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Organization of Embryonic Morphogenesis via Mechanical Information. Dev Cell 2019; 49:829-839.e5. [PMID: 31178400 DOI: 10.1016/j.devcel.2019.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 03/20/2019] [Accepted: 05/03/2019] [Indexed: 01/19/2023]
Abstract
Embryonic organizers establish gradients of diffusible signaling molecules to pattern the surrounding cells. Here, we elucidate an additional mechanism of embryonic organizers that is a secondary consequence of morphogen signaling. Using pharmacological and localized transgenic perturbations, 4D imaging of the zebrafish embryo, systematic analysis of cell motion, and computational modeling, we find that the vertebrate tail organizer orchestrates morphogenesis over distances beyond the range of morphogen signaling. The organizer regulates the rate and coherence of cell motion in the elongating embryo using mechanical information that is transmitted via relay between neighboring cells. This mechanism is similar to a pressure front in granular media and other jammed systems, but in the embryo the mechanical information emerges from self-propelled cell movement and not force transfer between cells. The propagation likely relies upon local biochemical signaling that affects cell contractility, cell adhesion, and/or cell polarity but is independent of transcription and translation.
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Joy JP, Pathak SN, Das D, Rajesh R. Shock propagation in locally driven granular systems. Phys Rev E 2017; 96:032908. [PMID: 29347038 DOI: 10.1103/physreve.96.032908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 06/07/2023]
Abstract
We study shock propagation in a system of initially stationary hard spheres that is driven by a continuous injection of particles at the origin. The disturbance created by the injection of energy spreads radially outward through collisions between particles. Using scaling arguments, we determine the exponent characterizing the power-law growth of this disturbance in all dimensions. The scaling functions describing the various physical quantities are determined using large-scale event-driven simulations in two and three dimensions for both elastic and inelastic systems. The results are shown to describe well the data from two different experiments on granular systems that are similarly driven.
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Affiliation(s)
- Jilmy P Joy
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sudhir N Pathak
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, India
| | - R Rajesh
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Barbier M, Villamaina D, Trizac E. Blast Dynamics in a Dissipative Gas. PHYSICAL REVIEW LETTERS 2015; 115:214301. [PMID: 26636851 DOI: 10.1103/physrevlett.115.214301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 06/05/2023]
Abstract
The blast caused by an intense explosion has been extensively studied in conservative fluids, where the Taylor-von Neumann-Sedov hydrodynamic solution is a prototypical example of self-similarity driven by conservation laws. In dissipative media, however, energy conservation is violated, yet a distinctive self-similar solution appears. It hinges on the decoupling of random and coherent motion permitted by a broad class of dissipative mechanisms. This enforces a peculiar layered structure in the shock, for which we derive the full hydrodynamic solution, validated by a microscopic approach based on molecular dynamics simulations. We predict and evidence a succession of temporal regimes, as well as a long-time corrugation instability, also self-similar, which disrupts the blast boundary. These generic results may apply from astrophysical systems to granular gases, and invite further cross-fertilization between microscopic and hydrodynamic approaches of shock waves.
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Affiliation(s)
- M Barbier
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - D Villamaina
- Laboratoire de Physique Théorique de l'ENS (CNRS UMR 8549) and Institut de Physique Théorique Philippe Meyer, 24 rue Lhomond 75005 Paris, France
| | - E Trizac
- Laboratoire de Physique Théorique et Modèles Statistiques (CNRS UMR 8626), Bâtiment 100, Université Paris-Sud, 91405 Orsay cedex, France
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Almazán L, Serero D, Salueña C, Pöschel T. Self-organized shocks in the sedimentation of a granular gas. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062214. [PMID: 26172712 DOI: 10.1103/physreve.91.062214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Indexed: 06/04/2023]
Abstract
A granular gas in gravity heated from below develops a certain stationary density profile. When the heating is switched off, the granular gas collapses. We investigate the process of sedimentation using computational hydrodynamics, based on the Jenkins-Richman theory, and find that the process is significantly more complex than generally acknowledged. In particular, during its evolution, the system passes several stages which reveal distinct spatial regions of inertial (supersonic) and diffusive (subsonic) dynamics. During the supersonic stages, characterized by Mach>1, the system develops supersonic shocks which are followed by a steep front of the hydrodynamic fields of temperature and density, traveling upward.
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Affiliation(s)
- Lidia Almazán
- Institute for Multiscale Simulation, Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany
| | - Dan Serero
- Institute for Multiscale Simulation, Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany
| | - Clara Salueña
- Departament d'Enginyeria Mecànica, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Thorsten Pöschel
- Institute for Multiscale Simulation, Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany
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Pathak SN, Jabeen Z, Das D, Rajesh R. Energy decay in three-dimensional freely cooling granular gas. PHYSICAL REVIEW LETTERS 2014; 112:038001. [PMID: 24484165 DOI: 10.1103/physrevlett.112.038001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Indexed: 06/03/2023]
Abstract
The kinetic energy of a freely cooling granular gas decreases as a power law t(-θ) at large times t. Two theoretical conjectures exist for the exponent θ. One based on ballistic aggregation of compact spherical aggregates predicts θ=2d/(d+2) in d dimensions. The other based on Burgers equation describing anisotropic, extended clusters predicts θ=d/2 when 2≤d≤4. We do extensive simulations in three dimensions to find that while θ is as predicted by ballistic aggregation, the cluster statistics and velocity distribution differ from it. Thus, the freely cooling granular gas fits to neither the ballistic aggregation or a Burgers equation description.
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Affiliation(s)
- Sudhir N Pathak
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai-600113, India
| | - Zahera Jabeen
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology, Bombay, Powai, Mumbai-400076, India
| | - R Rajesh
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai-600113, India
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Potiguar FQ, Ding Y. Lift and drag in intruders moving through hydrostatic granular media at high speeds. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012204. [PMID: 23944451 DOI: 10.1103/physreve.88.012204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 06/02/2023]
Abstract
Recently, experiments showed that forces on intruders dragged horizontally through dense, hydrostatic granular packings mainly depend on the local surface orientation and can be seen as the sum of the forces exerted on small surface elements. In order to understand such forces more deeply, we perform a two-dimensional soft-sphere molecular dynamics simulation, on a similar setup, of an intruder dragged through a 50-50 bi-disperse granular packing, with diameters 0.30 and 0.34 cm. We measure, for both circular and half-circle shapes, the forces parallel (drag) and perpendicular (lift) to the drag direction as functions of the drag speed, with V=10.3-309 cm/s, and intruder depths, with D=3.75-37.5 cm. The drag forces on an intruder monotonically increase with V and D, and are larger for the circle. However, the lift force does not depend monotonically on V and D, and this relationship is affected by the shape of the intruder. The vertical force was negative for the half-circle, but for a small range of V and D, we measure positive lift. We find no sign change for the lift on the circle, which is always positive. The explanation for the nonmonotonic dependence is related to the decrease in contacts on the intruder as V increases. This is qualitatively similar to supersonic flow detachment from an obstacle. The detachment picture is supported by simulation measurements of the velocity field around the intruder and force profiles measured on its surface.
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Affiliation(s)
- Fabricio Q Potiguar
- Universidade Federal do Pará, Departamento de Física, ICEN, Av. Augusto Correa, 1, Guamá 66075-110, Belém, Pará, Brazil.
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Boudet JF, Kellay H. Unstable blast shocks in dilute granular flows. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:052202. [PMID: 23767525 DOI: 10.1103/physreve.87.052202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Indexed: 06/02/2023]
Abstract
Shocks and blasts can be readily obtained in granular flows be they dense or dilute. Here, by examining the propagation of a blast shock in a dilute granular flow, we show that such a front is unstable with respect to transverse variations of the density of grains. This instability has a well-defined wavelength which depends on the density of the medium and has an amplitude which grows as an exponential of the distance traveled. These features can be understood using a simple model for the shock front, including dissipation which is inherent to granular flows. While this instability bears much resemblance to that anticipated in gases, it is distinct and has special features we discuss here.
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Affiliation(s)
- J F Boudet
- U. Bordeaux 1, Laboratoire Ondes et Matière d'Aquitaine (UMR CNRS 5798), 351 cours de la Libération, 33405 Talence, France
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Sano TG, Hayakawa H. Simulation of granular jets: is granular flow really a perfect fluid? PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:041308. [PMID: 23214581 DOI: 10.1103/physreve.86.041308] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/29/2012] [Indexed: 06/01/2023]
Abstract
We perform three-dimensional simulations of the impact of a granular jet for both frictional and frictionless grains. Small shear stress observed in the experiment [X. Cheng et al., Phys. Rev. Lett. 99, 188001 (2007)] is reproduced through our simulation. However, the fluid state after the impact is far from a perfect fluid, and thus the similarity between granular jets and quark gluon plasma is superficial because the observed viscosity is finite and its value is consistent with the prediction of the kinetic theory.
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Affiliation(s)
- Tomohiko G Sano
- Yukawa Institute for Theoretical Physics, Kyoto University Kitashirakawa Oiwakecho, Kyoto 606-8502 Japan
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Pathak SN, Jabeen Z, Ray P, Rajesh R. Shock propagation in granular flow subjected to an external impact. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061301. [PMID: 23005080 DOI: 10.1103/physreve.85.061301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 06/01/2023]
Abstract
We analyze a recent experiment [Boudet, Cassagne, and Kellay, Phys. Rev. Lett. 103, 224501 (2009)] in which the shock created by the impact of a steel ball on a flowing monolayer of glass beads is studied quantitatively. We argue that radial momentum is conserved in the process and hence show that in two dimensions the shock radius increases in time t as a power law t{1/3}. This is confirmed in event driven simulations of an inelastic hard sphere system. The experimental data are compared with the theoretical prediction and are shown to compare well at intermediate times. At long times the experimental data exhibit a crossover to a different scaling behavior. We attribute this to the problem becoming effectively three dimensional due to the accumulation of particles at the shock front and propose a simple hard sphere model that incorporates this effect. Simulations of this model capture the crossover seen in the experimental data.
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Affiliation(s)
- Sudhir N Pathak
- Institute of Mathematical Sciences, Central Institutes of Technology Campus, Taramani, Chennai 600 113, India.
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Shinde M, Das D, Rajesh R. Coarse-grained dynamics of the freely cooling granular gas in one dimension. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031310. [PMID: 22060364 DOI: 10.1103/physreve.84.031310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Indexed: 05/31/2023]
Abstract
We study the dynamics and structure of clusters in the inhomogeneous clustered regime of a freely cooling granular gas of point particles in one dimension. The coefficient of restitution is modeled as r(0)<1 or 1, depending on whether the relative speed is greater or smaller than a velocity scale δ. The effective fragmentation rate of a cluster is shown to rise sharply beyond a δ-dependent time scale. This crossover is coincident with the velocity fluctuations within a cluster becoming order δ. Beyond this crossover time, the cluster-size distribution develops a nontrivial power-law distribution, whose scaling properties are related to those of the velocity fluctuations. We argue that these underlying features are responsible for the recently observed nontrivial coarsening behavior in the one-dimensional freely cooling granular gas.
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Affiliation(s)
- Mahendra Shinde
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China.
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