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Fluctuations and Response in Active Materials: From Driven Granular Systems to Swarming Bacteria
“Driven dense granular matter as a da Vinci fluid”
The flow of dense granular materials is a long-standing fundamental scientific problem with a wide range of relevance to engineering fields, technological applications and natural phenomena that affect human society. It is also relevant to sanding in oil extraction, to flow of dense suspensions and to collapse of cavities in mines. In spite of centuries (!) of research, the rheology of dense granular matter is poorly understood.
I discuss a new model for the flow of dense particulates, where particles are in contact most of the time. A coarse-grained minimal model is derived from first principles - the da Vinci Fluid model. In da Vinci fluids, dissipation is dominated by solid friction rather than conventional viscosity.
I present initial results for both gravitational and Couette flows. In particular, I show that the da Vinci fluid model explains quantitatively formation and development of plugs (regions of vanishing velocity gradient) - a frequently observed phenomenon that has been notoriously difficult to model until now
“A bacterium’s perspective on chemosensing and exploration”
The detection, amplification, and processing of external chemical signals is affected by random fluctuations that arise within signaling pathways. In the case of the bacterial chemotaxis system we now have enough experimental data to go beyond ensemble averages. I will talk about our recent experimental and theoretical efforts to examine how the network design and spatial arrangement of this model signaling pathway shape the information processing and chemotactic capabilities of the single cell. An interesting result that emerges from this individual cell perspective is a molecular understanding of how cells resolve the compromise between the essential but likely competing behavioral modes of sensing and exploring.
Kenneth W. Foster
"The refined self-organized beating of cilia and their cellular control"
Cilia are slender cylindrical protrusions of a eukaryotic cell that propel a cell or move fluid. They also play a direct or developmental role in the sensors of fluid flow, light, sound, gravity, smells, touch, temperature and taste in mammals. Cilia are very complex nanostructures requiring at least 650 genes to make and control; more than ten times the components associated with a bacterial flagellum. Explaining how cilia propagate waves, oscillate, steer and have other behaviors has been a challenging problem. Part of the challenge is due to the many refinements and relatively independent control systems that have been overlaid on top of the basic system. From an evolutionary viewpoint prior to any controls came the insertion of dynein motors into the pre-existing cylindrical structure leading to self-generated oscillation. Refinements have included splitting into eight types of dynein motors which can be independently influenced, intricate compliance devices at the attachment site to the cell body, an interior ATP delivery system that rotates with the beating so that it always has the same phase relationship with the motor activity, and geometric changes that accentuate motor activity on the inside of bends. Starting from the observation of non-mammalian cilia and using hydrodynamics to determine the net force of the cilia on their environment, it has been promising to obtain reasonable and consistent estimates of their stiffness, base compliance properties and the relationship between force and sliding. A goal is to make a realistic model without any controlled switching between different modes for dynein behavior. To achieve a rich variety of functions the system has also been overlaid with cellular controls. Examples include control of steering associated with phototaxis and chemotaxis, of the stopping beating to facilitate mating, of the turning off of phototaxis when an obstacle is encountered, and of the optimum balance between ballistic and diffusive motion.
“Rheology and Flow of Geometrically Cohesive Granular Materials”
The ability of large aspect ratio granular particles to form solid plugs is now well-documented but, apart from a general phenomenological explanation of geometric entanglement, remains unexplained. The general class of materials whose particle geometry allows for pile cohesivity --- termed Geometrically Cohesive Granular Materials (GCGM) is much larger than just rods, including U-shaped staples and semi-circular arcs. In this talk, I'll begin by reporting on recent simulations of sheared granular rods, documenting bulk and shear modulii and preliminary data on particle mobility. Motion in the direction of shear appears ballistic, regardless of particle aspect ratio, and diffusive in the other two directions. I'll conclude by describing a framework that allows us to smoothly vary particle shape from a spherocylinder to an arc to a U-shape of arbitrary corner sharpness.
“Group dynamics in the fire ant Solenopsis invicta”
In this talk I will discuss two of our studies of collective behavior of the fire ant Solenopsis invicta. First I will discuss our work to understand the dynamics of fire ant nest construction. Fire ant colonies construct underground nest networks up to 3 meters in depth that house 10^5 colony members. In laboratory experiments we monitor quasi two-dimensional nests created by groups of 150 workers in a wetted granular medium to observe the growth and topology of the nest network. We find that network topology is independent of time. Nest growth stems from the digging and transport of grains by individual workers. By tracking digging workers in time we observe that on average only 20% of the worker population is engaged with digging during the test period. The final nest size was correlated with the average number of digging workers in each test which indicates that simple digging laws may regulate nest growth. Next, I will discuss a granular physics problem inspired by the self assembly and disassembly of groups of ants. When the nest is flooded, the colonies will cohere geometrically through interlinking of limbs and mandibles. Inspired by the fire ants, we study a passive granular system which displays similar particle interlinking. We use u-shaped particles to form piles of cohesive granular media which cohere through particle entanglement. We measure the stability of these piles by applying vertical oscillation of fixed frequency and controlled amplitude and measuring the characteristic collapse time. Column collapse time scales as tau; = 0 exp(Gamma;0=Gamma) with Gamma;0 a non-monotonic function of staple geometry. We model the relaxation as an activated hopping process and are able to explain the maximum of Gamma;0 as a competition between binding strength and packing efficiency. Nick Gravish and Daniel I. Goldman, June 7, 2011
“Inferring effective forces in collective motion”
Animal groups, such as bird flocks, fish schools, or insect swarms, often exhibit complex, coordinated collective dynamics resulting from individual interactions. Despite recent progress, it is still unknown how simple individual rules can achieve such synchronized, scalable, robust, and fast-responding behavior. I will present experimental analyses that use large datasets, obtained in recent experiments developed with Prof. Iain Couzin and his group at Princeton University, which allow us to unveil specific effective interaction forces within fish schools.
“Simple models for "granular bio-systems": From "sand-swimming" to cementing bacteria”
It is very fascinating when granular systems are influenced by or interact with biological system. On the one hand a "bio-system" can be actively interacting with the sand as, e.g., the so called "sand-swimmer", on the other hand microorganisms which are typically present in soils can influence the material behavior drastically.
Granular materials are able to act either as a solid, supporting a load, such as sand on a beach, or as a fluid, e.g., flowing in an hourglass. Some lizards are known to make use of this balance between solidlike and fluidlike properties to swim through sand beds. A simple model of a "sand-swimmer" is presented, being able to move in dense non-cohesive granular material . This swimmer also probes the granular material locally. Studies of "living quicksand"  indicate that bacteria can play an important role for stabilizing fragile structures of a looser material . In the present model the effects of the bacteria are included as specific cohesive bonds, additionally leading to a yield-stress material behavior.
 T. Shimada, D. Kadau, T. Shinbrot and H.J. Herrmann. Swimming in granular media. Rapid Communications to Physical Review E, 80, 020301R (2009).
 D. Kadau, H.J. Herrmann, J.S. Andrade Jr., A.D. Araujo, L.J.C. Bezerra and L.P. Maia. Living Quicksand. Brief Communications to Granular Matter, 11(1): 67-71 (2009).
 D. Kadau, H.J. Herrmann. Density profiles of loose and collapsed cohesive granular structures generated by ballistic deposition. Physical Review E 83, 031301 (2011).
All publications could be found on: http://sites.google.com/site/dirkkadau/publications
M. Cristina Marchetti
“Active Solids and Jamming”
The rich emergent behavior of active liquids has been discussed extensively in the literature in various contexts, from bacterial suspensions to mixture of cytoskeletal filaments and motor proteins to vibrated granular layers. In this talk I will focus on the behavior of ``active solids” as may be obtained in actomyosin systems by the addition of passive crosslinkers or in collections of self-propelled units by simply increasing the density. I will discuss two models of active solids that have been argued to exhibit glassy-like dynamics characteristic of jammed systems. The first is a continuum elastic theory of crosslinked gels aimed at describing a single cell and its cytoskeleton as an active material. In this system the interplay of activity and elastic recovery forces yields spontaneous contractility and sustained oscillations, as ubiquitously observed in cells. In the second part of the talk I will report on numerical studies of a model of self-propelled particles confined at high density on a substrate and show that this system exhibits an active jammed state with unusual oscillatory soft modes that control the collective dynamics of the system. This model is inspired by recent experiments on confluent layers of migrating epithelial cells that have been shown to exhibit collective glassy dynamics at high density.
“Self-propulsion and driven granular systems: introduction and update”
Abstract: My talk will be in three short sections: (i) The general framework of active matter, from the
perspective of self-propelled particle systems; (ii) Driven granular layers as
close analogues to self-driven systems; (iii) Recent results on dynamics,
fluctuations and instabilities in active matter -- stripes and drops.
“Breathing, sliding, proof reading: On how to access packed DNA”
Abstract: DNA in plants and animals are densely packed inside DNA-protein complexes called chromatin. In this talk I focus on the first level of compaction, the nucleosome. Nucleosomes are DNA-spools with a protein-core and engage about three quarter of DNA at any time. How DNA can nevertheless be accessed by the various proteins that have to bind to specific DNA target sequences will be the subject of my talk. I show how all the DNA is temporarily exposed through thermal fluctuations and why, nevertheless, nucleosomes are very stable against those fluctuations. I then discuss chromatin remodeller, active molecular machines, that can pull or push nucleosomes along DNA. Rather than discussing molecular details of those machines that yet have to be uncovered, I propose a possible kinetic proofreading scheme that might be at work inside chromatin.
“Identifying the Fingerprints of Molecular Motors in the Active Fluctuations of the Red Blood Cell Membrane”
The mechanical rigidity of cells has an important effect on their biological function, especially for red-blood cells (RBC) that have to be flexible and resilient at the same time, in order to pass unharmed through narrow capillaries in the body. The metabolic activity of the RBC controls its rigidity, and generates strong undulations of the cell membrane. The microscopic properties of the molecular motors that generate the RBC membrane activity are poorly understood. Our work enables to extract useful information regarding these elusive motors from a statistical analysis of the random fluctuations that these motors produce.
Recently, two experiments have attempted to characterize the active nature of RBC membrane fluctuations. We demonstrate that the two different measures used in these experiments can give conflicting behavior. Moreover, we show that the non-Gaussianity, or the deviation of the fluctuations from a thermal distribution, depends non-monotonically both on the activity of the microscopic motors, and on their number. Finally, we show that the “effective temperature” of the fluctuations, can depend non-monotonically on the measurement frequency. Our theoretical calculations can be used by future experiments in order to disentangle the mode of operation of the molecular motors in various biological systems.
E. Ben-Isaac, Y.K. Park, G. Popescu, F.L.H. Brown, N.S. Gov. and Y. Shokef
"Effective Temperature of Red Blood Cell Membrane Fluctuations"
Physical Review Letters - in press (June 2011)
"The flocks in you: liquid and crystalline flocking in cell membrane actin"
Flocking - the collective motion of large numbers of organisms or other self-propelled entities - exhibits a number of strange and baffling phenomena. Indeed, its very existence in two dimensions would appear to violate a fundamental theorem of statistical mechanics, while in any spatial dimension, flocks exhibit giant number fluctuations far in excess of those predicted by the "law of large numbers" of statistics.
In this talk, I`ll show that all of this mysteries can be explained by a very general "hydrodynamic" theory of flocks, which summarizes the behavior of ALL flocks in much the same way that the well-known Navier-Stokes equations summarize the behavior of all simple fluids. I`ll then discuss the impressive agreement between this theory and both simulations, and recent experiments showing giant number fluctuations of actin near cell walls.
“Jamming at high densities”
We extend studies of properties of jammed solids to volume fractions much higher than the jamming transition threshold. At zero temperature and shear stress, the whole jamming regime is divided into two distinct parts which are separated by a crossover volume fraction φd. Deeply jammed solids at φ >φd exhibit different critical scalings, structure, and vibrational properties from marginally jammed solids at φ <φd. Correspondingly, dynamical properties such as the glass transition temperature and dynamical heterogeneity show opposite volume fraction dependence on both sides of φd. Whether φdis indeed critical-like requires further studies.
Department of Physics & CAS Key Laboratory of Soft Matter Chemistry
University of Science and Technology of China - Hefei, Anhui 230026, P. R. China