrodynamic interactions are computed using a highly efficient and scalable fast multipole method, enabling the simulation of thousands of MTs. Our simulation method also takes into account the flexibility of MTs using Euler-Bernoulli beam theory as well as their dynamic instability. Using this technique, we simulate pronuclear migration in single-celled Caenorhabditis elegans embryos. Two different positioning mechanisms, based on the interactions of MTs with the motor proteins and the cell cortex, are explored: cytoplasmic pulling and cortical pushing. We find that although the pronuclear complex migrates towards the center of the cell in both models, the generated cytoplasmic flows are fundamentally different. This suggest that cytoplasmic flow visualization during pronuclear migration can be utilized to differentiate between the two mechanisms. [Preview Abstract] |
Monday, November 24, 2014 4:53PM - 5:06PM |
L5.00007: Characterization of Intracellular Streaming and Traction Forces in Migrating Physarum Plasmodia Shun Zhang, Ruedi Meili, Robert Guy, Juan Lasheras, Juan C. del Alamo Physarum plasmodium is a model organism for cell migration that exhibits fast intracellular streaming. Single amoebae were seeded and allowed to move on polyacrilamide gels that contained 0.5-micron fluorescent beads. Joint time-lapse sequences of intracellular streaming and gel deformation were acquired respectively in the bright and fluorescent fields under microscope. These images were analyzed using particle image velocimetry (PIV) algorithms, and the traction stresses applied by the amoebae on the surface were computed by solving the elastostatic equation for the gel using the measured bead displacements as boundary conditions. These measurements provide, for the first time, a joint characterization of intracellular mass transport and the forces applied on the substrate of motile amoeboid cells with high resolution in both time and space, enables a through study about the locomotive mechanism and the relation between intracellular flow and traction stress, shedding light on related biomimetic research. The results reveal a pronounced auto-oscillation character in intracellular flow, contact area, centroid speed and strain energy, all with the same periodicity about 100 seconds. Locomotion modes that were distinct in flow/ traction stress pattern as well as migration speed have been discovered and studied. [Preview Abstract] |
Monday, November 24, 2014 5:06PM - 5:19PM |
L5.00008: Coordination of Flow and Traction in Migration of Amoeboid Physarum polycephalum: Model and Measurement Owen Lewis, Robert Guy, Shun Zhang, Juan Carlos del Alamo In this research, we develop a computational model of crawling Physarum based on the Immersed Boundary Method. Our model incorporates the effects of cell cytoplasm, the internal cytoskeleton and adhesions to the substrate. Cytoplasmic flows and traction stresses predicted by the model are compared to experimentally measured values obtained using simultaneous Traction Force Microscopy (TFM) and Particle Image Velocimetry (PIV). Of particular interest are stresses generated by flow and how transmission of stresses to the substrate is coordinated. We identify methods of adhesion-flow coordination which are consistent with experiments. Certain consisten coordinations are seen to be ``optimal'' with regards to crawling speed, and robust to perturbations in the extracellular environment. [Preview Abstract] |
Monday, November 24, 2014 5:19PM - 5:32PM |
L5.00009: Viral video: Live imaging of virus-host encounters Kwangmin Son, Jeffrey S. Guasto, Andres Cubillos-Ruiz, Sallie W. Chisholm, Matthew B. Sullivan, Roman Stocker Viruses are non-motile infectious agents that rely on Brownian motion to encounter and subsequently adsorb to their hosts. Paradoxically, the viral adsorption rate is often reported to be larger than the theoretical limit imposed by the virus-host encounter rate, highlighting a major gap in the experimental quantification of virus-host interactions. Here we present the first direct quantification of the viral adsorption rate, obtained using live imaging of individual host cells and viruses for thousands of encounter events. The host-virus pair consisted of Prochlorococcus MED4, a 800 nm small non-motile bacterium that dominates photosynthesis in the oceans, and its virus PHM-2, a myovirus that has a 80 nm icosahedral capsid and a 200 nm long rigid tail. We simultaneously imaged hosts and viruses moving by Brownian motion using two-channel epifluorescent microscopy in a microfluidic device. This detailed quantification of viral transport yielded a 20-fold smaller adsorption efficiency than previously reported, indicating the need for a major revision in infection models for marine and likely other ecosystems. [Preview Abstract] |
Monday, November 24, 2014 5:32PM - 5:45PM |
L5.00010: Self-assembly of protein fibrils in stable circular Couette flow Samantha McBride, Christopher Tilger, Amir Hirsa, Juan Lopez Fluid flows are known to contribute to the chemical dynamics of self-assembling protein fibrils yet the roles of mixing and shear have not been elucidated. These long, crystalline structures are ubiquitous \emph{in-vivo} and strongly associated with many neurodegenerative disorders. Understanding the mechanism of formation is a significant challenge because of the variety of gradients proteins are exposed to in biological fluid channels. A stable circular Couette flow device was constructed in order to conduct comprehensive tests on the effects of pure shear on a protein solution initially free of any pre-existing aggregates. The protein insulin was sheared at various Reynolds numbers at normothermia ($37^{\circ}$C). Changes in fluid properties are observed at the onset of fibril precipitation, as the elongated structures generate complex particle-laden fluid dynamics. Measurements include fibrillization lag times, images of protein fibrils induced by shear, and changes to viscosity after exposure to shear. Discussion will cover biological implications and the role of fluid mechanics in pathogenesis of neurodegenerative disorders. [Preview Abstract] |
Monday, November 24, 2014 5:45PM - 5:58PM |
L5.00011: A Fast Multipole Method and a Metropolis Method for Coarse-grained Brownian Dynamics Simulations of a DNA with Hydrodynamic Interactions Szu-Pei Fu, Yuan-Nan Young, Shidong Jiang The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interaction with water molecules. The simulations are often numerically expensive for exploring long-time dynamics over meso-scales due to the amount of water molecules needed for capturing the non-local hydrodynamic interactions (HIs). In this paper a fast multipole method for computing the HIs and a metropolis method for molecular dynamics are validated by comparing against both experiments and simulations of a single DNA molecule in linear flow. In addition, it is shown that the Metropolis integration scheme for self--adjoint diffusions can be used to expedite the time it takes to prepare the initial configuration of the macromolecule for the BD simulations. Further numerical tests show that the fast multipole method scales linearly to the total number $N$ of beads for the long-chain molecule when $N \agt O(10^3)$ while other numerical algorithms scale to $O(N^2)$ (at least). [Preview Abstract] |
Monday, November 24, 2014 5:58PM - 6:11PM |
L5.00012: Modeling and design of light powered biomimicry micropump utilizing transporter proteins Jin Liu, Tsun-kay Jackie Sze, Prashanta Dutta The creation of compact micropumps to provide steady flow has been an on-going challenge in the field of microfluidics. We present a mathematical model for a micropump utilizing Bacteriorhodopsin and sugar transporter proteins. This micropump utilizes transporter proteins as method to drive fluid flow by converting light energy into chemical potential. The fluid flow through a microchannel is simulated using the Nernst-Planck, Navier-Stokes, and continuity equations. Numerical results show that the micropump is capable of generating usable pressure. Designing parameters influencing the performance of the micropump are investigated including membrane fraction, lipid proton permeability, illumination, and channel height. The results show that there is a substantial membrane fraction region at which fluid flow is maximized. The use of lipids with low membrane proton permeability allows illumination to be used as a method to turn the pump on and off. This capability allows the micropump to be activated and shut off remotely without bulky support equipment. This modeling work provides new insights on mechanisms potentially useful for fluidic pumping in self-sustained bio-mimic microfluidic pumps. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700