Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session B22: Biofluid Dynamics; Biological Pattern Formation; Biological Oscillators |
Hide Abstracts |
Sponsoring Units: DBIO Chair: Ofer Kimchi, Harvard University Room: 303 |
Monday, March 2, 2020 11:15AM - 11:27AM |
B22.00001: Flow due to chirality in suspensions of magnetotactic bacteria Andrejs Cebers Phenomena due to chirality are observed in suspensions of magnetotactic bacteria. As a particular example that is simple enough for analysis we consider a layer of magnetotactic bacteria suspension with thickness h and width 2d above a solid wall. The torque dipoles of the bacteria are oriented by an oblique magnetic field, leading to torques distributed on the free interface of the layer. As a result a boundary value problem for the 2D Stokes equation is formulated with a jump of the fluid velocity on the free interface and a no-slip condition on the solid wall. It is solved by the known methods of complex analysis where the flow field is defined by two analytical functions. The solution shows fluid motion perpendicular to the plane defined by the normal to the solid wall and the oblique magnetic field. The numerical value of the velocity and its dependence on the angle of the field inclination is in good agreement with the experimental data [1]. |
Monday, March 2, 2020 11:27AM - 11:39AM |
B22.00002: Active depinning of bacterial droplets due to gravity Harshitha Shankar Kotian, Amith Zafal Abdulla, Hithysini K. N., Varsha Singh, Manoj M Varma A bacterial culture on a nutrient rich agar plate exhibits swarming motility. Many species of swarming bacteria collectively extract water from the underlying agar and produce surfactants to enhance the spreading of the bacterial droplet to colonise the entire plate. When the agar plate is placed on an incline, this bacterial droplet de-pins to slide down the surface. This de-pinning has so far been presumed to be due to the reduction in surface tension of the droplet by the surfactants produced by the bacteria. Contrary to this belief, we present experimental evidence that motility of the individual bacteria and the stiffness of the agar dominates the de-pinning dynamics to an extent that de-pinning can happen even in mutant strains incapable of producing surfactants. We also present a fluid dynamical model to describe this active de-pinning mechanism of droplets containing surfactant producing bacteria such as Pseudomonas aeruginosa and Bacillus subtilis. |
Monday, March 2, 2020 11:39AM - 11:51AM |
B22.00003: Optimal Geometry of Perfusion in Flow Networks Tatyana Gavrilchenko, Eleni Katifori In organ capillaries, oxygen detaches from red blood cells and diffuses through a porous membrane into the nearby tissue, eventually getting absorbed by tissue cells. Motivated by this system, we study networks where flow is laden with nutrients able to diffuse out of the vessels and into the surrounding faces. In a uniform network with a single flow source and sink, the nutrients become depleted far from the source, forming a gradient of nutrient density that may leave some tissue undersupplied. Nonetheless, organs have developed capillary bed networks that avoid tissue starvation. In anticipation of engineering networks for artificial organs, we explore theoretical network designs for uniform perfusion over an extended area. Here, we first propose an algorithm with rules to induce local topological changes in a flow network, which serves to generate a wide range of network topologies. We then use vertex model dynamics to tune the vertex positions in a way that equalizes nutrient distribution. Ultimately, we hope to use this uniformly perfusing network ensemble to identify topological features that serve to dissipate an undesirable nutrient gradient. |
Monday, March 2, 2020 11:51AM - 12:03PM |
B22.00004: Confined Diffusion of a Colloidal Particle Between Two Parallel Walls: Quantifying Diffusing Diffusivity Gary W. Slater, Maxime Ignacio, Le Qiao "Anomalous yet Brownian" diffusion has been observed in numerous physical and biological systems over the last few years, both experimentally and in simulations. The concept of Diffusing Diffusivity, which we proposed to explain such phenomena, has also been studied extensively. As shown by the Bechhoefer group (PRE 96, 042604, 2017), the simplest experimental system is possibly that of a particle confined to a slit since its diffusion coefficient does depend on the distance to a wall. We revisit this problem using Lattice Boltzmann simulations of a particle between two walls in the absence of external forces, a simpler situation since no external force is present. Instead of using the Kurtosis as a measure of the non-ideality of the diffusion motion, we introduce a new empirical fitting function with a tunable exponent and a critical time scale. We test our results with an alternative Monte Carlo simulation and discuss the implications. |
Monday, March 2, 2020 12:03PM - 12:15PM |
B22.00005: Fluid flow dynamics in networks of compliant vessels Sean Fancher, Eleni Katifori Flow networks appear in a wide variety of natural and artificial contexts, and as such, a significant number of works have aimed to study their properties. However, most of these previous efforts have focused on continuous and dynamically invariant flow through networks of rigid vessels. Here, we develop a theoretical model of pulsatile flow using compliant vessels that interact with the flow and are capable of storing material and elastic energy. Pressure pulses can propagate, dissipate and scatter in such a fluidic network, and the system can support complex and rich dynamics. We solve for the flow and pressure profiles at any point within the network as a function of the properties of the input and output pressure or current waveforms, and we study the sensitivity of the dynamic flow profile to alterations or complete removal of single vessels. We use this to calculate not only the necessary power needed to maintain such a flow profile but also the power required to alter the profile, and show how a network can be optimized with respect to both. Finally, we explore possible applications of this work to biological systems such as the human vasculature network. |
Monday, March 2, 2020 12:15PM - 12:27PM |
B22.00006: Optimization of solute dissemination in complex flow networks Georgios Gounaris, Miguel Ruiz Garcia, Eleni Katifori Flow networks efficiently transport nutrients in many physical systems, such as plant and animal vasculature. In the case of the animal circulatory system, the oxygen and nutrient distribution are crucial for the survival of tissue. Homogeneity of the nutrient distribution provides a fitness advantage as waste is minimized while all tissue gets enough nutrients to survive. Can biological flow networks self-organize and remodel to optimally perfuse the tissue? We propose a local adaptation rule for the vessel radii that is able to equalize perfusion, while minimizing energy dissipation to circulate the flow and a cost constraint. These different objective functions compete to produce complex network morphologies including hierarchy and asymmetry between the network input and output. |
Monday, March 2, 2020 12:27PM - 12:39PM |
B22.00007: Probing in-mouth texture perception with a biomimetic tongue Alexis Prevost, Jean-Baptiste Thomazo, Javier Contreras Pastenes, Christopher J Pipe, Benjamin Le Révérend, Elie Wandersman An experimental biomimetic tongue–palate system has been developed to probe human in-mouth texture perception. Model tongues are made from soft elastomers patterned with fibrillar structures analogous to human filiform papillae. The palate is represented by a rigid flat plate parallel to the plane of the tongue. To probe the behavior under physiological flow conditions, deflections of model papillae are measured using a novel fluorescent imaging technique enabling sub-micrometer resolution of the displacements. Using optically transparent Newtonian liquids under steady shear flow, we show that deformations of the papillae allow their viscosity to be determined from 1 Pa s down to the viscosity of water (1 mPa.s), in full quantitative agreement with an elastohydrodynamics model. |
Monday, March 2, 2020 12:39PM - 12:51PM |
B22.00008: Towards a synthetic post-translational protein oscillator Ofer Kimchi, Carl Goodrich, Agnese Curatolo, Alexis Courbet, Nick Woodall, Dmitri Zorine, David Baker, Michael Phillip Brenner Synthetic protein circuits have the potential to significantly change the landscape of biomimicry engineering. While synthetic gene circuits have already borne fruit over the past several decades, post-translational circuits engineered to bypass transcription/translation machinery can offer more immediate responses and more direct coupling to endogenous systems. However, engineering dynamic phenomena such as oscillations in these circuits remains an outstanding challenge. Only a few known biological systems, such as the KaiABC system regulating the circadian clock in cyanobacteria, offer examples of post-translational oscillators, creating a need for theoretical work to fill in the gaps. Here, we develop two distinct post-translational oscillators, each using a small number of components which interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes which respectively interfere with and enhance this self-assembly. We will describe the systems, the intuition behind them, and their dependence on the (few) kinetic parameters. |
Monday, March 2, 2020 12:51PM - 1:03PM |
B22.00009: Protein recruitment through indirect mechanochemical interactions Andriy Goychuk, Atul Mohite, Erwin A Frey Some proteins have the ability to recruit other proteins from the cytosol to phospholipid membranes. This binding cooperativity plays a major role for the formation of protein patterns, which provide spatiotemporal control over many cellular processes. For example, Min oscillations guide the positioning of division axis in E. coli, and members of the Rho family of GTPases control contractility and migration of eukaryotic cells. However, the physical basis for this recruitment is still unclear. We suggest a generic feedback mechanism that explains how cooperativity can directly arise from mechanochemical coupling between the membrane and proteins. Such a mechanochemical coupling leads to membrane deformation, which in turn affects the affinity of proteins for the membrane, leading to a positive feedback in the protein binding rates. Our theory predicts that the mechanical properties of the membrane strongly affect protein recruitment, and therefore also protein pattern formation. |
Monday, March 2, 2020 1:03PM - 1:15PM |
B22.00010: Modelling the Ear with Electronic Oscillators: The Wien Bridge Oscillator as a Physical Analogue for the Hair Cell Courtney Fleming, Randall Tagg, Masoud Asadi-Zeydabadi The hair cell is the sensory organ of the human ear. In the vestibule, hair cells allow us to detect linear accelerations and rotations of the head. In the cochlea, patterns of hair cell activation along the dynamic basilar membrane allow us to encode information about complex sounds such as speech and music. A particularly important feature of hair cells is their intrinsic nonlinearity which gives rise to both a quiescent and oscillatory regime. This nonlinearity has been approached in the literature by treating the hair cell as a Hopf-type oscillator, wherein cochlear hair cells are poised just below the bifurcation point. In our research, we sought to construct and model a simple physical system that exhibited this same Hopf-type nonlinearity. We chose as our model system the Wien bridge electronic oscillator, an affordable and relatively simple circuit which mimics many of the essential features of the hair cell. We will introduce our theoretical model for nonlinearity and resonance within the Wien bridge oscillator based on experimental results, and discuss parallels between the dynamics of the Wien bridge oscillator and the dynamics of the hair cell. |
Monday, March 2, 2020 1:15PM - 1:27PM |
B22.00011: Bulk-surface coupling reconciles Min-protein pattern formation in vitro and in vivo Fridtjof Brauns, Grzegorz Pawlik, Jacob Halatek, Jacob Kerssemakers, Erwin A Frey, Cees Dekker The Min system of E. coli exhibits a rich variety of protein patterns whose phenomenology differs qualitatively and quantitatively between in vitro and in vivo settings. Here, we combine experiments and theory to show that this variety of patterns originates from distinct pattern-forming mechanisms (oscillation modes) that operate at different ratios of cytosolic volume to membrane surface area. Experiments in vitro, using laterally wide microchambers show qualitatively distinct patterns at different bulk heights, from standing waves, and sustained large-scale oscillations, to traveling waves. Our theoretical analysis shows that in vitro patterns at low bulk height are driven by the same lateral oscillation mechanism as in vivo pole-to-pole oscillations. Two distinct vertical oscillation modes – anti-phase oscillations between the opposite membrane surfaces and membrane-to-bulk oscillations – set in at larger bulk heights, marking the transition from the in vivo to the in vitro regime. We predict and experimentally confirm vertical pattern-synchronization (in-phase and anti-phase) between the microchambers' top and bottom surface and multistability of patterns in the transition regime. |
Monday, March 2, 2020 1:27PM - 1:39PM |
B22.00012: Low dimensional structures in cardiac alternans Hector Velasco Perez, Flavio H Fenton Our understanding of cardiac dynamics is frequently limited by our lack of knowledge of the ionic interactions at the microscopic level and how they drive the macroscopic phenomena. This has generated a series of complex models that are computationally demanding, inflexible and not generalizable. Nevertheless, there are characteristics or patterns that consistently show up in all of them, such as traveling waves and spiral waves. These patterns turn out to be low dimensional structures in an optimal basis, and optimal frame of reference. Here, we will focus on the study of traveling waves with alternans, that is, the change in the action potential wave length and/or amplitude in time. It is known that alternans are one of the main contributors to the initiation of fibrillation, which can be lethal if not attended. I will illustrate the derivation and properties of two types of reduced order models of cardiac tissue exhibiting various levels of alternans. These model reductions are based on proper orthogonal decomposition and sparse regression methods. We will compare the properties of both models and discuss the applications to other systems. |
Monday, March 2, 2020 1:39PM - 1:51PM |
B22.00013: Acoustic Coupling between Active Oscillators Allows for their Synchronization and Explains Identical-Frequency Sounds Emitted from the Two Ears Daibhid O Maoileidigh, Yuttana Roongthumskul, AJ Hudspeth Our ears emit sounds spontaneously, known as spontaneous otoacoustic emissions (SOAEs). It is unclear, however, why some animals emit sounds with identical frequencies from their two ears. In most nonmammalian tetrapods, acoustic coupling between the eardrums through the head cavity might influence SOAE production. |
Monday, March 2, 2020 1:51PM - 2:03PM |
B22.00014: Patterns make patterns: how hierarchical self-organization couples cell shape to biochemical dynamics Tzer Han Tan, Manon Wigbers, Fridtjof Brauns, Zachary Swartz, Erwin A Frey, Nikta Fakhri Many biological processes rely on the precise positioning of proteins on the membrane to perform complex tasks. Such protein patterns are susceptible to cell shape changes, raising the question of how these patterns can be robust in a mechanically dynamic environment. Here, we elucidate a mechanism that pattern protein localization on the membrane robustly despite cell shape deformations. By combining experiments in starfish oocytes with mathematical modelling, we find that cell shape information encoded in a cytosolic gradient can be decoded by a bistable front of a RhoA regulator. In turn, this bistable front precisely positions RhoA by locally triggering excitable dynamics. We posit that this hierarchical coupling between a biochemical gradient and protein self-organization provides mechanochemical feedback for cell shape sensing and control. |
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