Workshop Programme

for period 24 - 28 June 2013

Dynamics of active suspensions, gels, cells and tissues

24 - 28 June 2013

Timetable

 Monday 24 June 09:00-09:45 Registration at INI 09:45-10:30 Goldstein, R (University of Cambridge) Spontaneous Circulation of Confined Active Suspensions Sem 1 Many active fluid systems encountered in biology are set in total geometric confinement. Cytoplasmic streaming in plant cells is a prominent and ubiquitous example, in which cargo-carrying molecular motors move along polymer filaments and generate coherent cell-scale flow. In this talk I will summarize theoretical and experimental work in my group that addresses the possibility that the ordered patterns of streaming seen in nature can arise from a process of self-organization. 10:30-11:00 Morning Coffee at INI 11:00-11:45 Stark, H (Technische Universität Berlin) Active motion: under external fields and collective dynamics Sem 1 Active motion of microorganisms or artificial microswimmers, such as active colloids, is an appealing subject which has attracted much attention recently. Since these swimmers move constantly in non-equilibrium, they give rise to novel phenomena which, in particular, occur when external fields are applied or when they move collectively. The talk reviews our recent work on how active Brownian particles behave in external fields and in confinement. For example, they develop orientational order in a gravitational field [1] and exhibit an interesting instability in dense suspensions when they are bottom-heavy. They also create active fluid pumps in a harmonic trap. Finally, under Poiseuille flow they show nonlinear dynamics reminiscent of the nonlinear pendulum where the bounding walls introduce "dissipation" [2]. We also study the collective motion of so-called squirmers in a quasi 2D geometry by means of multi-particle collision dynamics. We observe dynamical clustering, phase separation, and active jamming which is strongly influenced by hydrodynamic near-field interactions. In dense suspensions rotational diffusion is greatly enhanced and the critical volume fraction for crystallisation is different for pushers and pullers. [1] M. Enculescu and H. Stark, Phys. Rev. Lett. 106, 208103 (2011). [2] A. Zoettl and H. Stark, Phys. Rev. Lett. 108, 218104 (2012). Co-authors: Marc Hennes (Institute of Theoretical Physics, Technische Universität Berlin), Katrin Wolff (Institute of Theoretical Physics, Technische Universität Berlin), Andreas Zoettl (Institute of Theoretical Physics, Technische Universität Berlin) 11:45-12:30 Keaveny, E (Imperial College London) Optimisation of chiral structures for micro-scale propulsion Sem 1 In micron-scale hydrodynamics, shape and geometry play a strong role in determining the speed at which a body can move through fluid. This shape dependence is particularly important to the design of many microfluidic devices, including magnetically actuated micro-structures fabricated and studied for biomedical applications. In this talk, I will discuss several important experimentally-realisable micro-structures whose shapes couple their rotations and translations. I will address the optimal design of these devices through an infinite-dimensional optimisation problem, obtaining geometries that maximise speed for a given applied torque. Our optimisations show that attached payloads have a significant effect on optimal micro-structure shapes and current designs can be improved by upwards of 450%. 12:30-13:30 Lunch at Wolfson Court 14:00-14:30 Koepf, M (Technion - Israel Institute of Technology) A continuum model of epithelial spreading Sem 1 We present a continuum model of unconstrained epithelial spreading. The tissue is described as a polarizable and chemo-mechanically interacting layer with neo-Hookean elasticity. Our model reproduces the spontaneous formation of finger-like protrusions commonly observed in experiment. Statistics of velocity orientation obtained from numerical simulation show strong alignment in the fingers opposed to an isotropic distribution in the bulk, as has been measured by Reffay et al. (Reffay et al., Biophysical Journal, 2011). The results faithfully reproduce faster relative advance of cells close to the leading edge of the tissue, as well as spatial velocity correlations and stress accumulation within the tissue, which proceeds in form of a "mechanical wave", traveling from the wound edge inwards (cf. Serra-Picamal et al., Nature Physics, 2012). M H Koepf, L M Pismen: A continuum model of epithelial spreading (2013) submitted M H Koepf, L M Pismen: Non-equilibrium patterns in polarizable active layers (2013) submitted Co-author: Leonid M. Pismen (Department of Chemical Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel) 14:30-15:00 Menzel, A (Heinrich-Heine-Universität Düsseldorf) Traveling and resting crystals in crowds of self-propelled particles Sem 1 When the density within a crowd of self-propelled particles is high enough and when the interactions between these particles are strong enough, then it is plausible to expect that crystallization will occur. We are interested in the formation and in the behavior of such active crystals that are composed of self-propelled particles. To study this kind of materials using a field approach, we combine the classical phase field crystal model by Elder and Grant with the Toner-Tu theory for active media. In this way we obtain an active phase field crystal model. Our approach can further be justified from dynamic density functional theory. The active crystals that we identify can be classified into two groups: either the crystal is resting, meaning that no net density flux is observed, or it is traveling, meaning that the lattice peaks collectively migrate into one direction. As a central result we find that a transition from a resting to a traveling crystal can occur at a threshold value of the active drive. Consequently a variety of different crystalline phases can be identified: resting hexagonal, traveling hexagonal, swinging hexagonal, traveling rhombic, traveling quadratic, resting lamellar, traveling lamellar, resting honeycomb, and traveling honeycomb. Upon quenching from the fluid phase, the traveling crystals emerge through a coarse-graining process from domains of different directions of collective motion. Qualitatively we also studied the impact of additional hydrodynamic interactions between the lattice peaks. Since the properties and response of active crystals can be very different from their equilibrium counterparts, the knowledge of, classification of, and control of the different crystalline states can provide a starting point for the design of new active materials. Co-author: Hartmut Lowen (Heinrich Heine University Dusseldorf, Germany) 15:00-15:30 Banerjee, S (Syracuse University) Collective mechanics of epithelial cell colonies on elastic substrates Sem 1 Crosstalk between cell-cell and cell-matrix adhesions plays an essential role in the mechanical function of tissues. The traction stresses exerted by cohesive keratinocyte colonies with strong cell-cell adhesions are mostly concentrated at the colony periphery. In contrast, for weak cadherin-based intercellular adhesions, individual cells in a colony interact with their matrix independently, with disorganized distribution of traction stresses extending throughout the colony. In this talk I will present a minimal physical model of the colony as adherent contractile elastic media coupled to an elastic substrate. The model captures the spatial distribution of traction forces seen in experiments. For cell colonies with strong cell-cell adhesions, the total traction force of the colony measured in experiments is found to scale with the colony’s geometrical size. This scaling suggests the emergence of an effective surface tension of magnitude comparable to that measured fo r non-adherent, three-dimensional cell aggregates. The physical model supports the scaling and indicates that the surface tension may be controlled by acto-myosin contractility. Co-authors: Aaron F. Mertz (Yale University), M. Cristina Marchetti (Syracuse University), Eric R. Dufresne (Yale University), Valerie Horsley (Yale University) 15:30-16:00 Afternoon Tea at INI 16:00-17:00 Lubensky, T (University of Pennsylvania) Rigidity, Zero Modes, States of Self Stress, and Surface Phonons in Periodic and Diluted Periodic Networks near their Instability Limit Sem 1 Frames consisting of nodes connected pairwise by rigid rods or central-force springs, possibly with preferred relative angles controlled by bending forces, are useful models for systems as diverse as architectural structures, crystalline and amorphous solids, sphere packings and granular matter, networks of semi-flexible polymers, and protein structure. The rigidity of these networks depends on the average coordination number z of the nodes: If z is small enough, the frames have internal zero-frequency modes, and they are "floppy"; if z is large enough, they have no internal zero modes and they are rigid. The critical point separating these two regimes occurs at a rigidity threshold, which corresponds closely to what is often referred to as the isostatic point, that for central forces in d-dimensions occurs at coordination number zc = 2d. At and near the rigidity threshold, elastic frames exhibit unique and interesting properties, including extreme sensitivity to boundary conditions, power-law scaling of elastic moduli with (z- zc), and diverging length and time scales. This talk will explore elastic and mechanical properties and mode structures of model periodic and diluted periodic lattices, such as the square and kagome lattices with central-force springs, that are just on verge of mechanical instability, and 4-coordinated lattices in two and three dimensions that are stabilized by bending forces. It will discuss the origin and nature of zero modes of these structures under both periodic (PBC) and free boundary conditions (FBC), and it will derive general conditions under which (a) the zero modes under the two boundary conditions are essentially identical and (b) under which zero modes do not appear in the periodic spectrum but do appear as surface Rayleigh waves in the free spectrum. In the former situation, lattices are generally in a type of critical state that admits states of self-stress in which there can be tension in bars with zero force on any node, and distortions away from that state give rise to surface modes under free boundary conditions whose degree of penetration into the bulk diverges at the critical state. This general phenomenon also occurs in sub-isostatic lattices like the honeycomb lattice. The talk will also explore diluted 4-coordinated lattices as models for networks of semi-flexible polymers, discuss the special properties that result when constituent polymers adopt strictly straight configurations. 17:00-18:00 Welcome Wine Reception at INI
 Tuesday 25 June 09:00-09:45 Crowdy, D (Imperial College London) Models of low-Reynolds-number swimmers and colloidal particles in confined domains Sem 1 The talk will survey some simple mathematical models to gain insights into the dynamics of particles or swimmers of various kinds moving at zero Reynolds numbers in geometrically complex domains bounded by no-slip walls and/or free surfaces. 09:45-10:30 Spagnolie, S (University of Wisconsin-Madison) Locomotion of helical bodies in viscoelastic fluids Sem 1 Many microorganisms swim by rotating one or many helical flagella, often propelling themselves through fluids that exhibit both viscous and elastic qualities in response to deformations. In an effort to better understand the complex interaction between the fluid and body in such systems, we have studied numerically the force-free swimming of a rotating helix in a viscoelastic (Oldroyd-B) fluid. The introduction of viscoelasticity can either enhance or retard the swimming speed depending on the body geometry and the properties of the fluid (through a dimensionless Deborah number). The numerical results show how small-amplitude theoretical calculations connect smoothly to large-amplitude experimental measurements. Co-authors: Bin Liu (Brown University), Thomas R. Powers (Brown University) 10:30-11:00 Morning Coffee at INI 11:00-11:45 Subramanian, G (Engineering Mechanics Unit, JNCASR, Bangalore) Concentration fluctuations in a bacterial suspension Sem 1 Recent analyses and simulations have identified an instability of a quiescent bacterial suspension above a threshold concentration, (nL3)crit = (5/C)(L/U\tau), where n is the bacterium number density, L and U the bacterium length and swimming speed, t the mean interval between tumbles, and C a measure of the intrinsic force-dipole. This instability is thought to underlie the large-scale coherent motions observed in experiments. There, however, remains a discrepancy between theory and simulations. While the former predicts a spatially homogeneous instability with coupled orientation and velocity fluctuations, simulations have observed large-scale concentration fluctuations. Even in the stable regime, solutions of the linearized equations reveal significant concentration fluctuations. We will formulate an analytical solution that illustrates the linearized evolution of the velocity, orientation and concentration fields in a bacterial suspension starting from an arbitrary initial condition. The analysis relies on a remarkable correspondence between orientation fluctuations in a bacterial suspension and vorticity fluctuations in an inviscid fluid. The governing operators in both cases possess singular continuous spectra in addition to discrete modes. The dynamics of the singular orientation modes leads to transient growth of concentration fluctuations in the manner that the singular vorticity modes lead to kinetic energy growth in high-Reynolds-number shearing flows. We will discuss the velocity, orientation and stress correlations, emerging from an uncorrelated Poisson field, both below and above the critical concentration. We also analyze the role of tumbling as a source of fluctuations. Regarding a tumble as a ‘linear collision’ governed by Poisson statistics allows one to write down the orientation-space noise, and this in turn leads to the analog of the fluctuating hydrodynamic equations for a bacterial suspension. Co-author: Donald Koch (Chemical and bio-molecular engineering, Cornell University, NY, USA.) 11:45-12:30 Graham, M (University of Wisconsin-Madison) Hydrodynamic coordination of bacterial motions: from bundles to biomixing Sem 1 Many bacteria propel themselves though their fluid environment by means of multiple rotating flagella that self-assemble to form bundles. At a larger scale, the fluid motion generated by an individual microbe as it swims affects the motions of its neighbors. Experimental observations indicate the presence of long-range order and enhanced transport in suspensions of bacteria -- these phenomena may be important in many aspects of bacterial dynamics including chemotaxis and development of biofilms. This talk focuses on the role of fluid dynamics in the bundling of flagella and the interactions between swimming organisms. We first describe theory and simulations of hydrodynamically interacting microorganisms, using very simple models of the individual organisms. In the dilute limit, simple arguments reveal the dependence of swimmer and tracer velocities and diffusivities on concentration. As concentration increases, we show that cases exist in which the swimming motion generates large-scale flows and dramatically enhanced transport in the fluid. A physical argument supported by a mean field theory sheds light on the origin of these effects. The second part of the talk focuses on the dynamics of the flagellar bundling process, using a mathematical model that incorporates the fluid motion generated by each flagellum as well as the finite flexibility of the flagella. The initial stage of bundling is driven purely by hydrodynamics, while the final state of the bundle is determined by a nontrivial and delicate balance between hydrodynamics and elasticity. As the flexibility of the flagella increases a regime is found where, depending on initial conditions, one finds bundles that are either tight, with the flagella in mechanical contact, or loose, with the flagella intertwined but not touching. That is, multiple coexisting states of bundling are found. The parameter regime at which this multiplicity occurs is comparable to the parameters for a number of bacteria. 12:30-13:30 Lunch at Wolfson Court 14:00-14:45 Yeomans, J (University of Oxford) Active Nematics CMS MR2 Active systems, such as the cytoskeleton and bacterial suspensions, provide their own energy and hence operate out of thermodynamic equilibrium. Continuum models describing active systems are closely related to those describing liquid crystal hydrodynamics, together with an additional ‘active’ stress term. We discuss how the behaviour of the active continuum models depends on model parameters, such as the strength of the activity and the liquid crystal tumbling parameter, and we compare our results to recent experiments on cytoskeletal gels. 14:45-15:30 Dogic, Z (Brandeis University) Hierarchical active matter: from extensible bundles to active gels, streaming liquid crystals and motile emulsions CMS MR2 The emerging field of active matter promises an entirely new category of materials, with highly sought after properties such as autonomous motility and internally generated flows. In this vein, I will describe recent experiments that have focused on reconstituting dynamical structures from purified biochemical components. In particular I will describe recent advances that include: (1) assembly of a minimal model of synthetic cilia capable of generating periodic beating patterns, and conditions under which they exhibit metachronal traveling waves, (2) study of 2D active nematic liquid crystals whose streaming flows are determined by internal fractures and self-healing as well as spontaneous unbinding and recombination of oppositely charged disclination defects, (3) reconstitution of active gels characterized by highly tunable and controllable spontaneous internal flows, and (4) assembly of active emulsions in which aqueous droplets spontaneously crawl when in contact with a ha rd wall. 15:30-16:00 Afternoon Tea at INI 16:00-16:45 Toner, J (University of Oregon) Rice, Locusts and Chemical Waves: A Hydrodynamic Theory of Polar Active Smectics CMS MR2 We present a hydrodynamic theory of polar active smectics, by which we mean active striped systemsactive systems, both with and without number conservation. For the latter, we find quasi long-ranged smectic order in $d=2$ and long-ranged smectic order in $d=3$. In $d=2$ there is a Kosterlitz-Thouless type phase transition from the smectic phase to the ordered fluid phase driven by increasing the noise strength. For the number conserving case, we find that giant number fluctuations are greatly suppressed by the smectic order; that smectic order is long-ranged in $d=3$; and that nonlinear effects become important in $d=2$. Co-author: Leiming Chen (The China University of Mining and Technology) 17:00-21:00 Walk to Grantchester, pub dinner* (either on Tues or Thu)
 Wednesday 26 June 09:00-09:45 Brady, J (CALTECH (California Institute of Technology)) The Five S's: Chemical Swimming, Sailing, Surfing, Squirming and Swarming Sem 1 The design of nanoengines that can convert stored chemical energy into motion is an important challenge of nanotechnology, especially for engines that can operate autonomously. Recent experiments have demonstrated that it is possible to power the motion of nanoscale and microscale objects by using surface catalytic reactions -- so-called catalytic nanomotors. The precise mechanism(s) responsible for this motion is(are) still debated, although a number of ideas have been put forth. Here, a very simple mechanism is discussed: A surface chemical reaction creates local concentration gradients of the reactant (the fuel) and product species. As these species diffuse in an attempt to re-establish equilibrium, they entrain the motor causing it to move. This process can be viewed either as osmotic propulsion or as self-diffusiophoresis. The simplest way to break symmetry and achieve motion is by an asymmetric reactivity on the motor surface. The mathematical description of suc h motion is analogous to that used to describe the swimming of microorganisms, hence the name 'chemical swimming.' However, symmetry can also be broken by the motor's shape and, even for uniform reactivity, propulsion can be achieved -- 'chemical sailing.' A motor particle at an air-water interface can change the local concentration of surface-active agents and propel itself -- 'chemical surfing.' And even local variations of hydrodynamic mobility and interactive potential between the motor and the fuel can lead to net motion, a form of 'chemical squirming.' The implications of these mechanisms on the attainable propulsive speeds as a function of reaction rate and fuel concentration will be discussed and compared with Brownian dynamics simulations. It will also be shown that chemically active particles can attract or repel each other through long-range 'Coulomb-like' interactions. And suspensions of active particles can exhibit Debye-like screening leading to 'chemical swarming.' 09:45-10:30 Lipowsky, R (Max-Planck-Institut für Kolloid- und Grenzflächenforschung) Remodelling of membrane compartments Sem 1 Biomembranes undergo continuous remodelling by budding and fission processes, which create new membrane compartments in the form of vesicles, as well as by adhesion and fusion, which combine two such compartments into a single one. The vesicles are transported by teams of molecular motors from donor membranes, where they are created, to acceptor membranes,into which they are incorporated by membrane fusion. In this talk, I will address the energetics and kinetics of these remodelling processes as well as their relevance for intracellular transport. 10:30-11:00 Morning Coffee at INI 11:00-11:45 Döbereiner, H-G (Universität Bremen) Physarum Polycephalum Percolation as a Paradigm for Topological Phase Transitions in Transportation Networks Sem 1 We study the formation of transportation networks of the true slime mold Physarum polycephalum after fragmentation by shear. Small fragments, called microplasmodia, fuse to form macroplasmodia in a percolation transition. At this topological phase transition, one single giant component forms, connecting most of the previously isolated microplasmodia. Employing the configuration model of graph theory for small link degree, we have found analytically an exact solution for the phase transition. The universality of percolation may be used as a general gauge in the analysis of transportation networks. Some malignant tissues derive their blood vessels not by angiogenesis, i.e., remodeling of existing vessels, but rather by denovo vascularization like embryos. Since topologically, percolation is independent from detailed mechanisms and even space dimensions, i.e., 2D versus 3D growth, it may serve as a reference point in space and time when comparing the dynamics of network formation in tumors of varying size and shape. Since restricting blood supply via hindering vessel percolation is paramount for suppressing tumor growth, this may foster development of antiangiogenic therapy. 11:45-12:30 Yoshinaga, N (Tohoku University) Spontaneous motion and deformation of a droplet driven by chemical reaction Sem 1 Spontaneous motion has been attracting lots of attention in last decades in nonlinear and nonequilibrium physics partially for its potential application to biological problems such as cell motility. Recently several model experiments showing spontaneous motion have been proposed in order to elucidate underlying mechanism of the motion. The systems in these works consist of relatively simple ingredients, for instance oil droplets in water, but nevertheless the results show rich motion and deformation of the droplet. Importantly, the system breaks symmetry and chooses one direction of motion. In this work, we theoretically derive a set of nonlinear equations exhibiting a transition between stationary and motile states starting from advection-reaction-diffusion equation driven away from an equilibrium state due to chemical reactions. A particular focus is on how hydrodynamic flow destabilizes an isotropic distribution of a concentration of chemicals. We also discuss a shape of the droplet. Due to self-propulsive motion and flow around the droplet, a spherical shape becomes unstable and it elongates perpendicular to the direction of motion. This fact would imply that the self-propulsion driven by chemical reaction is characterized as a pusher in terms of a flow field. 12:30-13:00 Lunch at Wolfson Court 14:00-14:30 Kevrekidis, IG (Princeton University) Data mining in swarming models Sem 1 14:30-16:00 Poster Session at INI 15:30-16:00 Afternoon Tea at INI 16:00-17:00 Free 19:30-22:00 Conference Dinner at Lucy Cavendish College