44 results on '"Aranson, Igor"'
Search Results
2. Patterns and collective behavior in granular media: Theoretical concepts
- Author
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Aranson, Igor S. and Tsimring, Lev S.
- Subjects
Granular materials -- Research ,Petrogenesis -- Research ,Physics - Abstract
A number of situations in which nontrivial patterns emerge in granular systems are surveyed and a theoretical description of granular systems is provided. General principles and models of pattern formation in complex systems that have been successfully applied to granular systems and statistical mechanics of dense granular systems are discussed.
- Published
- 2006
3. Nonlinear Field Equations for Aligning Self-Propelled Rods.
- Author
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Peshkov, Anton, Aranson, Igor S., Bertin, Eric, Chaté, Hugues, and Ginelli, Francesco
- Subjects
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NONLINEAR equations , *NEMATIC liquid crystals , *MICROSCOPY , *LINEAR dynamical systems , *NONLINEAR dynamical systems - Abstract
We derive a set of minimal and well-behaved nonlinear field equations describing the collective properties of self-propelled rods from a simple microscopic starting point, the Vicsek model with nematic alignment. Analysis of their linear and nonlinear dynamics shows good agreement with the original microscopic model. In particular, we derive an explicit expression for density-segregated, banded solutions, allowing us to develop a more complete analytic picture of the problem at the nonlinear level. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
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4. Physical Properties of Collective Motion in Suspensions of Bacteria.
- Author
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Sokolov, Andrey and Aranson, Igor S.
- Subjects
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SUSPENSIONS (Chemistry) , *PROPERTIES of matter , *MOTION , *BACTERIAL diseases , *HYDRODYNAMICS - Abstract
A suspension of microswimmers, the simplest realization of active matter, exhibits novel material properties: the emergence of collective motion, reduction in viscosity, increase in diffusivity, and extraction of useful energy. Bacterial dynamics in dilute suspensions suggest that hydrodynamic interactions and collisions between the swimmers lead to collective motion at higher concentrations. On the example of aerobic bacteria Bacillus subtilis, we report on spatial and temporal correlation functions measurements of collective state for various swimming speeds and concentrations. The experiments produced a puzzling result: while the energy injection rate is proportional to the swimming speed and concentration, the correlation length remains practically constant upon small speeds where random tumbling of bacteria dominates. It highlights two fundamental mechanisms: hydrodynamic interactions and collisions; for both of these mechanisms, the change of the swimming speed or concentration alters an overall time scale. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
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5. Hydrodynamics of a vibrated granular monolayer.
- Author
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Khain, Evgeniy and Aranson, Igor S.
- Subjects
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HYDRODYNAMICS , *GRANULAR materials , *COMPRESSIBILITY , *PHASE separation method (Engineering) , *NAVIER-Stokes equations - Abstract
We investigate the long-standing puzzle of phase separation in a granular monolayer vibrated from below. Although this system is three dimensional, an interesting dynamics occurs mostly in the horizontal plane, perpendicular to the direction of vibration. Experiments [Olafsen and Urbach, Phys. Rev. Lett. 81, 4369 (1998)] demonstrated that for a high amplitude of vibration the system is in the gaslike phase, but when the amplitude becomes smaller than a certain threshold, a phase separation occurs: A solidlike dense condensate of particles forms in the center of the system, surrounded by particles in the gaslike phase. We explain theoretically the experimentally observed coexistence of dilute and dense phases, employing Navier-Stokes granular hydrodynamics. We show that the phase separation is associated with a negative compressibility of granular gas. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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6. Self-organized superconducting textures in thin films.
- Author
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Glatz, Andreas, Aranson, Igor S., Baturina, Tatyana I., Chtchelkatchev, Nikolay M., and Vinokur, Valerii M.
- Subjects
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ELECTRIC conductivity , *SUPERFLUIDITY , *SOLID state electronics , *PARTICLES (Nuclear physics) , *COUPLING constants , *PHYSICAL metallurgy , *THIN films - Abstract
The interplay between the superconducting order parameter and elastic fields, which are intimately connected to the very existence of the superconductivity itself, can result in a novel superconducting state: a regular self-organized texture of superconducting islands. We study the formation of these islands in a system of a thin superconducting film coupled elastically to a more rigid substrate and derive the phase diagram below the superconducting critical temperature depending on the elastic coupling constant of both subsystems. The fact that this pattern is a result of the Ginzburg-Landau description of superconductivity indicates that the formation of regular structures may be a common feature of the superconductor transition in the presence of long-range coupling. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
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7. Cold Active Motion: How Time-Independent Disorder Affects the Motion of Self-Propelled Agents.
- Author
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Peruani, Fernando and Aranson, Igor S.
- Subjects
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PARTICLES (Nuclear physics) , *COLLECTIVE behavior , *QUENCHED disorder (Quantum mechanics) - Abstract
Assemblages of self-propelled particles, often termed active matter, exhibit collective behavior due to competition between neighbor alignment and noise-induced decoherence. However, very little is known of how the quenched (i.e., time-independent) disorder impacts active motion. Here we report on the effects of quenched disorder on the dynamics of self-propelled point particles. We identified three major types of quenched disorder relevant in the context of active matter: random torque, force, and stress. We demonstrate that even in the absence of external fluctuations ("cold active matter"), quenched disorder results in nontrivial dynamic phases not present in their "hot" counterpart. In particular, by analyzing when the equations of motion exhibit a Hamiltonian structure and when attractors may be present, we identify in which scenarios particle trapping, i.e., the asymptotic convergence of particle trajectories to bounded areas in space ("traps"), can and cannot occur. Our study provides new fundamental insights into active systems realized by self-propelled particles on natural and synthetic disordered substrates. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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8. Large-Scale Chaos and Fluctuations in Active Nematics.
- Author
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Ngo, Sandrine, Peshkov, Anton, Aranson, Igor S., Bertin, Eric, Ginelli, Francesco, and Chate, Hugues
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FLUCTUATIONS (Physics) , *NEMATIC liquid crystals , *QUANTUM chaos , *HYDRODYNAMICS , *SPATIOTEMPORAL processes - Abstract
We show that dry active nematics, e.g., collections of shaken elongated granular particles, exhibit large-scale spatiotemporal chaos made of interacting dense, ordered, bandlike structures in a parameter region including the linear onset of nematic order. These results are obtained from the study of both the well-known (deterministic) hydrodynamic equations describing these systems and of the self-propelled particle model they were derived from. We prove, in particular, that the chaos stems from the generic instability of the band solution of the hydrodynamic equations. Revisiting the status of the strong fluctuations and long-range correlations in the particle model, we show that the giant number fluctuations observed in the chaotic phase are a trivial consequence of density segregation. However anomalous, curvature-driven number fluctuations are present in the homogeneous quasiordered nematic phase and characterized by a nontrivial scaling exponent. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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9. Understanding Dense Active Nematics from Microscopic Models.
- Author
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Patelli, Aurelio, Djafer-Cherif, Ilyas, Aranson, Igor S., Bertin, Eric, and Chaté, Hugues
- Subjects
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TOPOLOGICAL dynamics , *PHASE diagrams - Abstract
We study dry, dense active nematics at both particle and continuous levels. Specifically, extending the Boltzmann-Ginzburg-Landau approach, we derive well-behaved hydrodynamic equations from a Vicsek-style model with nematic alignment and pairwise repulsion. An extensive study of the phase diagram shows qualitative agreement between the two levels of description. We find in particular that the dynamics of topological defects strongly depends on parameters and can lead to "arch" solutions forming a globally polar, smecticlike arrangement of Néel walls. We show how these configurations are at the origin of the defect ordered states reported previously. This work offers a detailed understanding of the theoretical description of dense active nematics directly rooted in their microscopic dynamics. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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10. Minimal model of directed cell motility on patterned subs trates.
- Author
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Mizuhara, Matthew S., Berlyand, Leonid, and Aranson, Igor S.
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CELL motility , *NERON models , *POLYMERIZATION - Abstract
Crawling cell motility is vital to many biological processes such as wound healing and the immune response. Using a minimal model we investigate the effects of patterned substrate adhesiveness and biophysical cell parameters on the direction of cell motion. We show that cells with low adhesion site formation rates may move perpendicular to adhesive stripes while those with high adhesion site formation rates results in motility only parallel to the substrate stripes. We explore the effects of varying the substrate pattern geometry and the strength of actin polymerization on the directionality of the crawling cell. These results reveal that high strength of actin polymerization results in motion perpendicular to substrate stripes only when the substrate is relatively nonadhesive; in particular, this suggests potential applications in motile cell sorting and guiding on engineered substrates. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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11. Phase slips in superconducting weak links.
- Author
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Kimmel, Gregory, Glatz, Andreas, and Aranson, Igor S.
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SUPERCONDUCTIVITY , *DYNAMICS , *SPHEROMAKS - Abstract
Superconducting vortices and phase slips are primary mechanisms of dissipation in superconducting, superfluid, and cold-atom systems. While the dynamics of vortices is fairly well described, phase slips occurring in quasi-one-dimensional superconducting wires still elude understanding. The main reason is that phase slips are strongly nonlinear time-dependent phenomena that cannot be cast in terms of small perturbations of the superconducting state. Here we study phase slips occurring in superconducting weak links. Thanks to partial suppression of superconductivity in weak links, we employ a weakly nonlinear approximation for dynamic phase slips. This approximation is not valid for homogeneous superconducting wires and slabs. Using the numerical solution of the time-dependent Ginzburg-Landau equation and bifurcation analysis of stationary solutions, we show that the onset of phase slips occurs via an infinite period bifurcation, which is manifested in a specific voltage-current dependence. Our analytical results are in good agreement with simulations. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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12. Collective Motion of Self-Propelled Particles with Memory.
- Author
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Nagai, Ken H., Yutaka Sumino, Montagne, Raul, Aranson, Igor S., and Chaté, Hugues
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MEMORY , *ANGULAR distribution (Nuclear physics) , *SELF-propelled artillery , *MOTION detectors , *DOUBLE consciousness (Sociology) , *GENETICS - Abstract
We show that memory, in the form of underdamped angular dynamics, is a crucial ingredient for the collective properties of self-propelled particles. Using Vicsek-style models with an Omstein-Uhlenbeck process acting on angular velocity, we uncover a rich variety of collective phases not observed in usual overdamped systems, including vortex lattices and active foams. In a model with strictly nematic interactions the smectic arrangement of Vicsek waves giving rise to global polar order is observed. We also provide a calculation of the effective interaction between vortices in the case where a telegraphic noise process is at play, explaining thus the emergence and structure of the vortex lattices observed here and in motility assay experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
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13. Individual behavior and pairwise interactions between microswimmers in anisotropic liquid.
- Author
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Sokolov, Andrey, Shuang Zhou, Lavrentovich, Oleg D., and Aranson, Igor S.
- Subjects
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LYOTROPIC liquid crystals , *PAIRED comparisons (Mathematics) , *ANISOTROPY , *MEASUREMENT of viscosity , *FLUID dynamic measurements , *PHASE velocity - Abstract
A motile bacterium swims by generating flow in its surrounding liquid. Anisotropy of the suspending liquid significantly modifies the swimming dynamics and corresponding flow signatures of an individual bacterium and impacts collective behavior. We study the interactions between swimming bacteria in an anisotropic environment exemplified by lyotropic chromonic liquid crystal. Our analysis reveals a significant localization of the bacteriainduced flow along a line coaxial with the bacterial body, which is due to strong viscosity anisotropy of the liquid crystal. Despite the fact that the average viscosity of the liquid crystal is two to three orders of magnitude higher than the viscosity of pure water, the speed of bacteria in the liquid crystal is of the same order of magnitude as in water. We show that bacteria can transport a cargo (a fluorescent particle) along a predetermined trajectory defined by the direction of molecular orientation of the liquid crystal. We demonstrate that while the hydrodynamic interaction between flagella of two close-by bacteria is negligible, the observed convergence of the swimming speeds as well as flagella waves' phase velocities may occur due to viscoelastic interaction between the bacterial bodies. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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14. Phase Imprinting in Equilibrating Fermi Gases: The Transience of Vortex Rings and Other Defects.
- Author
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Scherpelz, Peter, Padavić, Karmela, Rançon, Adam, Glatz, Andreas, Aranson, Igor S., and Levin, K.
- Subjects
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ELECTRON gas , *COMPUTER simulation , *ULTRACOLD molecules , *FERMIONS , *SOLITONS - Abstract
We present numerical simulations of phase imprinting experiments in ultracold trapped Fermi gases, which were obtained independently and are in good agreement with recent experimental results. Our focus is on the sequence and evolution of defects using the fermionic time-dependent Ginzburg-Landau equation, which contains dissipation necessary for equilibration. In contrast to other simulations, we introduce small, experimentally unavoidable symmetry breaking, particularly that associated with thermal fluctuations and with the phase-imprinting tilt angle, and we illustrate their dramatic effects. As appears consistent with experiment, the former causes vortex rings in confined geometries to move to the trap surface and rapidly decay into more stable vortex lines. The latter aligns the precessing and relatively long-lived vortex filaments, rendering them difficult to distinguish from solitons. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
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15. Transport Powered by Bacterial Turbulence.
- Author
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Kaiser, Andreas, Peshkov, Anton, Sokolov, Andrey, ten Hagen, Borge, Löwen, Hartmut, and Aranson, Igor S.
- Subjects
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BACTERIAL physiology , *TURBULENCE , *MESOSCOPIC physics , *SIMULATION methods & models , *FLUCTUATIONS (Physics) - Abstract
We demonstrate that collective turbulentlike motion in a bacterial bath can power and steer the directed transport of mesoscopic carriers through the suspension. In our experiments and simulations, a micro- wedgelike "bulldozer" draws energy from a bacterial bath of varied density. We obtain that an optimal transport speed is achieved in the turbulent state of the bacterial suspension. This apparent rectification of random motion of bacteria is caused by polar ordered bacteria inside the cusp region of the carrier, which is shielded from the outside turbulent fluctuations. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
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16. Generic equilibration dynamics of planar defects in trapped atomic superfluids.
- Author
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Scherpelz, Peter, Padavić, Karmela, Murray, Andy, Glatz, Andreas, Aranson, Igor S., and Levin, K.
- Subjects
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ULTRACOLD molecules , *ATOM trapping , *SUPERFLUIDITY , *RELAXATION (Nuclear physics) , *CRYSTAL defects , *BOSE-Einstein condensation - Abstract
We investigate equilibration processes shortly after sudden perturbations are applied to ultracold trapped superfluids. We show the similarity of phase imprinting and localized density depletion perturbations, both of which initially are found to produce "phase walls." These planar defects are associated with a sharp gradient in the phase. Importantly they relax following a quite general sequence. Our studies, based on simulations of the complex time-dependent Ginzburg-Landau equation, address the challenge posed by these experiments: how a superfluid eventually eliminates a spatially extended planai' defect. The processes involved are necessarily more complex than equilibration involving simpler line vortices. An essential mechanism for relaxation involves repeated formation and loss of vortex rings near the trap edge. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
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17. Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise.
- Author
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Ryan, Shawn D., Haines, Brian M., Berlyand, Leonid, Ziebert, Falko, and Aranson, Igor S.
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VISCOSITY , *HYDRODYNAMICS , *STOCHASTIC analysis , *SIMULATION methods & models , *BACILLUS subtilis - Abstract
The viscosity of a suspension of swimming bacteria is investigated analytically and numerically. We propose a simple model that allows for efficient computation for a large number of bacteria. Our calculations show that long-range hydrodynamic interactions, intrinsic to self-locomoting objects in a viscous fluid, result in a dramatic reduction of the effective viscosity. In agreement with experiments on suspensions of Bacillus subtilis, we show that the viscosity reduction is related to the onset of large-scale collective motion due to interactions between the swimmers. The simulations reveal that the viscosity reduction occurs only for relatively low concentrations of swimmers: Further increases of the concentration yield an increase of the viscosity. We derive an explicit asymptotic formula for the effective viscosity in terms of known physical parameters and show that hydrodynamic interactions are manifested as self-induced noise in the absence of any explicit stochasticity in the system. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
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18. Direct Lattice Shaking of Bose Condensates: Finite Momentum Superfluids.
- Author
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Anderson, Brandon M., Clark, Logan W., Crawford, Jennifer, Glatz, Andreas, Aranson, Igor S., Scherpelz, Peter, Lei Feng, Cheng Chin, and Levin, K.
- Subjects
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BOSE-Einstein condensation , *SUPERFLUIDITY , *FLOQUET theory - Abstract
We address band engineering in the presence of periodic driving by numerically shaking a lattice containing a bosonic condensate. By not restricting to simplified band structure models we are able to address arbitrary values of the shaking frequency, amplitude, and interaction strengths g. For "near-resonant" shaking frequencies with moderate g, a quantum phase transition to a finite momentum superfluid is obtained with Kibble-Zurek scaling and quantitative agreement with experiment. We use this successful calibration as a platform to support a more general investigation of the interplay between (one particle) Floquet theory and the effects associated with arbitrary g. Band crossings lead to superfluid destabilization, but where this occurs depends on g in a complicated fashion. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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19. Reversals and collisions optimize protein exchange in bacterial swarms.
- Author
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Amiri, Aboutaleb, Harvey, Cameron, Buchmann, Amy, Christley, Scott, Shrout, Joshua D., Aranson, Igor S., and Alber, Mark
- Subjects
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BACTERIA , *QUORUM sensing - Abstract
Swarming groups of bacteria coordinate their behavior by self-organizing as a population to move over surfaces in search of nutrients and optimal niches for colonization. Many open questions remain about the cues used by swarming bacteria to achieve this self-organization. While chemical cue signaling known as quorum sensing is well-described, swarming bacteria often act and coordinate on time scales that could not be achieved via these extracellular quorum sensing cues. Here, cell-cell contact-dependent protein exchange is explored as a mechanism of intercellular signaling for the bacterium Myxococcus xanthus. A detailed biologically calibrated computational model is used to study how M. xanthus optimizes the connection rate between cells and maximizes the spread of an extracellular protein within the population. The maximum rate of protein spreading is observed for cells that reverse direction optimally for swarming. Cells that reverse too slowly or too fast fail to spread extracellular protein efficiently. In particular, a specific range of cell reversal frequencies was observed to maximize the cell-cell connection rate and minimize the time of protein spreading. Furthermore, our findings suggest that predesigned motion reversal can be employed to enhance the collective behavior of biological synthetic active systems. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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20. Confinement and Collective Escape of Active Particles.
- Author
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Aranson IS and Pikovsky A
- Abstract
Active matter broadly covers the dynamics of self-propelled particles. While the onset of collective behavior in homogenous active systems is relatively well understood, the effect of inhomogeneities such as obstacles and traps lacks overall clarity. Here, we study how interacting, self-propelled particles become trapped and released from a trap. We have found that captured particles aggregate into an orbiting condensate with a crystalline structure. As more particles are added, the trapped condensates escape as a whole. Our results shed light on the effects of confinement and quenched disorder in active matter.
- Published
- 2022
- Full Text
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21. Reduction of viscosity in suspension of swimming bacteria.
- Author
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Sokolov A and Aranson IS
- Subjects
- Computer Simulation, Models, Biological, Rheology, Viscosity, Bacillus subtilis physiology, Movement physiology
- Abstract
Measurements of the shear viscosity in suspensions of swimming Bacillus subtilis in free-standing liquid films have revealed that the viscosity can decrease by up to a factor of 7 compared to the viscosity of the same liquid without bacteria or with nonmotile bacteria. The reduction in viscosity is observed in two complementary experiments: one studying the decay of a large vortex induced by a moving probe and another measuring the viscous torque on a rotating magnetic particle immersed in the film. The viscosity depends on the concentration and swimming speed of the bacteria.
- Published
- 2009
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22. Three-dimensional model for the effective viscosity of bacterial suspensions.
- Author
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Haines BM, Sokolov A, Aranson IS, Berlyand L, and Karpeev DA
- Subjects
- Rheology, Suspensions, Viscosity, Bacteria chemistry, Models, Molecular
- Abstract
We derive the effective viscosity of dilute suspensions of swimming bacteria from the microscopic details of the interaction of an elongated body with the background flow. An individual bacterium propels itself forward by rotating its flagella and reorients itself randomly by tumbling. Due to the bacterium's asymmetric shape, interactions with a prescribed generic (such as planar shear or straining) background flow cause the bacteria to preferentially align in directions in which self-propulsion produces a significant reduction in the effective viscosity, in agreement with recent experiments on suspensions of Bacillus subtilis.
- Published
- 2009
- Full Text
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23. Effect of noise on solid-to-liquid transition in small granular systems under shear.
- Author
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Melhus MF, Aranson IS, Volfson D, and Tsimring LS
- Abstract
The effect of noise on the solid-to-liquid transition of a dense granular assembly under planar shear is studied numerically using soft-particle molecular dynamics simulations in two dimensions. We focus on small systems in a thin planar Couette cell, examining the bistable region while increasing shear, with varying amounts of random noise, and determine statistics of the shear required for fluidization. In the absence of noise, the threshold value of the shear stress depends on the preparation of the system and has a broad distribution. However, adding force fluctuations both lowers the mean threshold value of the shear stress and decreases its variability. This behavior is interpreted as thermoactivated escape through a fluctuating barrier.
- Published
- 2009
- Full Text
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24. Enhanced mixing and spatial instability in concentrated bacterial suspensions.
- Author
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Sokolov A, Goldstein RE, Feldchtein FI, and Aranson IS
- Subjects
- Bacillus subtilis metabolism, Movement, Suspensions, Tomography, Optical Coherence, Bacillus subtilis cytology
- Abstract
High-resolution optical coherence tomography is used to study the onset of a large-scale convective motion in free-standing thin films of adjustable thickness containing suspensions of swimming aerobic bacteria. Clear evidence is found that beyond a threshold film thickness there exists a transition from quasi-two-dimensional collective swimming to three-dimensional turbulent behavior. The latter state, qualitatively different from bioconvection in dilute bacterial suspensions, is characterized by enhanced diffusivities of oxygen and bacteria. These results emphasize the impact of self-organized bacterial locomotion on the onset of three-dimensional dynamics, and suggest key ingredients necessary to extend standard models of bioconvection to incorporate effects of large-scale collective motion.
- Published
- 2009
- Full Text
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25. Motor-mediated alignment of microtubules in semidilute mixtures.
- Author
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Swaminathan S, Ziebert F, Karpeev D, and Aranson IS
- Abstract
We propose and study a model of molecular motor-induced ordering in a cytoskeletal filament solution for the semidilute case. Motors attach to a pair of filaments and walk along the pair bringing them into closer alignment. In the semidilute regime multiple motors can bind a filament to several others and, for a critical motor density, induce a transition to an ordered phase with a nonzero mean orientation. The motors, on the one hand, cause closer filament alignment, and, on the other hand, induce fluctuations that are dependent on the relative orientation of the filaments to which the motors are attached. We develop a spatially homogenous, mean-field theory that explicitly accounts for a force-dependent detachment rate of motors, which in turn affects the mean and the fluctuations of the net force acting on a filament. This model considers each filament to be in motor contact with all other filaments in the solution. We show that the transition to the oriented state changes from second order to first order when the force-dependent detachment becomes important.
- Published
- 2009
- Full Text
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26. Nonlocal rheological properties of granular flows near a jamming limit.
- Author
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Aranson IS, Tsimring LS, Malloggi F, and Clément E
- Abstract
We study the rheology of sheared granular flows close to a jamming transition. We use the approach of partially fluidized theory (PFT) with a full set of equations extending the thin layer approximation derived previously for the description of the granular avalanches phenomenology. This theory provides a picture compatible with a local rheology at large shear rates [G. D. R. Midi, Eur. Phys. J. E 14, 341 (2004)] and it works in the vicinity of the jamming transition, where a description in terms of a simple local rheology comes short. We investigate two situations displaying important deviations from local rheology. The first one is based on a set of numerical simulations of sheared soft two-dimensional circular grains. The next case describes previous experimental results obtained on avalanches of sandy material flowing down an incline. Both cases display, close to jamming, significant deviations from the now standard Pouliquen's flow rule [O. Pouliquen, Phys. Fluids 11, 542 (1999); 11, 1956 (1999)]. This discrepancy is the hallmark of a strongly nonlocal rheology and in both cases, we relate the empirical results and the outcomes of PFT. The numerical simulations show a characteristic constitutive structure for the fluid part of the stress involving the confining pressure and the material stiffness that appear in the form of an additional dimensionless parameter. This constitutive relation is then used to describe the case of sandy flows. We show a quantitative agreement as far as the effective flow rules are concerned. A fundamental feature is identified in PFT as the existence of a jammed layer developing in the vicinity of the flow arrest that corroborates the experimental findings. Finally, we study the case of solitary erosive granular avalanches and relate the outcome with the PFT analysis.
- Published
- 2008
- Full Text
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27. Bundle dynamics of interacting polar rods.
- Author
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Swaminathan S, Karpeev D, and Aranson IS
- Abstract
We use a probabilistic model of microtubule interaction via molecular motors to study microtubule bundle interaction. Our model indicates that initially disordered systems of interacting polar rods exhibit an orientational instability resulting in spontaneous ordering. We study the existence and dynamic interaction of microtubule bundles analytically and numerically. Our results show a long term attraction and coalescing of bundles indicating a clear coarsening in the system; Microtubule bundles concentrate into fewer orientations on a slow logarithmic time scale.
- Published
- 2008
- Full Text
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28. Simulation studies of self-organization of microtubules and molecular motors.
- Author
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Jia Z, Karpeev D, Aranson IS, and Bates PW
- Subjects
- Computer Simulation, Dimerization, Multiprotein Complexes chemistry, Multiprotein Complexes ultrastructure, Protein Conformation, Crystallization methods, Microtubules chemistry, Microtubules ultrastructure, Models, Chemical, Models, Molecular, Molecular Motor Proteins chemistry, Molecular Motor Proteins ultrastructure
- Abstract
We perform Monte Carlo type simulation studies of self-organization of microtubules interacting with molecular motors. We model microtubules as stiff polar rods of equal length exhibiting anisotropic diffusion in the plane. The molecular motors are implicitly introduced by specifying certain probabilistic collision rules resulting in realignment of the rods. This approximation of the complicated microtubule-motor interaction by a simple instant collision allows us to bypass the "computational bottlenecks" associated with the details of the diffusion and the dynamics of motors and the reorientation of microtubules. Consequently, we are able to perform simulations of large ensembles of microtubules and motors on a very large time scale. This simple model reproduces all important phenomenology observed in in vitro experiments: Formation of vortices for low motor density and raylike asters and bundles for higher motor density.
- Published
- 2008
- Full Text
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29. Rheological and structural properties of dilute active filament solutions.
- Author
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Ziebert F and Aranson IS
- Subjects
- Computer Simulation, Elasticity, Motion, Protein Conformation, Solutions, Stress, Mechanical, Viscosity, Intermediate Filament Proteins chemistry, Intermediate Filament Proteins ultrastructure, Microfluidics methods, Models, Chemical, Models, Molecular, Molecular Motor Proteins chemistry, Molecular Motor Proteins ultrastructure
- Abstract
The rheology and the structure of a dilute semiflexible biofilament solution, like F-actin, interacting via molecular motors is probed by molecular dynamics simulations. Oscillatory external shear is used to measure the storage and loss moduli as a function of motor activity in a range of frequencies and for low shear rates. The overall effect of the motor activity on the rheological properties is interpreted as an increase of the temperature, with the effective temperature proportional to the density of motors. However, the effect of motors on the structural properties of the solution, such as the orientation correlation function, is opposite: the motors drastically increase the orientation correlation length whereas thermal fluctuations decrease it.
- Published
- 2008
- Full Text
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30. Spreading of a granular droplet.
- Author
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Sánchez I, Raynaud F, Lanuza J, Andreotti B, Clément E, and Aranson IS
- Abstract
The influence of controlled vibrations on the granular rheology is investigated in a specifically designed experiment in which a granular film spreads under the action of horizontal vibrations. A nonlinear diffusion equation is derived theoretically that describes the evolution of the deposit shape. A self-similar parabolic shape (the "granular droplet") and a spreading dynamics are predicted that both agree quantitatively with the experimental results. The theoretical analysis is used to extract effective friction coefficients between the base and the granular layer under sustained and controlled vibrations. A shear thickening regime characteristic of dense granular flows is evidenced at low vibration energy, both for glass beads and natural sand. Conversely, shear thinning is observed at high agitation.
- Published
- 2007
- Full Text
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31. Interactions of semiflexible filaments and molecular motors.
- Author
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Karpeev D, Aranson IS, Tsimring LS, and Kaper HG
- Subjects
- Computer Simulation, Elasticity, Motion, Stress, Mechanical, Intermediate Filament Proteins chemistry, Models, Chemical, Models, Molecular, Molecular Motor Proteins chemistry
- Abstract
This paper summarizes the results of numerical simulations of the interaction of a pair of biofilaments mediated by a molecular motor. The filaments are modeled as flexible rods, and the results are applicable to microtubules, which are relatively stiff, as well as to much softer filaments, such as actin. The results provide insight into the effects of flexibility on cytoskeleton formation and the rheology of semiflexible filament networks. The simulations are based on a nonlinear elasticity equation. The results show that flexibility enhances the tendency of filaments to align. The enhancement in turn favors the formation of large-scale structures in multifilament systems. Simulations for soft filaments show that the action of the motor can result in the formation of multiple loops of the filaments as a result of buckling, which can affect the structure of a cross-linked network and thereby its rheology. The estimate for the minimal buckling length as a function of the motor speed, the viscosity of the solvent, and the bending stiffness of the filament is derived analytically.
- Published
- 2007
- Full Text
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32. Swirling motion in a system of vibrated elongated particles.
- Author
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Aranson IS, Volfson D, and Tsimring LS
- Abstract
Large-scale collective motion emerging in a monolayer of vertically vibrated elongated particles is studied. The motion is characterized by recurring swirls, with the characteristic scale exceeding several times the size of an individual particle. Our experiments identified a small horizontal component of the oscillatory acceleration of the vibrating plate in combination with orientation-dependent bottom friction (with respect to horizontal acceleration) as a source for the swirl formation. We developed a continuum model operating with the velocity field and local alignment tensor, which is in qualitative agreement with the experiment.
- Published
- 2007
- Full Text
- View/download PDF
33. Concentration dependence of the collective dynamics of swimming bacteria.
- Author
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Sokolov A, Aranson IS, Kessler JO, and Goldstein RE
- Subjects
- Locomotion physiology, Bacillus subtilis physiology, Models, Biological
- Abstract
At concentrations near the maximum allowed by steric repulsion, swimming bacteria form a dynamical state exhibiting extended spatiotemporal coherence. The viscous fluid into which locomotive energy of individual microorganisms is transferred also carries interactions that drive the coherence. The concentration dependence of correlations in the collective state is probed here with a novel technique that herds bacteria into condensed populations of adjustable concentration. For the particular thin-film geometry employed, the correlation lengths vary smoothly and monotonically through the transition from individual to collective behavior.
- Published
- 2007
- Full Text
- View/download PDF
34. Model for dynamical coherence in thin films of self-propelled microorganisms.
- Author
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Aranson IS, Sokolov A, Kessler JO, and Goldstein RE
- Abstract
Concentrated bacterial suspensions spontaneously develop transient spatiotemporal patterns of coherent locomotion whose correlation lengths greatly exceed the size of individual organisms. Continuum models have indicated that a state of uniform swimming order is linearly unstable at finite wavelengths, but have not addressed the nonlinear dynamics of the coherent state, with its biological implications for mixing, transport, and intercellular communication. We investigate a specific model incorporating hydrodynamic interactions in thin-film geometries and show by numerical studies that it displays large scale persistently recurring vortices, as actually observed.
- Published
- 2007
- Full Text
- View/download PDF
35. Theory of self-assembly of microtubules and motors.
- Author
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Aranson IS and Tsimring LS
- Subjects
- Biomechanical Phenomena, Motion, Microtubules physiology, Models, Biological, Molecular Motor Proteins physiology
- Abstract
We derive a model describing spatiotemporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel, we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes an orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments. We derive the specific form of the interaction kernel from the detailed analysis of microscopic interaction of two filaments mediated by a moving molecular motor and extend our results to include variable motor density and motor attachment to the substrate.
- Published
- 2006
- Full Text
- View/download PDF
36. Transverse instability of avalanches in granular flows down an incline.
- Author
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Aranson IS, Malloggi F, and Clément E
- Abstract
Avalanche experiments on an erodible substrate are analyzed using the "partial fluidization" model of dense granular flows. The model identifies a family of propagating solitonlike avalanches with shape and velocity controlled by the inclination angle and the depth of the substrate. At high inclination angles, the solitons display a transverse instability, followed by coarsening and fingering similar to recent experimental observation. A primary cause for the transverse instability is directly related to the dependence of the soliton velocity on the granular mass trapped in the avalanche.
- Published
- 2006
- Full Text
- View/download PDF
37. Pattern formation of microtubules and motors: inelastic interaction of polar rods.
- Author
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Aranson IS and Tsimring LS
- Subjects
- Computer Simulation, Elasticity, Models, Molecular, Molecular Conformation, Motion, Multiprotein Complexes chemistry, Multiprotein Complexes physiology, Protein Conformation, Static Electricity, Structure-Activity Relationship, Microtubules chemistry, Microtubules physiology, Models, Biological, Models, Chemical, Molecular Motor Proteins chemistry, Molecular Motor Proteins physiology
- Abstract
We derive a model describing spatiotemporal organization of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments.
- Published
- 2005
- Full Text
- View/download PDF
38. Dendritic flux avalanches and nonlocal electrodynamics in thin superconducting films.
- Author
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Aranson IS, Gurevich A, Welling MS, Wijngaarden RJ, Vlasko-Vlasov VK, Vinokur VM, and Welp U
- Abstract
We report a mechanism of nonisothermal dendritic flux penetration in superconducting films. Our numerical and analytical analysis of coupled nonlinear Maxwell and thermal diffusion equations shows that dendritic flux pattern formation results from spontaneous branching of propagating flux filaments due to nonlocal magnetic flux diffusion and positive feedback between flux motion and Joule heating. The branching is triggered by a thermomagnetic edge instability, which causes stratification of the critical state. The resulting distribution of thermomagnetic microavalanches is not universal, because it depends on a spatial distribution of defects. Our results are in good agreement with experiments on Nb films.
- Published
- 2005
- Full Text
- View/download PDF
39. Stick-slip dynamics of a granular layer under shear.
- Author
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Volfson D, Tsimring LS, and Aranson IS
- Abstract
Stick-slip regime of shear granular flows is studied theoretically and numerically. Numerical experiments are carried out for a thin Couette cell using soft-particle molecular dynamics code in two dimensions. We apply order parameter theory of partially fluidized granular flows and find a good agreement with simulations and experiments by Nasuno et al.
- Published
- 2004
- Full Text
- View/download PDF
40. Partially fluidized shear granular flows: continuum theory and molecular dynamics simulations.
- Author
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Volfson D, Tsimring LS, and Aranson IS
- Abstract
The continuum theory of partially fluidized shear granular flows is tested and calibrated using two-dimensional soft particle molecular dynamics simulations. The theory is based on the relaxational dynamics of the order parameter that describes the transition between static and flowing regimes of granular material. We define the order parameter as a fraction of static contacts among all contacts between particles. We also propose and verify by direct simulations the constitutive relation based on the splitting of the shear stress tensor into a"fluid part" proportional to the strain rate tensor, and a remaining "solid part." The ratio of these two parts is a function of the order parameter. The rheology of the fluid component agrees well with the kinetic theory of granular fluids even in the dense regime. Based on the hysteretic bifurcation diagram for a thin shear granular layer obtained in simulations, we construct the "free energy" for the order parameter. The theory calibrated using numerical experiments with the thin granular layer is applied to the surface-driven stationary two-dimensional granular flows in a thick granular layer under gravity.
- Published
- 2003
- Full Text
- View/download PDF
41. Order parameter description of stationary partially fluidized shear granular flows.
- Author
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Volfson D, Tsimring LS, and Aranson IS
- Abstract
We carry out a detailed comparison of soft-particle molecular dynamics simulations with the theory of partially fluidized shear granular flows. We verify by direct simulations a constitutive relation based on the separation of the shear stress tensor into a fluid part proportional to the strain rate tensor, and a remaining solid part. The ratio of these two components is determined by the order parameter. Based on results of the simulations we construct the "free energy" function for the order parameter. We also present the simulations of the stationary deep 2D granular flows driven by an upper wall and compare it with the continuum theory.
- Published
- 2003
- Full Text
- View/download PDF
42. Vortex glass and vortex liquid in oscillatory media.
- Author
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Brito C, Aranson IS, and Chaté H
- Abstract
We study the disordered, multispiral solutions of two-dimensional oscillatory media for parameter values at which the single-spiral/vortex solution is fully stable. Using the complex Ginzburg-Landau (CGLE) equation, we show that these states, heretofore believed to be static, actually evolve extremely slowly. This is achieved via a reduction of the CGLE to the evolution of the sole vortex coordinates. This true defect-mediated turbulence occurs in two distinct phases, a vortex liquid characterized by normal diffusion of spirals, and a slowly relaxing, intermittent, "vortex glass."
- Published
- 2003
- Full Text
- View/download PDF
43. Model of coarsening and vortex formation in vibrated granular rods.
- Author
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Aranson IS and Tsimring LS
- Abstract
Neicu et al. observed experimentally spontaneous formation of the long-range orientational order and large-scale vortices in a system of vibrated macroscopic rods. We propose a phenomenological theory of this phenomenon based on a coupled system of equations for local rods density and tilt. The density evolution is described by the modified Cahn-Hilliard equation, while the tilt is described by the Ginzburg-Landau type equation. Our analysis shows that, in accordance with the Cahn-Hilliard dynamics, islands of the ordered phase appear spontaneously and grow due to coarsening. The generic vortex solutions of the Ginzburg-Landau equation for the tilt correspond to the vortical motion of the rods around the cores which are located near the centers of the islands.
- Published
- 2003
- Full Text
- View/download PDF
44. Continuum theory of partially fluidized granular flows.
- Author
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Aranson IS and Tsimring LS
- Abstract
A continuum theory of partially fluidized granular flows is developed. The theory is based on a combination of the equations for the flow velocity and shear stresses coupled with the order-parameter equation which describes the transition between the flowing and static components of the granular system. We apply this theory to several important granular problems: avalanche flow in deep and shallow inclined layers, rotating drums, and shear granular flows between two plates. We carry out quantitative comparisons between the theory and experiment.
- Published
- 2002
- Full Text
- View/download PDF
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