Clustering of lipids driven by integrin.

Integrin is an important transmembrane receptor protein which remodels the actin network and anchors the cell membrane towards the extracellular matrix via mechanochemical pathways. The clustering of specific lipids and lipid-anchored proteins, which is essential for a certain type of endocytosis process, is facilitated at integrin-mediated active regions. To study this, we propose a minimal exactly solvable model which includes the interplay of stochastic shuttling between integrin on and off states with the intrinsic dynamics of the membrane. We propose a two-step mechanism in which the integrin induces an aster-like arrangement in the actin network, followed by clustering of lipids in that region. We obtain an analytic expression for the deformation and local membrane velocity, and thereby the evolution of clustering mediated by a single integrin. The deformation evolves nonmonotonically and its dependence on the stochastic shuttling timescales and membrane properties is elucidated. Our estimates of the area of the deformed region and the number of lipids in it indicate strong clustering.

Coarsening, condensates, and extremes in aggregation-fragmentation models.

We use extreme value statistics to study the dynamics of coarsening in aggregation-fragmentation models which form condensates in the steady state. The dynamics is dominated by the formation of local condensates on a coarsening length scale which grows in time in both the zero range process and conserved mass aggregation model. The local condensate mass distribution exhibits scaling, which implies anomalously large fluctuations, with mean and standard deviation both proportional to the coarsening length. Remarkably, the state of the system during coarsening is governed not by the steady state, but rather a preasymptotic state in which the condensate mass fluctuates strongly.

Active random walks in one and two dimensions.

We investigate active lattice walks: biased continuous time random walks which perform orientational diffusion between lattice directions in one and two spatial dimensions. We study the occupation probability of an arbitrary site on the lattice in one and two dimensions and derive exact results in the continuum limit. Next, we compute the large deviation free-energy function in both one and two dimensions, which we use to compute the moments and the cumulants of the displacements exactly at late times. Our exact results demonstrate that the cross-correlations between the motion in the x and y directions in two dimensions persist in the large deviation function. We also demonstrate that the large deviation function of an active particle with diffusion displays two regimes, with differing diffusive behaviors. We verify our analytic results with kinetic Monte Carlo simulations of an active lattice walker in one and two dimensions.

Phase transitions in XY models with randomly oriented crystal fields.

We obtain a representation of the free energy of an XY model on a fully connected graph with spins subjected to a random crystal field of strength D and with random orientation α. Results are obtained for an arbitrary probability distribution of the disorder using large deviation theory, for any D. We show that the critical temperature is insensitive to the nature and strength of the distribution p(α), for a large family of distributions which includes quadriperiodic distributions, with p(α)=p(α+π/2), which includes the uniform and symmetric bimodal distributions. The specific heat vanishes as temperature T→0 if D is infinite, but approaches a constant if D is finite. We also studied the effect of asymmetry on a bimodal distribution of the orientation of the random crystal field and obtained the phase diagram comprising four phases: a mixed phase (in which spins are canted at angles which depend on the degree of disorder), an x-Ising phase, a y-Ising phase, and a paramagnetic phase, all of which meet at a tetracritical point. The canted mixed phase is present for all finite D, but vanishes when D→∞.

Size-stretched exponential relaxation in a model with arrested states.

We study the effect of a rapid quench to zero temperature in a model with competing interactions, evolving through conserved spin dynamics. In a certain regime of model parameters, we find that the model belongs to the broader class of kinetically constrained models, however, the dynamics is different from that of a glass. The system shows stretched exponential relaxation with the unusual feature that the relaxation time diverges as a power of the system size. Explicitly, we find that the spatial correlation function decays as exp(-2r/sqrt[L]) as a function of spatial separation r in a system with L sites in the steady state, while the temporal autocorrelation function follows exp[-(t/τ_{L})^{1/2}], where t is the time and τ_{L} proportional to L. In the coarsening regime, after time t_{w}, there are two growing length scales, namely L(t_{w})∼t_{w}^{1/2} and R(t_{w})∼t_{w}^{1/4}; the spatial correlation function decays as exp[-r/R(t_{w})]. Interestingly, the stretched exponential form of the autocorrelation function of a single typical sample in the steady state differs markedly from that averaged over an ensemble of initial conditions resulting from different quenches; the latter shows a slow power-law decay at large times.

Interface growth driven by a single active particle.

We study pattern formation, fluctuations, and scaling induced by a growth-promoting active walker on an otherwise static interface. Active particles on an interface define a simple model for energy-consuming proteins embedded in the plasma membrane, responsible for membrane deformation and cell movement. In our model, the active particle overturns local valleys of the interface into hills, simulating growth, while itself sliding and seeking new valleys. In one dimension, this "overturn-slide-search" dynamics of the active particle causes it to move superdiffusively in the transverse direction while pulling the immobile interface upward. Using Monte Carlo simulations, we find an emerging tentlike mean profile developing with time, despite large fluctuations. The roughness of the interface follows scaling with the growth, dynamic, and roughness exponents, derived using simple arguments as ß=2/3, z=3/2, and α=1/2, respectively, implying a breakdown of the usual scaling law ß=α/z, due to very local growth of the interface. The transverse displacement of the puller on the interface scales as ∼t^{2/3} and the probability distribution of its displacement is bimodal, with an unusual linear cusp at the origin. Both the mean interface pattern and probability distribution display scaling. A puller on a static two-dimensional interface also displays aspects of scaling in the mean profile and probability distribution. We also show that a pusher on a fluctuating interface moves subdiffusively leading to a separation of timescale in pusher motion and interface response.

Dynamics of coupled modes for sliding particles on a fluctuating landscape.

The recently developed formalism of nonlinear fluctuating hydrodynamics (NLFH) has been instrumental in unraveling many new dynamical universality classes in coupled driven systems with multiple conserved quantities. In principle, this formalism requires knowledge of the exact expression of locally conserved current in terms of local density of the conserved components. However, for most nonequilibrium systems an exact expression is not available and it is important to know what happens to the predictions of NLFH in these cases. We address this question here in a system with coupled time evolution of sliding particles on a fluctuating energy landscape. In the disordered phase this system shows short-ranged correlations, the exact form of which is not known, and so the exact expression for current cannot be obtained. We use approximate expressions based on mean-field theory and corrections to it, to test the prediction of NLFH using numerical simulations. In this process we also discover important finite size effects and show how they affect the predictions of NLFH. We find that our system is rich enough to show a large variety of universality classes. From our analytics and simulations we have been able to find parameter values which lead to diffusive, Karder-Parisi-Zhang (KPZ), 5/3 Lévy, and modified KPZ universality classes. Interestingly, the scaling function in the modified KPZ case turns out to be close to the Prähofer-Spohn function, which is known to describe usual KPZ scaling. Our analytics also predict the golden mean and the 3/2 Lévy universality classes within our model but our simulations could not verify this, perhaps due to strong finite size effects.

Reversals in infinite-Prandtl-number Rayleigh-Bénard convection.

Using direct numerical simulations, we study the statistical properties of reversals in two-dimensional Rayleigh-Bénard convection for infinite Prandtl number. We find that the large-scale circulation reverses irregularly, with the waiting time between two consecutive genuine reversals exhibiting a Poisson distribution on long timescales, while the interval between successive crossings on short timescales shows a power-law distribution. We observe that the vertical velocities near the sidewall and at the center show different statistical properties. The velocity near the sidewall shows a longer autocorrelation and 1/f^{2} power spectrum for a wide range of frequencies, compared to shorter autocorrelation and a narrower scaling range for the velocity at the center. The probability distribution of the velocity near the sidewall is bimodal, indicating a reversing velocity field. We also find that the dominant Fourier modes capture the dynamics at the sidewall and at the center very well. Moreover, we show a signature of weak intermittency in the fluctuations of velocity near the sidewall by computing temporal structure functions.

Time evolution of intermittency in the passive slider problem.

How does a steady state with strong intermittency develop in time from an initial state which is statistically random? For passive sliders driven by various fluctuating surfaces, we show that the approach involves an indefinitely growing length scale which governs scaling properties. A simple model of sticky sliders suggests scaling forms for the time-dependent flatness and hyperflatness, both measures of intermittency and these are confirmed numerically for passive sliders driven by a Kardar-Parisi-Zhang surface. Aging properties are studied via a two-time flatness. We predict and verify numerically that the time-dependent flatness is, remarkably, a nonmonotonic function of time with different scaling forms at short and long times. The scaling description remains valid when clustering is more diffuse as for passive sliders evolving through Edwards-Wilkinson driving or under antiadvection, although exponents and scaling functions differ substantially.

Ordered phases in coupled nonequilibrium systems: Dynamic properties.

We study the dynamical properties of the ordered phases obtained in a coupled nonequilibrium system describing advection of two species of particles by a stochastically evolving landscape. The local dynamics of the landscape also gets affected by the particles. In a companion paper we have presented static properties of different phases that arise as the two-way coupling parameters are varied. In this paper we discuss the dynamics. We show that in the ordered phases macroscopic particle clusters move over an ergodic time scale growing exponentially with system size but the ordered landscape shows dynamics over a faster time scale growing as a power of system size. We present a scaling ansatz that describes several dynamical correlation functions of the landscape measured in steady state.

Ordered phases in coupled nonequilibrium systems: Static properties.

We study a coupled driven system in which two species of particles are advected by a fluctuating potential energy landscape. While the particles follow the potential gradient, each species affects the local shape of the landscape in different ways. As a result of this two-way coupling between the landscape and the particles, the system shows interesting new phases, characterized by different sorts of long-ranged order in the particles and in the landscape. In all these ordered phases, the two particle species phase separate completely from each other, but the underlying landscape may either show complete ordering, with macroscopic regions with distinct average slopes, or may show coexistence of ordered and disordered regions, depending on the differential nature of effect produced by the particle species on the landscape. We discuss several aspects of static properties of these phases in this paper, and we discuss the dynamics of these phases in the sequel.

Publisher's Note: Ordered phases in coupled nonequilibrium systems: Dynamic properties [Phys. Rev. E 96, 022128 (2017)].

This corrects the article DOI: 10.1103/PhysRevE.96.022128.

Coarsening and persistence in a one-dimensional system of orienting arrowheads: Domain-wall kinetics with A+B→0.

We demonstrate the large-scale effects of the interplay between shape and hard-core interactions in a system with left- and right-pointing arrowheads <> on a line, with reorientation dynamics. This interplay leads to the formation of two types of domain walls, >< (A) and <> (B). The correlation length in the equilibrium state diverges exponentially with increasing arrowhead density, with an ordered state of like orientations arising in the limit. In this high-density limit, the A domain walls diffuse, while the B walls are static. In time, the approach to the ordered state is described by a coarsening process governed by the kinetics of domain-wall annihilation A+B→0, quite different from the A+A→0 kinetics pertinent to the Glauber-Ising model. The survival probability of a finite set of walls is shown to decay exponentially with time, in contrast to the power-law decay known for A+A→0. In the thermodynamic limit with a finite density of walls, coarsening as a function of time t is studied by simulation. While the number of walls falls as t^{-1/2}, the fraction of persistent arrowheads decays as t^{-θ} where θ is close to 1/4, quite different from the Ising value. The global persistence too has θ=1/4, as follows from a heuristic argument. In a generalization where the B walls diffuse slowly, θ varies continuously, increasing with increasing diffusion constant.

Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae.

A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.

Large compact clusters and fast dynamics in coupled nonequilibrium systems.

We demonstrate particle clustering on macroscopic scales in a coupled nonequilibrium system where two species of particles are advected by a fluctuating landscape and modify the landscape in the process. The phase diagram generated by varying the particle-landscape coupling, valid for all particle densities and in both one and two dimensions, shows novel nonequilibrium phases. While particle species are completely phase separated, the landscape develops macroscopically ordered regions coexisting with a disordered region, resulting in coarsening and steady state dynamics on time scales which grow algebraically with size, not seen earlier in systems with pure domains.

Order-parameter scaling in fluctuation-dominated phase ordering.

In systems exhibiting fluctuation-dominated phase ordering, a single order parameter does not suffice to characterize the order, and it is necessary to monitor a larger set. For hard-core sliding particles on a fluctuating surface and the related coarse-grained depth (CD) models, this set comprises the long-wavelength Fourier components of the density profile, which capture the breakup and remerging of particle-rich regions. We study both static and dynamic scaling laws obeyed by the Fourier modes Q_{mL} and find that the mean value obeys the static scaling law 〈Q_{mL}〉∼L^{-ϕ}f(m/L) with ϕ≃2/3 and ϕ≃3/5 for Edwards-Wilkinson (EW) and Kardar-Parisi-Zhang (KPZ) surface evolution, respectively, and ϕ≃3/4 for the CD model. The full probability distribution P(Q_{mL}) exhibits scaling as well. Further, time-dependent correlation functions such as the steady-state autocorrelation and cross-correlations of order-parameter components are scaling functions of t/L^{z}, where L is the system size and z is the dynamic exponent, with z=2 for EW and z=3/2 for KPZ surface evolution. In addition we find that the CD model shows temporal intermittency, manifested in the dynamical structure functions of the density and the weak divergence of the flatness as the scaled time approaches 0.

Condensation and intermittency in an open-boundary aggregation-fragmentation model.

We study real space condensation in aggregation-fragmentation models where the total mass is not conserved, as in phenomena such as cloud formation and intracellular trafficking. We study the scaling properties of the system with influx and outflux of mass at the boundaries using numerical simulations, supplemented by analytical results in the absence of fragmentation. The system is found to undergo a phase transition to an unusual condensate phase, characterized by strong intermittency and giant fluctuations of the total mass. A related phase transition also occurs for biased movement of large masses, but with some crucial differences which we highlight.

Driven k-mers: correlations in space and time.

Steady-state properties of hard objects with exclusion interaction and a driven motion along a one-dimensional periodic lattice are investigated. The process is a generalization of the asymmetric simple exclusion process (ASEP) to particles of length k, and is called the k-ASEP. Here, we analyze both static and dynamic properties of the k-ASEP. Density correlations are found to display interesting features, such as pronounced oscillations in both space and time, as a consequence of the extended length of the particles. At long times, the density autocorrelation decays exponentially in time, except at a special k-dependent density when it decays as a power law. In the limit of large k at a finite density of occupied sites, the appropriately scaled system reduces to a nonequilibrium generalization of the Tonks gas describing the motion of hard rods along a continuous line. This allows us to obtain in a simple way the known two-particle distribution for the Tonks gas. For large but finite k, we also obtain the leading-order correction to the Tonks result.

Multispecies model with interconversion, chipping, and injection.

Motivated by the phenomenology of transport through the Golgi apparatus of cells, we study a multispecies model with boundary injection of one species of particle, interconversion between the different species of particle, and driven diffusive movement of particles through the system by chipping of a single particle from a site. The model is analyzed in one dimension using equations for particle currents. It is found that, depending on the rates of various processes and the asymmetry in the hopping, the system may exist either in a steady phase, in which the average mass at each site attains a time-independent value, or in a "growing" phase, in which the total mass grows indefinitely in time, even in a finite system. The growing phases have interesting spatial structure. In particular, we find phases in which some spatial regions of the system have a constant average mass, while other regions show unbounded growth.