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## Full-Text Articles in Physics

Generic Phases Of Cross-Linked Active Gels: Relaxation, Oscillation And Contractility, Shiladitya Banerjee, Tanniemola B. Liverpool, M. C. Marchetti

#### Generic Phases Of Cross-Linked Active Gels: Relaxation, Oscillation And Contractility, Shiladitya Banerjee, Tanniemola B. Liverpool, M. C. Marchetti

*Physics*

We study analytically and numerically a generic continuum model of an isotropic active solid with internal stresses generated by non-equilibrium `active' mechano-chemical reactions. Our analysis shows that the gel can be tuned through three classes of dynamical states by increasing motor activity: a constant unstrained state of homogeneous density, a state where the local density exhibits sustained oscillations, and a steady-state which is spontaneously contracted, with a uniform mean density.

Substrate Rigidity Deforms And Polarizes Active Gels, Shiladitya Banerjee, M. C. Marchetti

#### Substrate Rigidity Deforms And Polarizes Active Gels, Shiladitya Banerjee, M. C. Marchetti

*Physics*

We present a continuum model of the coupling between cells and substrate that accounts for some of the observed substrate-stiffness dependence of cell properties. The cell is modeled as an elastic active gel, adapting recently developed continuum theories of active viscoelastic fluids. The coupling to the substrate enters as a boundary condition that relates the cell's deformation field to local stress gradients. In the presence of activity, the coupling to the substrate yields spatially inhomogeneous contractile stresses and deformations in the cell and can enhance polarization, breaking the cell's front-rear symmetry.

Active Jamming: Self-Propelled Soft Particles At High Density, Silke Henkes, Yaouen Fily, M. Christina Marchetti

#### Active Jamming: Self-Propelled Soft Particles At High Density, Silke Henkes, Yaouen Fily, M. Christina Marchetti

*Physics*

We study numerically the phases and dynamics of a dense collection of self-propelled particles with soft repulsive interactions in two dimensions. The model is motivated by recent in vitro experiments on confluent monolayers of migratory epithelial and endothelial cells. The phase diagram exhibits a liquid phase with giant number fluctuations at low packing fraction and high self-propulsion speed and a jammed phase at high packing fraction and low self-propulsion speed. The dynamics of the jammed phase is controlled by the low frequency modes of the jammed packing.

Nonlinear Hydrodynamics Of Disentangled Flux-Line Liquids, Panayotis Benetatos, M. Cristina Marchetti

#### Nonlinear Hydrodynamics Of Disentangled Flux-Line Liquids, Panayotis Benetatos, M. Cristina Marchetti

*Physics*

In this paper we use non-Gaussian hydrodynamics to study the magnetic response of a flux-line liquid in the mixed state of a type-II superconductor. Both the derivation of our model, which goes beyond conventional Gaussian flux liquid hydrodynamics, and its relationship to other approaches used in the literature are discussed. We focus on the response to a transverse tilting field which is controlled by the tilt modulus, c44, of the flux array. We show that interaction effects can enhance c44 even in infinitely thick clean materials. This enhancement can be interpreted as the appearance of a disentangled flux-liquid fraction. In ...

Theory Of Double-Sided Flux Decorations, M. Cristina Marchetti, David R. Nelson

#### Theory Of Double-Sided Flux Decorations, M. Cristina Marchetti, David R. Nelson

*Physics*

A novel two-sided Bitter decoration technique was recently employed by Yao et al. to study the structure of the magnetic vortex array in high-temperature superconductors. Here we discuss the analysis of such experiments. We show that two-sided decorations can be used to infer {\it quantitative} information about the bulk properties of flux arrays, and discuss how a least squares analysis of the local density differences can be used to bring the two sides into registry. Information about the tilt, compressional and shear moduli of bulk vortex configurations can be extracted from these measurements.

Cooperative Self-Propulsion Of Active And Passive Rotors, Yaouen Fily, Aparna Baskaran, M. Cristina Marchetti

#### Cooperative Self-Propulsion Of Active And Passive Rotors, Yaouen Fily, Aparna Baskaran, M. Cristina Marchetti

*Physics*

Using minimal models for low Reynolds number passive and active rotors in a fluid, we characterize the hydrodynamic interactions among rotors and the resulting dynamics of a pair of interacting rotors. This allows us to treat in a common framework passive or externally driven rotors, such as magnetic colloids driven by a rotating magnetic field, and active or internally driven rotors, such as sperm cells confined at boundaries. The hydrodynamic interaction of passive rotors contains an azimuthal component 1/r2 to dipolar order that can yield the recently discovered “cooperative self-propulsion” of a pair of rotors of opposite vorticity. While ...

Motor-Driven Dynamics Of Cytoskeletal Filaments In Motility Assays, Shiladitya Banerjee, M. Cristina Marchetti, Kristian Muller-Nedebock

#### Motor-Driven Dynamics Of Cytoskeletal Filaments In Motility Assays, Shiladitya Banerjee, M. Cristina Marchetti, Kristian Muller-Nedebock

*Physics*

We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as linear springs and motor heads that bind to the filament. As in related models of rigid and soft two-state motors, the binding/unbinding dynamics of the motor heads and the dependence of the transition rates on the load exerted by the motor tails play a crucial role in controlling the filament's dynamics. Our work shows that the filament effectively ...

Polar Patterns In Active Fluids, Luca Giomi, M. Cristina Marchetti

#### Polar Patterns In Active Fluids, Luca Giomi, M. Cristina Marchetti

*Physics*

We study the spatio-temporal dynamics of a model of polar active fluid in two dimensions. The system exhibits a transition from an isotropic to a polarized state as a function of density. The uniform polarized state is, however, unstable above a critical value of activity. Upon increasing activity, the active fluids displays increasingly complex patterns, including traveling bands, traveling vortices and chaotic behavior. The advection arising from the particles self-propulsion and unique to polar fluids yields qualitatively new behavior as compared to that obtain in active nematic, yielding traveling-wave structures. We show that the nonlinear hydrodynamic equations can be mapped ...

Instabilities And Oscillations In Isotropic Active Gels, Shiladitya Banerjee, M. Cristina Marchetti

#### Instabilities And Oscillations In Isotropic Active Gels, Shiladitya Banerjee, M. Cristina Marchetti

*Physics*

We present a generic formulation of the continuum elasticity of an isotropic crosslinked active gel. The gel is described by a two-component model consisting of an elastic network coupled frictionally to a permeating fluid. Activity is induced by active crosslinkers that undergo an ATP-activated cycle and transmit forces to the network. The on/off dynamics of the active crosslinkers is described via rate equations for unbound and bound motors. For large activity motors yield a contractile instability of the network. At smaller values of activity, the on/off motor dynamics provides an effective inertial drag on the network that opposes ...

Fluctuations And Pattern Formation In Self-Propelled Particles, Shradha Mishra, Aparna Baskaran, M. Cristina Marchetti

#### Fluctuations And Pattern Formation In Self-Propelled Particles, Shradha Mishra, Aparna Baskaran, M. Cristina Marchetti

*Physics*

We consider a coarse-grained description of a system of self-propelled particles given by hydrodynamic equations for the density and polarization fields. We find that the ordered moving or flocking state of the system is unstable to spatial fluctuations beyond a threshold set by the self-propulsion velocity of the individual units. In this region, the system organizes itself into an inhomogeneous state of well-defined propagating stripes of flocking particles interspersed with low density disordered regions. Further, we find that even in the regime where the homogeneous flocking state is stable, the system exhibits large fluctuations in both density and orientational order ...

Nonequilibrium Statistical Mechanics Of Self-Propelled Hard Rods, Aparna Baskaran, M. Cristina Marchetti

#### Nonequilibrium Statistical Mechanics Of Self-Propelled Hard Rods, Aparna Baskaran, M. Cristina Marchetti

*Physics*

Using tools of nonequilibirum mechanics, we study a model of self-propelled hard rods on a substrate in two dimensions to quantify the interplay of self-propulsion and excluded-volume effects. We derive of a Smoluchowski equation for the configurational probability density of self-propelled rods that contains several modifications as compared to the familiar Smoluchowski equation for thermal rods. As a side-product of out work, we also present a purely dynamical derivation of the Onsager form of the mean field excluded volume interaction among thermal hard rods.

Sheared Active Fluids: Thickening, Thinning And Vanishing Viscosity, Luca Giomi, Tanniemola B. Liverpool, M. Cristina Marchetti

#### Sheared Active Fluids: Thickening, Thinning And Vanishing Viscosity, Luca Giomi, Tanniemola B. Liverpool, M. Cristina Marchetti

*Physics*

We analyze the behavior of a suspension of active polar particles under shear. In the absence of external forces, orientationally ordered active particles are known to exhibit a transition to a state of non-uniform polarization and spontaneous flow. Such a transition results from the interplay between elastic stresses, due to the liquid crystallinity of the suspension, and internal active stresses. In the presence of an external shear we find an extremely rich variety of phenomena, including an effective reduction (increase) in the apparent viscosity depending on the nature of the active stresses and the flow-alignment property of the particles, as ...

Mechanical Response Of Active Gels, Tanniemola B. Liverpool, M. Cristina Marchetti, J-F. Joanny, J. Prost

#### Mechanical Response Of Active Gels, Tanniemola B. Liverpool, M. Cristina Marchetti, J-F. Joanny, J. Prost

*Physics*

We study a model of an active gel of cross-linked semiflexible filaments with additional active linkers such as myosin II clusters. We show that the coupling of the elasticity of the semiflexible filaments to the mechanical properties of the motors leads to contractile behavior of the gel, in qualitative agreement with experimental observations. The motors, however, soften the zero frequency elastic constant of the gel. When the collective motor dynamics is incorporated in the model, a stiffening of the network at high frequencies is obtained. The frequency controlling the crossover between low and high frequency network elasticity is estimated in ...

Enhanced Diffusion And Ordering Of Self-Propelled Rods, Aparna Baskaran, M. Cristina Marchetti

#### Enhanced Diffusion And Ordering Of Self-Propelled Rods, Aparna Baskaran, M. Cristina Marchetti

*Physics*

Starting from a minimal physical model of self propelled hard rods on a substrate in two dimensions, we derive a modified Smoluchowski equation for the system. Self -propulsion enhances longitudinal diffusion and modifies the mean field excluded volume interaction. From the Smoluchowski equation we obtain hydrodynamic equations for rod concentration, polarization and nematic order parameter. New results at large scales are a lowering of the density of the isotropic-nematic transition and a strong enhancement of boundary effects in confined self-propelled systems.

Complex Spontaneous Flows And Concentration Banding In Active Polar Films, Luca Giomi, M. Cristina Marchetti, Tanniemola B. Liverpool

#### Complex Spontaneous Flows And Concentration Banding In Active Polar Films, Luca Giomi, M. Cristina Marchetti, Tanniemola B. Liverpool

*Physics*

We study the dynamical properties of active polar liquid crystalline films. Like active nematic films, active polar films undergo a dynamical transitions to spontaneously flowing steady-states. Spontaneous flow in polar fluids is, however, always accompanied by strong concentration inhomogeneities or "banding" not seen in nematics. In addition, a spectacular property unique to polar active films is their ability to generate spontaneously oscillating and banded flows even at low activity. The oscillatory flows become increasingly complicated for strong polarity.

Mode-Locking In Driven Disordered Systems As A Boundary-Value Problem, William Kung, M. Cristina Marchetti

#### Mode-Locking In Driven Disordered Systems As A Boundary-Value Problem, William Kung, M. Cristina Marchetti

*Physics*

We study mode-locking in disordered media as a boundary-value problem. Focusing on the simplest class of mode-locking models which consists of a single driven overdamped degree-of-freedom, we develop an analytical method to obtain the shape of the Arnol'd tongues in the regime of low ac-driving amplitude or high ac-driving frequency. The method is exact for a scalloped pinning potential and easily adapted to other pinning potentials. It is complementary to the analysis based on the well-known Shapiro's argument that holds in the perturbative regime of large driving amplitudes or low driving frequency, where the effect of pinning is ...

Poisson-Bracket Approach To The Dynamics Of Bent-Core Molecules, William Kung, M. Cristina Marchetti

#### Poisson-Bracket Approach To The Dynamics Of Bent-Core Molecules, William Kung, M. Cristina Marchetti

*Physics*

We generalize our previous work on the phase stability and hydrodynamic of polar liquid crystals possessing local uniaxial

C1v-symmetry to biaxial systems exhibiting local C2v -symmetry. Our work is motivated by the recently discovered examples of thermotropic biaxial nematic liquid crystals comprising bent-core mesogens, whose molecular structure is characterized by a non-polar body axis (n) as well as a polar axis (p) along the bisector of the bent mesogenic core which is coincident with a large, transverse dipole moment. The free energy for this system differs from that of biaxial nematic liquid crystals in that it contains terms violating the ...

Hydrodynamics Of Polar Liquid Crystals, William Kung, M. Cristina Marchetti, Karl Saunders

#### Hydrodynamics Of Polar Liquid Crystals, William Kung, M. Cristina Marchetti, Karl Saunders

*Physics*

Starting from a microscopic definition of an alignment vector proportional to the polarization, we discuss the hydrodynamics of polar liquid crystals with local

C1v-symmetry. The free energy for polar liquid crystals differs from that of nematic liquid crystals (D1h) in that it contains terms violating the n −n symmetry. First we show that these Z2-odd terms induce a general splay instability of a uniform polarized state in a range of parameters. Next we use the general Poissonbracket formalism to derive the hydrodynamic equations of the system in the polarized state. The structure of the linear hydrodynamic modes confirms the existence ...

Depinning In A Two-Layer Model Of Plastic Flow, Pierre Le Doussal, M. Cristina Marchetti, Kay Jorg Wiese

#### Depinning In A Two-Layer Model Of Plastic Flow, Pierre Le Doussal, M. Cristina Marchetti, Kay Jorg Wiese

*Physics*

We study a model of two layers, each consisting of a d-dimensional elastic object driven over a random substrate, and mutually interacting through a viscous coupling. For this model, the mean-field theory (i.e. a fully connected model) predicts a transition from elastic depinning to hysteretic plastic depinning as disorder or viscous coupling is increased. A functional RG analysis shows that any small inter-layer viscous coupling destablizes the standard (decoupled) elastic depinning FRG fixed point for d4 most aspects of the mean-field theory are recovered. A one-loop study at non-zero velocity indicates, for d

Mean Field Theory Of Collective Transport With Phase Slips, Karl Saunders, J. M. Schwarz, M. Cristina Marchetti, Alan Middleton

#### Mean Field Theory Of Collective Transport With Phase Slips, Karl Saunders, J. M. Schwarz, M. Cristina Marchetti, Alan Middleton

*Physics*

The driven transport of plastic systems in various disordered backgrounds is studied within mean field theory. Plasticity is modeled using non-convex interparticle potentials that allow for phase slips. This theory most naturally describes sliding charge density waves; other applications include flow of colloidal particles or driven magnetic flux vortices in disordered backgrounds. The phase diagrams exhibit generic phases and phase boundaries, though the shapes of the phase boundaries depend on the shape of the disorder potential. The phases are distinguished by their velocity and coherence: the moving phase generically has finite coherence, while pinned states can be coherent or incoherent ...

Nematic And Polar Order In Active Filament Solutions, A. Ahmadi, Tanniemola B. Liverpool, M. Cristina Marchetti

#### Nematic And Polar Order In Active Filament Solutions, A. Ahmadi, Tanniemola B. Liverpool, M. Cristina Marchetti

*Physics*

Using a microscopic model of interacting polar biofilaments and motor proteins, we characterize the phase diagram of both homogeneous and inhomogeneous states in terms of experimental parameters. The polarity of motor clusters is key in determining the organization of the filaments in homogeneous isotropic, polarized and nematic states, while motor-induced bundling yields spatially inhomogeneous structures.

Driven Depinning Of Strongly Disordered Media And Anisotropic Mean-Field Limits, M. Cristina Marchetti, Alan Middleton, Karl Saunders, J. M. Schwarz

#### Driven Depinning Of Strongly Disordered Media And Anisotropic Mean-Field Limits, M. Cristina Marchetti, Alan Middleton, Karl Saunders, J. M. Schwarz

*Physics*

Extended systems driven through strong disorder are modeled generically using coarse-grained degrees of freedom that interact elastically in the directions parallel to the driving force and that slip along at least one of the directions transverse to the motion. A realization of such a model is a collection of elastic channels with transverse viscous couplings. In the infinite range limit this model has a tricritical point separating a region where the depinning is continuous, in the universality class of elastic depinning, from a region where depinning is hysteretic. Many of the collective transport models discussed in the literature are special ...

Depinning And Plasticity Of Driven Disordered Lattices, M. Cristina Marchetti

#### Depinning And Plasticity Of Driven Disordered Lattices, M. Cristina Marchetti

*Physics*

We review in these notes the dynamics of extended condensed matter systesm, such as vortex lattices in type-II superconductors and charge density waves in anisotropic metals, driven over quenched disorder. We focus in particular on the case of strong disorder, where topological defects are generated in the driven lattice. In this case the repsonse is plastic and the depinning transition may become discontinuous and hysteretic.

Viscoelasticity From A Microscopic Model Of Dislocation Dynamics, M. Cristina Marchetti, Karl Saunders

#### Viscoelasticity From A Microscopic Model Of Dislocation Dynamics, M. Cristina Marchetti, Karl Saunders

*Physics*

It is shown that the dynamics of a two-dimensional crystal with a finite concentration of dislocations, as well as vacancy and interstitial defects, is governed by the hydrodynamic equations of a viscoelastic medium. At the longest length scales the viscoelasticity is described by the simplest Maxwell model, whose shear and compressional relaxation times are obtained in terms of microscopic quantities, including the density of free dislocations. At short length scales, bond orientational order effects become important and lead to wavevector dependent corrections to the relaxation times.

Hydrodynamics Of Self-Propelled Hard Rods, Aparna Baskaran, M. Cristina Marchetti

#### Hydrodynamics Of Self-Propelled Hard Rods, Aparna Baskaran, M. Cristina Marchetti

*Physics*

Motivated by recent simulations and by experiments on aggregation of gliding bacteria, we study a model of the collective dynamics of self-propelled hard rods on a substrate in two dimensions. The rods have finite size, interact via excluded volume and their dynamics is overdamped by the interaction with the substrate. Starting from a microscopic model with non-thermal noise sources, a continuum description of the system is derived. The hydrodynamic equations are then used to characterize the possible steady states of the systems and their stability as a function of the particles packing fraction and the speed of self propulsion.

A Hydrodynamic Approach To The Bose-Glass Transition, Panayotis Benetatos, M. Cristina Marchetti

#### A Hydrodynamic Approach To The Bose-Glass Transition, Panayotis Benetatos, M. Cristina Marchetti

*Physics*

Nonlinear hydrodynamics is used to evaluate disorder-induced corrections to the vortex liquid tilt modulus for finite screening length and arbitrary disorder geometry. Explicit results for aligned columnar defects yield a criterion for locating the Bose glass transition line at all fields.

Hydrodynamics Of Liquids Of Arbitrarily Curved Flux-Lines And Vortex Loops, Panayotis Benetatos, M. Cristina Marchetti

#### Hydrodynamics Of Liquids Of Arbitrarily Curved Flux-Lines And Vortex Loops, Panayotis Benetatos, M. Cristina Marchetti

*Physics*

We derive a hydrodynamic model for a liquid of arbitrarily curved flux-lines and vortex loops using the mapping of the vortex liquid onto a liquid of relativistic charged quantum bosons in 2+1 dimensions recently suggested by Tesanovic and by Sudbo and collaborators. The loops in the flux-line system correspond to particle-antiparticle fluctuations in the bosons. We explicitly incorporate the externally applied magnetic field which in the boson model corresponds to a chemical potential associated with the conserved charge density of the bosons. We propose this model as a convenient and physically appealing starting point for studying the properties of ...

Vortex Physics In Confined Geometries, M. Cristina Marchetti, David R. Nelson

#### Vortex Physics In Confined Geometries, M. Cristina Marchetti, David R. Nelson

*Physics*

Patterned irradiation of cuprate superconductors with columnar defects allows a new generation of experiments which can probe the properties of vortex liquids by forcing them to flow in confined geometries. Such experiments can be used to distinguish experimentally between continuous disorder-driven glass transitions of vortex matter, such as the vortex glass or the Bose glass transition, and nonequilibrium polymer-like glass transitions driven by interaction and entanglement. For continuous glass transitions, an analysis of such experiments that combines an inhomogeneous scaling theory with the hydrodynamic description of viscous flow of vortex liquids can be used to infer the critical behavior. After ...

Glassy Motion Of Elastic Manifolds, Valerii M. Vinokur, M. Cristina Marchetti, Lee-Wen Chen

#### Glassy Motion Of Elastic Manifolds, Valerii M. Vinokur, M. Cristina Marchetti, Lee-Wen Chen

*Physics*

We discuss the low-temperature dynamics of an elastic manifold driven through a random medium. For driving forces well below the

T = 0 depinning force, the medium advances via thermally activated hops over the energy barriers separating favorable metastable states. We show that the distribution of waiting times for these hopping processes scales as a power-law. This power-law distribution naturally yields a nonlinear glassy response for the driven medium, v exp(−const x F−μ).

Vortex Dynamics And Defects In Simulated Flux Flow, Michael Chance Faleski, M. Cristina Marchetti, Alan Middleton

#### Vortex Dynamics And Defects In Simulated Flux Flow, Michael Chance Faleski, M. Cristina Marchetti, Alan Middleton

*Physics*

We present the results of molecular dynamic simulations of a two-dimensional vortex array driven by a uniform current through random pinning centers at zero temperature. We identify two types of flow of the driven array near the depinning threshold. For weak disorder the flux array contains few dislocation and moves via correlated displacements of patches of vortices in a {\it crinkle} motion. As the disorder strength increases, we observe a crossover to a spatially inhomogeneous regime of {\it plastic} flow, with a very defective vortex array and a channel-like structure of the flowing regions. The two regimes are characterized by ...