Rheology in dense assemblies of spherocylinders: Frictional vs. frictionless.

Using molecular dynamics simulations, we study the steady shear flow of dense assemblies of anisotropic spherocylindrical particles of varying aspect ratios. Comparing frictionless and frictional particles we discuss the specific role of frictional inter-particle forces for the rheological properties of the system. In the frictional system we evidence a shear-thickening regime, similar to that for spherical particles. Furthermore, friction suppresses the alignment of the spherocylinders along the flow direction. Finally, the jamming density in frictional systems is rather insensitive to variations in aspect ratio, quite contrary to what is known from frictionless systems.

Linear rheology of reversibly cross-linked biopolymer networks.

We suggest a simple model for reversible cross-links, binding, and unbinding to/from a network of semiflexible polymers. The resulting frequency dependent response of the network to an applied shear is calculated via Brownian dynamics simulations. It is shown to be rather complex with the time scale of the linkers competing with the excitations of the network. If the lifetime of the linkers is the longest time scale, as is indeed the case in most biological networks, then a distinct low frequency peak of the loss modulus develops. The storage modulus shows a corresponding decay from its plateau value, which for irreversible cross-linkers extends all the way to the static limit. This additional relaxation mechanism can be controlled by the relative weight of reversible and irreversible linkers.

Transition from a Linear to a Harmonic Potential in Collective Dynamics of a Multifilament Actin Bundle.

Attractive depletion forces between rodlike particles in highly crowded environments have been shown through recent modeling and experimental approaches to induce different structural and dynamic signatures depending on relative orientation between rods. For example, it has been demonstrated that the axial attraction between two parallel rods yields a linear energy potential corresponding to a constant contractile force of 0.1 pN. Here, we extend pairwise, depletion-induced interactions to a multifilament level with actin bundles, and find contractile forces up to 3 pN. Forces generated due to bundle relaxation were not constant, but displayed a harmonic potential and decayed exponentially with a mean decay time of 3.4 s. Through an analytical model, we explain these different fundamental dynamics as an emergent, collective phenomenon stemming from the additive, pairwise interactions of filaments within a bundle.

Thermalized connectivity networks of jammed packings.

Jammed packings of repulsive elastic spheres have emerged as a rich model system within which the elastic properties of disordered glassy materials may be elucidated. Most of the work on these packings has focused on the case of vanishing temperature. Here, we explore the elastic properties of the associated connectivity network for finite temperatures, ignoring the breaking of bonds and the formation of new ones. Using extensive Monte Carlo simulations, we find that, as the temperature is increased, the resulting spring network shrinks and exhibits a rapidly softening bulk modulus via a cusp. Moreover, the shear modulus stiffens in a fixed volume ensemble but not in a fixed pressure ensemble. These counter-intuitive behaviors may be understood from the characteristic spectrum of soft modes near isostaticity, which resembles the spectrum of a rod near its buckling instability. Our results suggest a generic mechanism for negative thermal expansion coefficients in marginal solids. We discuss some consequences of bond breaking and an apparent analogy between thermalization and shear.

Free volume under shear.

Using an athermal quasistatic simulation protocol, we study the distribution of free volumes in sheared hard-particle packings close to, but below, the random-close packing threshold. We show that under shear, and independent of volume fraction, the free volumes develop features similar to close-packed systems - particles self-organize in a manner as to mimick the isotropically jammed state. We compare athermally sheared packings with thermalized packings and show that thermalization leads to an erasure of these structural features. The temporal evolution in particular the opening-up and the closing of free-volume patches is associated with the single-particle dynamics, showing a crossover from ballistic to diffusive behavior.

Impact of attractive interactions on the rheology of dense athermal particles.

Using numerical simulations, the rheological response of an athermal assembly of soft particles with tunable attractive interactions is studied in the vicinity of jamming. At small attractions, a fragile solid develops and a finite yield stress is measured. Moreover, the measured flow curves have unstable regimes, which lead to persistent shear banding. These features are rationalized by establishing a link between the rheology and the interparticle connectivity, which also provides a minimal model to describe the flow curves.

(Ir)reversibility in dense granular systems driven by oscillating forces.

We use computer simulations to study highly dense systems of granular particles that are driven by oscillating forces. We implement different dissipation mechanisms that are used to extract the injected energy. In particular, the action of a simple local Stokes' drag is compared with non-linear and history-dependent frictional forces that act either between particle pairs or between particles and an external container wall. The Stokes' drag leads to particle motion that is periodic with the driving force, even at high densities around close packing where particles undergo frequent collisions. With the introduction of inter-particle frictional forces this "interacting absorbing state" is destroyed and particles start to diffuse around. By reducing the density of the material we go through another transition to a "non-interacting" absorbing state, where particles independently follow the force-induced oscillations without collisions. In the system with particle-wall frictional interactions this transition has signs of a discontinuous phase transition. It is accompanied by a diverging relaxation time, but not by a vanishing order parameter, which rather jumps to zero at the transition.

Elasto-plastic response of reversibly crosslinked biopolymer bundles.

We study the response of F-actin bundles to driving forces through a simple analytical model. We consider two filaments connected by reversibly bound crosslinks and driven by an external force. Two failure modes under load can be defined. Brittle failure is observed when crosslinks suddenly and collectively unbind, leading to catastrophic loss of bundle integrity. During ductile failure, on the other hand, bundle integrity is maintained, however at the cost of crosslink reorganization and defect formation. We present phase diagrams for the onset of failure, highlighting the importance of the crosslink stiffness for these processes. Crossing the phase boundaries, force-deflection curves display (frequency-dependent) hysteresis loops, reflecting the first-order character of the failure processes. We evidence how the introduction of defects can lead to complex elasto-plastic relaxation processes, once the force is switched off. Depending on, both the time-scale for defect motion and the crosslink stiffness, bundles can remain in a quasi-permanent plastically deformed state for a very long time.

Melting a granular glass by cooling.

Driven granular systems readily form glassy phases at high particle volume fractions and low driving amplitudes. We use computer simulations of a driven granular glass to evidence a reentrance melting transition into a fluid state, which, contrary to intuition, occurs by reducing the amplitude of the driving. This transition is accompanied by anomalous particle dynamics and superdiffusive behavior on intermediate time scales. We highlight the special role played by frictional interactions, which help particles to escape their glassy cages. Such an effect is in striking contrast to what friction is expected to do: reduce particle mobility by making them stick.

Shear flow of non-Brownian suspensions close to jamming.

The dynamical mechanisms controlling the rheology of dense suspensions close to jamming are investigated numerically, using simplified models for the relevant dissipative forces. We show that the velocity fluctuations control the dissipation rate and therefore the effective viscosity of the suspension. These fluctuations are similar in quasi-static simulations and for finite strain rate calculations with various damping schemes. We conclude that the statistical properties of grain trajectories-in particular the critical exponent of velocity fluctuations with respect to volume fraction φ-only weakly depend on the dissipation mechanism. Rather they are determined by steric effects, which are the main driving forces in the quasistatic simulations. The critical exponent of the suspension viscosity with respect to φ can then be deduced, and is consistent with experimental data.

Cross-linked biopolymer bundles: cross-link reversibility leads to cooperative binding/unbinding phenomena.

We consider a biopolymer bundle consisting of filaments that are cross-linked together. The cross-links are reversible: they can dynamically bind and unbind adjacent filament pairs as controlled by a binding enthalpy. The bundle is subjected to a bending deformation and the corresponding distribution of cross-links is measured. For a bundle consisting of two filaments, upon increasing the bending amplitude, a first-order transition is observed. The transition is from a state where the filaments are tightly coupled by many bound cross-links, to a state of nearly independent filaments with only a few bound cross-links. For a bundle consisting of more than two filaments, a series of first-order transitions is observed. The transitions are connected with the formation of an interface between regions of low and high cross-link densities. Combining umbrella sampling Monte Carlo simulations with analytical calculations, we present a detailed picture of how the competition between cross-link shearing and filament stretching drives the transitions. We also find that, when the cross-links become soft, collective behavior is not observed: the cross-links then unbind one after the other leading to a smooth decrease of the average cross-link density.

Transiently crosslinked F-actin bundles.

F-actin bundles are prominent cytoskeletal structures in eukaryotes. They provide mechanical stability in stereocilia, microvilli, filopodia, stress fibers and the sperm acrosome. Bundles are typically stabilized by a wide range of specific crosslinking proteins, most of which exhibit off-rates on the order of 1s(-1). Yet F-actin bundles exhibit structural and mechanical integrity on time scales that are orders of magnitude longer. By applying large deformations to reconstituted F-actin bundles using optical tweezers, we provide direct evidence of their differential mechanical response in vitro: bundles exhibit fully reversible, elastic response on short time scales and irreversible, elasto-plastic response on time scales that are long compared to the characteristic crosslink dissociation time. Our measurements show a broad range of characteristic relaxation times for reconstituted F-actin bundles. This can be reconciled by considering that bundle relaxation behavior is also modulated by the number of filaments, crosslinking type and occupation number as well as the consideration of defects due to filament ends.

Theory of crosslinked bundles of helical filaments: intrinsic torques in self-limiting biopolymer assemblies.

Inspired by the complex influence of the globular crosslinking proteins on the formation of biofilament bundles in living organisms, we study and analyze a theoretical model for the structure and thermodynamics of bundles of helical filaments assembled in the presence of crosslinking molecules. The helical structure of filaments, a universal feature of biopolymers such as filamentous actin, is shown to generically frustrate the geometry of crosslinking between the "grooves" of two neighboring filaments. We develop a coarse-grained model to investigate the interplay between the geometry of binding and mechanics of both linker and filament distortion, and we show that crosslinking in parallel bundles of helical filaments generates intrinsic torques, of the type that tend to wind the bundle superhelically about its central axis. Crosslinking mediates a non-linear competition between the preference for bundle twist and the size-dependent mechanical cost of filament bending, which in turn gives rise to feedback between the global twist of self-assembled bundles and their lateral size. Finally, we demonstrate that above a critical density of bound crosslinkers, twisted bundles form with a thermodynamically preferred radius that, in turn, increases with a further increase in crosslinking bonds. We identify the stiffness of crosslinking bonds as a key parameter governing the sensitivity of bundle structure and assembly to the availability and affinity of crosslinkers.

Start-up shear of spherocylinder packings: Effect of friction.

We study the response to shear deformations of packings of long spherocylindrical particles that interact via frictional forces with friction coefficient µ. The packings are produced and deformed with the help of molecular dynamics simulations combined with minimization techniques performed on a GPU. We calculate the linear shear modulus g_{∞}, which is orders of magnitude larger than the modulus g_{0} in the corresponding frictionless system. The motion of the particles responsible for these large frictional forces is governed by and increases with the length ℓ of the spherocylinders. One consequence of this motion is that the shear modulus g_{∞} approaches a finite value in the limit ℓ→∞, even though the density of the packings vanishes, ρ∝ℓ^{-2}. By way of contrast, the frictionless modulus decreases to zero, g_{0}∼ℓ^{-2}, in accordance with the behavior of density. Increasing the strain beyond a value γ_{c}∼µ, the packing strain weakens from the large frictional to the smaller frictionless modulus when contacts saturate at the Coulomb inequality and start to slide. In this regime, sliding friction contributes a "yield stress" σ_{y}=g_{∞}γ_{c} and the stress behaves as σ=σ_{y}+g_{0}γ. The interplay between static and sliding friction gives rise to hysteresis in oscillatory shear simulations.

Packings of frictionless spherocylinders.

We present simulation results on the properties of packings of frictionless spherocylindrical particles. Starting from a random distribution of particles in space, a packing is produced by minimizing the potential energy of interparticle contacts until a force-equilibrated state is reached. For different particle aspect ratios α=10⋯40, we calculate contacts z, pressure as well as bulk and shear modulus. Most important is the fraction f_{0}(α) of spherocylinders with contacts at both ends, as it governs the jamming threshold z_{c}(α)=8+2f_{0}(α). These results highlight the important role of the axial "sliding" degree of freedom of a spherocylinder, which is a zero-energy mode but only if no end contacts are present.

Unsteady flow, clusters, and bands in a model shear-thickening fluid.

We analyze the flow curves of a two-dimensional assembly of granular particles which are interacting via frictional contact forces. For packing fractions slightly below jamming, the fluid undergoes a large scale instability, implying a range of stress and strain rates where no stationary flow can exist. Whereas small systems were shown previously to exhibit hysteretic jumps between the low and high stress branches, large systems exhibit continuous shear thickening arising from averaging unsteady, spatially heterogeneous flows. The observed large scale patterns as well as their dynamics are found to depend on strain rate: At the lower end of the unstable region, force chains merge to form giant bands that span the system in the compressional direction and propagate in the dilational direction. At the upper end, we observe large scale clusters which extend along the dilational direction and propagate along the compressional direction. Both patterns, bands and clusters, come in with infinite correlation length similar to the sudden onset of system-spanning plugs in impact experiments.

Cytoskeletal bundle mechanics.

The mechanical properties of cytoskeletal actin bundles play an essential role in numerous physiological processes, including hearing, fertilization, cell migration, and growth. Cells employ a multitude of actin-binding proteins to actively regulate bundle dimensions and cross-linking properties to suit biological function. The mechanical properties of actin bundles vary by orders of magnitude depending on diameter and length, cross-linking protein type and concentration, and constituent filament properties. Despite their importance to cell function, the molecular design principles responsible for this mechanical behavior remain unknown. Here, we examine the mechanics of cytoskeletal bundles using a molecular-based model that accounts for the discrete nature of constituent actin filaments and their distinct cross-linking proteins. A generic competition between filament stretching and cross-link shearing determines three markedly different regimes of mechanical response that are delineated by the relative values of two simple design parameters, revealing the universal nature of bundle-bending mechanics. In each regime, bundle-bending stiffness displays distinct scaling behavior with respect to bundle dimensions and molecular composition, as observed in reconstituted actin bundles in vitro. This mechanical behavior has direct implications on the physiological bending, buckling, and entropic stretching behavior of cytoskeletal processes, as well as reconstituted actin systems. Results are used to predict the bending regimes of various in vivo cytoskeletal bundles that are not easily accessible to experiment and to generate hypotheses regarding implications of the isolated behavior on in vivo bundle function.

Rheology of Membrane-Attached Minimal Actin Cortices.

The actin cortex is a thin cross-linked network attached to the plasma membrane, which is responsible for the cell's shape during migration, division, and growth. In a reductionist approach, we created a minimal actin cortex (MAC) attached to a lipid membrane to correlate the filamentous actin architecture with its viscoelastic properties. The system is composed of a supported 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine bilayer doped with the receptor lipid phosphatidylinositol(4,5)-bisphosphate (PtdIns(4,5)P2) to which a constitutively active mutant of ezrin, which is a direct membrane-cytoskeleton linker, is bound. The formation of the MAC on the supported lipid bilayer is analyzed as a function of increasing PtdIns(4,5)P2/ezrin pinning points, revealing an increase in the intersections between actin filaments, that is, the node density of the MAC. Bead tracking microrheology on the membrane-attached actin network provides information about its viscoelastic properties. The results show that ezrin serves as a dynamic cross-linker for the actin cortex attached to the lipid bilayer and that the stiffness of the network is influenced by the pinning point density, relating the plateau storage modulus G0 to the node density of the MAC.

Role of architecture in the elastic response of semiflexible polymer and fiber networks.

We study the elasticity of cross-linked networks of thermally fluctuating stiff polymers. As compared to their purely mechanical counterparts, it is shown that these thermal networks have a qualitatively different elastic response. By accounting for the entropic origin of the single-polymer elasticity, the networks acquire a strong susceptibility to polydispersity and structural randomness that is completely absent in athermal models. In extensive numerical studies we systematically vary the architecture of the networks and identify a wealth of phenomena that clearly show the strong dependence of the emergent macroscopic moduli on the underlying mesoscopic network structure. In particular, we highlight the importance of the polymer length, which to a large extent controls the elastic response of the network, surprisingly, even in parameter regions where it does not enter the macroscopic moduli explicitly. Understanding these subtle effects is only possible by going beyond the conventional approach that considers the response of typical polymer segments only. Instead, we propose to describe the elasticity in terms of a typical polymer filament and the spatial distribution of cross-links along its backbone. We provide theoretical scaling arguments to relate the observed macroscopic elasticity to the physical mechanisms on the microscopic and mesoscopic scales.

Nonaffine rubber elasticity for stiff polymer networks.

We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams, stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces ("stretching"). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic characterization of the deformation field in terms of "floppy modes"-low-energy bending excitations that retain a high degree of nonaffinity. The length scale characterizing the emergent nonaffinity is given by the "fiber length" lf, defined as the scale over which the polymers remain straight. The calculated scaling properties for the shear modulus are in excellent agreement with the results of recent simulations obtained in two-dimensional model networks. Furthermore, our theory can be applied to rationalize bulk rheological data in reconstituted actin networks.