Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session R66: Pattern Formation and Oscillations in BiologyFocus
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Sponsoring Units: DBIO GSNP GSOFT Chair: David Lubensky, Univ of Michigan - Ann Arbor Room: BCEC 261 |
Thursday, March 7, 2019 8:00AM - 8:36AM |
R66.00001: Mitotic traveling waves in the Drosophila embryo Invited Speaker: Stefano di Talia Early embryogenesis of most metazoans is characterized by rapid and synchronous cleavage divisions. While diffusion is too slow for synchronization of mitosis across large spatial scales, traveling waves represent a possible process of synchronization. I will discuss our recent work dissecting the molecular and physical mechanisms for the generation of traveling waves of activity of Cdk1, the master regulator of the cell cycle. I will show that the in vivo dynamics of Cdk1 are captured by a transiently bistable reaction-diffusion model, where time-dependent reaction terms account for the growing level of cyclins and Cdk1 activation across the cell cycle. I will discuss two distinct regimes. The first one is observed in mutants of the mitotic switch. There, waves are triggered by the classical mechanism of a stable state invading a metastable one. Conversely, waves in wild type reflect a transient phase that preserves the Cdk1 spatial gradients while the overall level of Cdk1 activity is swept upward by the time-dependent reaction terms. This unique mechanism generates a wave-like spreading (sweep-waves) that differs from bistable waves for its dependence on dynamic parameters and its faster speed. I will also discuss how the integration of biochemical and mechanical processes is required for the early establishment of synchronization of the cell cycle. |
Thursday, March 7, 2019 8:36AM - 9:12AM |
R66.00002: Tuning the Xenopus mitotic oscillator in artificial cells Invited Speaker: Qiong Yang We study biological oscillations and self-organization phenomena in both artificially constructed mitotic cells and live zebrafish embryos. We focus on how the network structures of biological clocks are linked to their functions, such as tunability and robustness, and how individuals coordinate through biochemical and mechanical signals to generate collective spatiotemporal patterns. To pin down the physical mechanisms that give rise to these complex phenomena, we integrate modeling, time-lapse fluorescence microscopy, microfluidics, and systems and synthetic biology approaches. |
Thursday, March 7, 2019 9:12AM - 9:24AM |
R66.00003: Identifying How Single Cells Modulate Population-Wide Pattern Formation Allyson Sgro One of the key outstanding challenges in understanding multicellular pattern formation is identifying what single cells tune within themselves to change population-wide patterns. A major driver of multicellular patterns is oscillations in single-cell signaling networks, but it is unknown what features single cells naturally modulate in these oscillations to change global patterns. An ideal system for addressing this challenge exists in the social amoeba, Dictyostelium discoideum. Dictyostelium uses travelling waves of chemoattractant molecules between cells to drive aggregation into a multicellular state when starving. These waves originate within single cells that release this molecule to the environment, and the single-cell signaling network phenomena that drive the creation of these waves are well-characterized. However, it is still unknown what parameters a single cell naturally controls to change the observed population pattern. Using new experimental data in conjunction with an existing phenomenological model, I explore what parameters single cells can modulate to control signaling oscillations and pattern formation. |
Thursday, March 7, 2019 9:24AM - 9:36AM |
R66.00004: Single-Mode Turbulence in Pattern-Forming Protein Systems Jonas Denk, Jacob Halatek, Fridtjof Brauns, Korbinian Pöppel, Erwin Frey Protein pattern formation often relies on proteins that cycle between a cyctosolic bulk and a membrane at which they undergo molecular interactions. On a flat membrane, this cycling can lead to intriguing protein patterns including spiral waves as well as more irregular dynamics such as chemical turbulence. While theoretical approaches have been able to reproduce various experimentally observed protein patterns, the underlying mechanisms for pattern selection remain poorly understood. Motivated by the bacterial Min protein system, we present a spatially reduced reaction-diffusion model to study pattern selection in protein systems with bulk-membrane coupling. Remarkably, we find that already a single-mode instability can lead to turbulent dynamics at the onset of pattern formation. Further away from this onset, we observe a transition from turbulent to coherent patterns, which can be explained on the basis of diffusively coupled local equilibria. Our study yields insights into a novel route to chaos for a widespread class of mass-conserving reaction-diffusion systems with bulk-boundary coupling. |
Thursday, March 7, 2019 9:36AM - 9:48AM |
R66.00005: Directed and Spiral Wave Propagation in Communities with Correlated Heterogeneity Xiaoling Zhai, Joseph Larkin, Gurol Suel, Andrew Mugler Directed signal propagation in cellular communities is an important and ubiquitous phenomenon. However, heterogeneity in these communities may pose a challenge to directed propagation. Additionally, spatial correlations in the heterogeneity may alter the dynamic behavior. In general, the relationship between correlated heterogeneity and wave propagation is poorly understood. Here we use a FitHugh Nagumo-type model to investigate wave propagation in a two-dimensional heterogeneous community. Our model predicts three dynamic regimes in which waves either propagate directly, die out, or spiral indefinitely. In some parameter regimes, correlations in the heterogeneity enhance directionality and suppress spiraling, as expected. In contrast, in other regimes, correlations promote spiraling, a surprising feature that we explain by demonstrating that these spirals form by a second, distinct mechanism. Finally, we characterize the dependence of the spiral period on the degree of heterogeneity and connect our results to percolation theory. Our work reveals that the spatial structure of cell-to-cell heterogeneity can have important consequences for directed signal propagation in cellular communities, and provides predictions that can be tested in experiments. |
Thursday, March 7, 2019 9:48AM - 10:00AM |
R66.00006: Coexistence and coupling of Min protein patterns in heterogenous systems Jacob Halatek, Fridtjof Brauns, Grzegorz Pawlik, Laeschkir Hassan, Cees Dekker, Erwin Frey In the past two decades, the Min protein system has been established as paradigmatic model system for self-organized protein pattern formation. Much of this success is owned to the advances made in the reconstitution of Min protein patterns in vitro, which allowed precise control over experimental conditions and thereby the pattern forming phenomena. However, up until recently a theoretical description for in vitro Min protein patterns has been missing. Lately, we proposed a novel theoretical framework for pattern formation in mass-conserved reaction-diffusion systems [1]. One of the key predictions are transitions between chaotic, standing, and travelling wave patterns induced by variations in the system geometry or protein numbers. Here, we present the first experimental confirmation of these predictions. An extension of the theoretical framework enables us to forecast the entire time evolution of patterns and their dynamic transitions in systems with heterogeneous geometry or kinetic parameters. Strikingly, the theory predicts the coexistence of patterns in large heterogeneous systems, which we confirm experimentally. |
Thursday, March 7, 2019 10:00AM - 10:12AM |
R66.00007: Rectified adaptation - a variance sensor for processing time-varying inputs Kabir Husain, Jackson D O'Brien, Weerapat Pittayakanchit, Parthiv Patel, Savas Tay, Arvind Murugan The role of chemical identity and spatial distribution of biomolecules in pattern formation and cell fate decision making has long been appreciated. However, recent experiments have revealed that the temporal dynamics of molecular concentrations also plays an important role and can affect gene regulation, cell fate decisions and accelerate pattern formation. We identify a general phenomenological behavior - ``rectified adaptation'' - that plays a critical role in processing oscillatory, pulsatile and fluctuating temporal signals in these diverse biological contexts. Like conventional adaptation, rectified adaptation describes a transient response to step changes in an input signal but the response to step ups and step downs is strongly asymmetric. We show how simple implementations of rectified adaptation can sense the variance of an input signal on specific timescales, helping make decisions in immune response and in embryonic patterning. |
Thursday, March 7, 2019 10:12AM - 10:24AM |
R66.00008: Critical dynamics in bursts of δ and θ-rhythms across the sleep-wake cycle Fabrizio Lombardi, Manuel Gomez-Extremera, Pedro Bernaola-Galvan, Thomas E Scammell, Plamen Ch Ivanov Solid evidences indicate that different cortical rhythms characterize distinct phases (sleep stages) of the sleep-wake cycle. Sleep stages are not stable, and sleep periods exhibit numerous transitions among different stages, including short awakenings/arousals. Nature and dynamics of such transitions, as well as origin and functions of arousals, remain elusive. Recently, it has been shown that brief awakenings/arousals do not have a characteristic duration and consistently follow a power-law distributions across different species. Since arousals can be viewed as 'active' states of the brain that interrupt the 'inactive' phase represented by sleep periods, such a scale-free statistics has been interpreted as a fingerprint of criticality in sleep dynamics, suggesting that arousals are an integral part of sleep regulation. In this talk, I will present recent results on the dynamics of relevant cortical rhythms across the sleep-wake cycle that seem to support such a hypothesis. I will show that wake-related θ- and sleep-related δ-bursts exhibit a robust scale invariant temporal organization closely reminiscent of other non-equilibrium phenomena, and discuss their dynamics and coupling in relation to the neuronal circuitry responsible for wake and sleep control in rats. |
Thursday, March 7, 2019 10:24AM - 10:36AM |
R66.00009: Phase space geometry of reaction--diffusion systems Fridtjof Brauns, Jacob Halatek, Erwin Frey Self-organized pattern formation — typically studied in terms of spatially extended dynamical systems — is as ubiquitous in nature as it is difficult to deal with conceptually and mathematically. We build on the phase space geometric methods of Nonlinear Dynamics, using geometric structures like nullclines and fixed points, to develop a comprehensive theory for two-component mass-conserving reaction–diffusion systems — a paradigmatic model class for pattern formation, e.g. intracellular polarization. A dissection of space into (notional) compartments enables us to characterize the spatio-temporal dynamics based on the ODE phase space of local reactions. Diffusive coupling leads to mass redistribution between the compartments which, in turn, changes the local phase space properties. |
Thursday, March 7, 2019 10:36AM - 10:48AM |
R66.00010: Emergence of traveling waves in linear arrays of electromechanical oscillators Yong Dou, Shashank Pandey, Charles Cartier, Olivia Miller, Kyle J. M. Bishop Traveling waves of mechanical actuation provide a versatile strategy for locomotion and transport in both natural and engineered systems across many scales. These rhythmic motor patterns are often orchestrated by systems of coupled oscillators such as beating cilia or firing neurons. Here, we show that similar motions can be realized in linear arrays of electromechanical oscillators that move and interact via electrostatic forces. Conductive spheres oscillate between biased electrodes through cycles of contact charging and electrostatic actuation. The combination of repulsive interactions among the particles and spatial gradients in their natural frequencies lead to phase locked states characterized by gradients in the oscillation phase. The frequency and wavelength of these traveling waves can be specified independently by varying the applied voltage and the electrode separation. We demonstrate how traveling wave synchronization can enable the directed transport of material cargo. Our results suggest that simple energy inputs can power complex patterns of mechanical actuation with potential opportunities for soft robotics and colloidal machines. |
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