Bulletin of the American Physical Society
72nd Annual Meeting of the APS Division of Fluid Dynamics
Volume 64, Number 13
Saturday–Tuesday, November 23–26, 2019; Seattle, Washington
Session L32: Biological Fluid Dynamics: Single Cells and Bacteria III |
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Chair: Gwynn Elfring, University of British Columbia Room: 614 |
Monday, November 25, 2019 1:45PM - 1:58PM |
L32.00001: Effects of Extracellular Transforming Growth Factor-mediated Fibroblast Activation in Tumor Microenvironment Robert Dillon, Adnan Morshed, Prashanta Dutta The transforming growth factor (TGF) is known to prevent differentiation of benign tumor cells to malignancy. Paradoxically, cancer cells exploit the immune regulation and microenvironment modulatory functions of TGF to their advantage. This makes TGF response highly sensitive to tumor progression. In vitro experimental data for several intercellular and cell surface reactions involving the fibroblasts indicate a switch-like behavior based on extracellular TGF conditions. We modeled a single tumor cell with surrounding fibroblasts to create a specific tumor microenvironment. The extracellular transport through advection, reaction and diffusion as well as cell surface reactions are captured through an immersed interface approach. Flow of extracellular nutrients and fluid-structure interactions are modeled with an immersed boundary description. The unknown reaction parameters were estimated using Bayesian inference with experimental data on the PE25 cell line. Variation in spatial distance and arrangement of tumor cells and fibroblasts showed significant change in reaction dynamics and intracellular TGF production. Microfluidic results also highlight the clinical relevance and therapeutic potential of TGF/Smad pathway. [Preview Abstract] |
Monday, November 25, 2019 1:58PM - 2:11PM |
L32.00002: Molecular Simulations of Synaptotagmin-like Protein4-a during the Vesicle Docking and Fusion with Endothelial Cells upon Ca$^{\mathrm{2+}}$ Binding Jin Liu, Quyen Dinh, Prashanta Dutta Synaptotagmin-like protein4-a (Slp4-a) is a calcium sensor protein which plays critical roles in triggering the vesicle docking and fusion with blood-brain barrier endothelial cells during the exocytosis process. Upon binding Ca$^{\mathrm{2+}}$, Slp4-a undergoes a series of global translational/rotational movements and conformational changes, actively interacts with the SNARE complex, penetrates into the membrane bilayer, and triggers the pore opening. The exact molecular mechanism of how Ca$^{\mathrm{2+}}$ binding to Slp4-a leads to vesicle-cell fusion is not fully understood. In this work, we implement a hybrid coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the responses of Slp4-a upon Ca$^{\mathrm{2+}}$ binding. The hybrid coarse-grained molecular simulations enable us to explore large scale protein changes while retaining detailed molecular interactions. Our simulation results show that the binding of calcium ions causes dramatic reorientation and structural reorganization of Slp4-a. These changes induce local re-arrangement of membrane lipids at the Slp4-a-membrane contact areas leading to stronger attractive force between vesicle and endothelial cell membranes, which clearly indicate the initial docking and fusion process. [Preview Abstract] |
Monday, November 25, 2019 2:11PM - 2:24PM |
L32.00003: Investigation of the Key Parameters Impacting the Receptor Dependent Clathrin-mediated Endocytosis through Stochastic Modeling and Simulations Md Muhtasim Billah, Hua Deng, Prashanta Dutta, Jin Liu Receptor dependent clathrin-mediated endocytosis (CME) is one of the most important endocytic pathways taken by bioparticles, such as viruses and drug carriers, to enter the cells. During CME, the ligand-receptor interactions, assembly/disassembly of clathrin-coated pit (CCP) and membrane deformation all act together to drive the internalization of bioparticles. Study of CME through experiments is significantly challenging because of the number of parameters impacting this complex biological process. In this work, we develop a stochastic computational model for the CME based on the Metropolis Monte Carlo simulations. After validation, we implement the model to systematically investigate effects of a wide range of biochemical and geometrical parameters on the overall internalization efficiency of particles. Specifically, results from our simulations demonstrate that the particle size and shape play critical roles during internalization. In addition, the ligand-receptor parameters, such as the receptor flexural rigidity/size and ligand-receptor reaction cutoff/energy, also significantly impact the internalization efficiency. Our model and simulations yield critical insights into CME and may provide guidelines for intra/transcellular drug delivery design. [Preview Abstract] |
Monday, November 25, 2019 2:24PM - 2:37PM |
L32.00004: Filter Flows at Low Reynolds Number Anders Andersen Filter feeders that create flows through fibrous structures to capture prey particles are common among the plankton. Often the filter is external to the organism, and depending on the filter permeability and the overall motion of fluid and filter, the flow may or may not circumvent the filter. To capture small prey particles it may be advantageous to have small spacing between the filter elements, but at the same time, small filter spacing corresponds to low permeability and may result in filter circumvention and low flow rate through the filter. To explore this trade-off, we focus on low Reynolds number flow perpendicular to a thin, circular filter (permeable disk), and we determine an analytical solution for the flow through and around the filter. We compare the solution with the well-known solution for the flow past an impermeable disk, and we determine the dependence of the flow rate through the filter on its permeability and size. Finally, we discuss the possible biological implications of the results for planktonic organisms. [Preview Abstract] |
Monday, November 25, 2019 2:37PM - 2:50PM |
L32.00005: Pinning and hydrodynamic coupling determine the motility pattern of interfacially trapped bacteria Jiayi Deng, Mehdi Molaei, Nicholas Chisholm, Kathleen Stebe Fluid interfaces are unique environments for swimming bacteria, which display complex motility patterns influenced by concomitant capillary forces and hydrodynamic interactions. In 3-d suspension, \textit{P aeruginosa }swims along symmetric straight paths in run and reverse motions by altering the rotation direction of its flagellum to switch between pusher and puller modes. Near solid walls, the straight trajectories become circular paths due to the well understood hydrodynamic interactions. Trajectories of \textit{P. aeruginosa} trapped at an oil-water interface, however, display a diverse set of trajectory types: fast and straight visitors, Brownian diffusive cells, stable curly paths, and pirouettes. Which of these patterns occurs depends on the trapping state of the cell and its orientation with respect to the interface. An analysis of the curly paths reveals that highly asymmetric trajectories occur with higher angular velocity and curvature for pullers and higher linear velocity and lower curvature for pushers. Our hydrodynamic analysis suggests that this motion is regulated by the re-orientation of the bacterial flagellum, which pivots normal to the interface in the puller mode and parallel to the interface in the pusher mode. [Preview Abstract] |
Monday, November 25, 2019 2:50PM - 3:03PM |
L32.00006: The colloidal hydrodynamics of intracellular transport Roseanna Zia, Akshay Maheshwari, Alp Sunol, Emma Gonzalez, Drew Endy Many representations of intra-cellular behavior rely on abstractions that do not account for how macromolecules are organized and move inside the cell. For many questions in biology and medicine these simpler models have been sufficient. However, fundamental gaps in understanding of many cell functions persist; physics may provide a bridge to close such gaps. I will discuss our computational and theoretical models of spherically confined colloidal suspensions, as a simple model cell, where biomolecules and their interactions can be physically represented individually and explicitly. A primary challenge in models of confined colloidal suspensions is the accurate and efficient representation of many-body hydrodynamic interactions, Brownian motion, and the enclosure.~ To this end, we developed the Cellular Stokesian dynamics framework. Utilizing this model, we studied diffusion, cooperative motion, and self-organization with confinement and crowding levels representative of a cell interior. I will discuss the qualitative influence of hydrodynamics, confinement and crowding on transport behavior, as well as the consequences of neglecting such influences. ~Connections to underlying structure are made, and implications for cellular function are discussed. [Preview Abstract] |
Monday, November 25, 2019 3:03PM - 3:16PM |
L32.00007: Fluid forces and flows in muscle's contractile lattice Sage Malingen, Kaitlyn Hood, Anette Hosoi, Thomas Daniel Muscle cells are specialized for large, rapid shape change. Their contraction is powered by the collective action of molecular motors anchored to long protein filaments (thick filaments) that form a densely packed, fluid filled lattice. Molecular motors bind to thin filaments and pull them past the thick filaments. These motors are estimated to produce 5 pN forces. As filaments slide they shear with the surrounding fluid. Additionally, the lattice volume can change during contraction, causing flows that create axial and radial shear forces. With an inter-filament gap distance of only \textasciitilde 30 nm surface-to-surface, viscous drag forces could be non-trivial and have not been measured. Using a finite element model (COMSOL) of the contractile machinery we estimate that viscous drag forces on single filaments are on the order of 10 fN. We estimate that the energy dissipated by viscous drag over all filaments is less that 1{\%} of the energy used by the system. However additional proteins occupying the gaps between filaments, variable inter-filament spacing and viscosity values greater than that of water may influence this result. [Preview Abstract] |
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