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Motivated by the sidewise motions of dynein motors shown in experiments, we use a variant of the exclusion process to model the multistep dynamics of dyneins on a cylinder with open ends. Due to the varied step sizes of the particles in a quasi-two-dimensional topology, we observe the emergence of a novel phase diagram depending on the various load conditions. Under high-load conditions, our numerical findings yield results similar to the TASEP model with the presence of all three standard TASEP phases, namely the low-density (LD), high-density (HD), and maximal-current (MC) phases. However, for medium- to low-load conditions, for all chosen influx and outflux rates, we only observe the LD and HD phases, and the maximal-current phase disappears. Further, we also measure the dynamics for a single dynein particle which is logarithmically slower than a TASEP particle with a shorter waiting time. Our results also confirm experimental observations of the dwell time distribution. The dwell time distribution for dyneins is exponential in less crowded conditions, whereas a double exponential emerges under overcrowded conditions.

We explore linear control of the one-dimensional non-linear Kardar--Parisi--Zhang (KPZ) equation with the goal to understand the effects the control process has on the dynamics and on the stationary state of the resulting stochastic growth kinetics. In linear control, the intrinsic non-linearity of the system is maintained at all times. In our protocol, the control is applied to only a small number $n_c$ of Fourier modes. The stationary-state roughness is obtained analytically in the small-$n_c$ regime with weak non-linear coupling wherein the controlled growth process is found to result in Edwards--Wilkinson dynamics. Furthermore, when the non-linear KPZ coupling is strong, we discern a regime where the controlled dynamics shows scaling in accordance to the KPZ universality class. We perform a detailed numerical analysis to investigate the controlled dynamics subject to weak as well as strong non-linearity. A first-order perturbation theory calculation supports the simulation results in the weak non-linear regime. For strong non-linearity, we find a temporal crossover between KPZ and dispersive growth regimes, with the crossover time scaling with the number $n_c$ of controlled Fourier modes. We observe that the height distribution is positively skewed, indicating that as a consequence of the linear control, the surface morphology displays fewer and smaller hills than in the uncontrolled growth process, and that the inherent size-dependent stationary-state roughness provides an upper limit for the roughness of the controlled system.

We discuss the use of Langevin molecular dynamics in the investigation of the non-equilibrium properties of disordered vortex matter. Our special focus is set on values of system parameters that are realistic for disordered high-$T_c$ superconductors such as YBCO. Using a discretized elastic line model, we study different aspects of vortices far from thermal equilibrium. On the one hand we investigate steady-state properties of driven magnetic flux lines in a disordered environment, namely the current-voltage characteristics, the gyration radius, and the pinning time statistics. On the other hand we study the complex relaxation processes and glassy-like dynamics that emerge in type-II superconductors due to the intricate competition between the long-range vortex-vortex repulsion and flux pinning due to randomly placed point defects. To this end we consider different types of sudden perturbations: temperature, magnetic field, and external current quenches., Comment: 15 pages, 7 figures, to appear in Molecular Simulation for a special issue on "Nonequilibrium Systems"

Vortex lines in type-II superconductors display complicated relaxation processes due to the intricate competition between their mutual repulsive interactions and pinning to attractive point or extended defects. We perform extensive Monte Carlo simulations for an interacting elastic line model with either point-like or columnar pinning centers. From measurements of the space- and time-dependent height-height correlation function for lateral flux line fluctuations, we extract a characteristic correlation length that we use to investigate different non-equilibrium relaxation regimes. The specific time dependence of this correlation length for different disorder configurations displays characteristic features that provide a novel diagnostic tool to distinguish between point-like pinning centers and extended columnar defects., Comment: 12 pages, 3 figures, version to appear in J. Stat. Mech

We study the effects of rapid temperature and magnetic field changes on the non-equilibrium relaxation dynamics of magnetic vortex lines in disordered type-II superconductors by employing an elastic line model and performing Langevin molecular dynamics simulations. In a previously equilibrated system, either the temperature is suddenly changed, or the magnetic field is instantaneously altered which is reflected in adding or removing flux lines to or from the system. The subsequent aging properties are investigated in samples with either randomly distributed point-like or extended columnar defects, which allows to distinguish the complex relaxation features that result from either type of pinning centers. One-time observables such as the radius of gyration and the fraction of pinned line elements are employed to characterize steady-state properties, and two-time correlation functions such as the vortex line height autocorrelations and their mean-square displacement are analyzed to study the non-linear stochastic relaxation dynamics in the aging regime., Comment: 17 pages, 14 figures, to appear in Phys. Rev. E (2015)

We study the pinning dynamics of magnetic flux (vortex) lines in a disordered type-II superconductor. Using numerical simulations of a directed elastic line model, we extract the pinning time distributions of vortex line segments. We compare different model implementations for the disorder in the surrounding medium: discrete, localized pinning potential wells that are either attractive and repulsive or purely attractive, and whose strengths are drawn from a Gaussian distribution; as well as continuous Gaussian random potential landscapes. We find that both schemes yield power law distributions in the pinned phase as predicted by extreme-event statistics, yet they differ significantly in their effective scaling exponents and their short-time behavior., Comment: 7 pages, 5 figures, to appear in Phys. Rev. E

We employ Monte Carlo simulations to investigate the non-equilibrium relaxation properties of the two- and three-dimensional Coulomb glass with different long-range repulsive interactions. Specifically, we explore the aging scaling laws in the two-time density autocorrelation function. We find that in the time window and parameter range accessible to us, the scaling exponents are not universal, depending on the filling fraction and temperature: As either the temperature decreases or the filling fraction deviates more from half-filling, the exponents reflect markedly slower relaxation kinetics. In comparison with a repulsive Coulomb potential, appropriate for impurity states in strongly disordered semiconductors, we observe that for logarithmic interactions, the soft pseudo-gap in the density of states is considerably broader, and the dependence of the scaling exponents on external parameters is much weaker. The latter situation is relevant for flux creep in the disorder-dominated Bose glass phase of type-II superconductors subject to columnar pinning centers., Comment: 11 pages, 11 figures, to appear in Phys. Rev. E (2014)

The universal critical behavior of the driven-dissipative non-equilibrium Bose-Einstein condensation transition is investigated employing the field-theoretical renormalization group method. Such criticality may be realized in broad ranges of driven open systems on the interface of quantum optics and many-body physics, from exciton-polariton condensates to cold atomic gases. The starting point is a noisy and dissipative Gross-Pitaevski equation corresponding to a complex valued Landau-Ginzburg functional, which captures the near critical non-equilibrium dynamics, and generalizes Model A for classical relaxational dynamics with non-conserved order parameter. We confirm and further develop the physical picture previously established by means of a functional renormalization group study of this system. Complementing this earlier numerical analysis, we analytically compute the static and dynamical critical exponents at the condensation transition to lowest non-trivial order in the dimensional epsilon expansion about the upper critical dimension d_c = 4, and establish the emergence of a novel universal scaling exponent associated with the non-equilibrium drive. We also discuss the corresponding situation for a conserved order parameter field, i.e., (sub-)diffusive Model B with complex coefficients., Comment: 17 pages, 6 figures, to appear in Phys. Rev. X (2014)

In contrast to the neutral population cycles of the deterministic mean-field Lotka--Volterra rate equations, including spatial structure and stochastic noise in models for predator-prey interactions yields complex spatio-temporal structures associated with long-lived erratic population oscillations. Environmental variability in the form of quenched spatial randomness in the predation rates results in more localized activity patches. Population fluctuations in rare favorable regions in turn cause a remarkable increase in the asymptotic densities of both predators and prey. Very intriguing features are found when variable interaction rates are affixed to individual particles rather than lattice sites. Stochastic dynamics with demographic variability in conjunction with inheritable predation efficiencies generate non-trivial time evolution for the predation rate distributions, yet with overall essentially neutral optimization., Comment: 28 pages, 10 figures, Proceedings paper of the STATPHYS 25 conference

Field theory tools are applied to analytically study fluctuation and correlation effects in spatially extended stochastic predator-prey systems. In the mean-field rate equation approximation, the classic Lotka-Volterra model is characterized by neutral cycles in phase space, describing undamped oscillations for both predator and prey populations. In contrast, Monte Carlo simulations for stochastic two-species predator-prey reaction systems on regular lattices display complex spatio-temporal structures associated with persistent erratic population oscillations. The Doi-Peliti path integral representation of the master equation for stochastic particle interaction models is utilized to arrive at a field theory action for spatial Lotka-Volterra models in the continuum limit. In the species coexistence phase, a perturbation expansion with respect to the nonlinear predation rate is employed to demonstrate that spatial degrees of freedom and stochastic noise induce instabilities toward structure formation, and to compute the fluctuation corrections for the oscillation frequency and diffusion coefficient. The drastic downward renormalization of the frequency and the enhanced diffusivity are in excellent qualitative agreement with Monte Carlo simulation data., Comment: 36 pages, 7 figures included, to appear in J. Phys. A: Math. Theor. 45 (2012)

We investigate the competing effects and relative importance of intrinsic demographic and environmental variability on the evolutionary dynamics of a stochastic two-species Lotka-Volterra model by means of Monte Carlo simulations on a two-dimensional lattice. Individuals are assigned inheritable predation efficiencies; quenched randomness in the spatially varying reaction rates serves as environmental noise. We find that environmental variability enhances the population densities of both predators and prey while demographic variability leads to essentially neutral optimization., Comment: 5 pages, 4 figures included; to appear in Phys. Rev. Lett. (2013)

We employ Monte Carlo simulations to study the non-equilibrium relaxation of driven Ising lattice gases in two dimensions. Whereas the temporal scaling of the density auto-correlation function in the non-equilibrium steady state does not allow a precise measurement of the critical exponents, these can be accurately determined from the aging scaling of the two-time auto-correlations and the order parameter evolution following a quench to the critical point. We obtain excellent agreement with renormalization group predictions based on the standard Langevin representation of driven Ising lattice gases., Comment: 5 pages, 4 figures included; to appear in Phys. Rev. Lett. (2012)

These notes provide a concise introduction to important applications of the renormalization group (RG) in statistical physics. After reviewing the scaling approach and Ginzburg-Landau theory for critical phenomena, Wilson's momentum shell RG method is presented, and the critical exponents for the scalar Phi^4 model are determined to first order in an eps expansion about d_c = 4. Subsequently, the technically more versatile field-theoretic formulation of the perturbational RG for static critical phenomena is described. It is explained how the emergence of scale invariance connects UV divergences to IR singularities, and the RG equation is employed to compute the critical exponents for the O(n)-symmetric Landau-Ginzburg-Wilson theory. The second part is devoted to field theory representations of non-linear stochastic dynamical systems, and the application of RG tools to critical dynamics. Dynamic critical phenomena in systems near equilibrium are efficiently captured through Langevin equations, and their mapping onto the Janssen-De Dominicis response functional, exemplified by the purely relaxational models with non-conserved (model A) / conserved order parameter (model B). The Langevin description and scaling exponents for isotropic ferromagnets (model J) and for driven diffusive non-equilibrium systems are also discussed. Finally, an outlook is presented to scale-invariant phenomena and non-equilibrium phase transitions in interacting particle systems. It is shown how the stochastic master equation associated with chemical reactions or population dynamics models can be mapped onto imaginary-time, non-Hermitian `quantum' mechanics. In the continuum limit, this Doi-Peliti Hamiltonian is represented through a coherent-state path integral, which allows an RG analysis of diffusion-limited annihilation processes and phase transitions from active to inactive, absorbing states., Comment: 28 pages; 49th Schladming Theoretical Physics Winter School lecture notes; to appear in Nucl. Phys. B Proc. Suppl. (2012)

We aim to clarify the relationship between interacting three-species models and the two-species Lotka-Volterra (LV) model. We utilize mean-field theory and Monte Carlo simulations on two-dimensional square lattices to explore the temporal evolution characteristics of two different interacting three-species predator-prey systems: (1) a cyclic rock-paper-scissors (RPS) model with conserved total particle number but strongly asymmetric reaction rates that lets the system evolve towards one corner of configuration space; (2) a hierarchical food chain where an additional intermediate species is inserted between the predator and prey in the LV model. For model variant (1), we demonstrate that the evolutionary properties of both minority species in the steady state of this stochastic spatial three-species corner RPS model are well approximated by the LV system, with its emerging characteristic features of localized population clustering, persistent oscillatory dynamics, correlated spatio-temporal patterns, and fitness enhancement through quenched spatial disorder in the predation rates. In contrast, we could not identify any regime where the hierarchical model (2) would reduce to the two-species LV system. In the presence of pair exchange processes, the system remains essentially well-mixed, and we generally find the Monte Carlo simulation results for the spatially extended model (2) to be consistent with the predictions from the corresponding mean-field rate equations. If spreading occurs only through nearest-neighbor hopping, small population clusters emerge; yet the requirement of an intermediate species cluster obviously disrupts spatio-temporal correlations between predator and prey, and correspondingly eliminates many of the intriguing fluctuation phenomena that characterize the stochastic spatial LV system., Comment: 13 pages, 4 figures; to appear in Eur. Phys. J. B (2012)

It is well-established that including spatial structure and stochastic noise in models for predator-prey interactions invalidates the classical deterministic Lotka-Volterra picture of neutral population cycles. In contrast, stochastic models yield long-lived, but ultimately decaying erratic population oscillations, which can be understood through a resonant amplification mechanism for density fluctuations. In Monte Carlo simulations of spatial stochastic predator-prey systems, one observes striking complex spatio-temporal structures. These spreading activity fronts induce persistent correlations between predators and prey. In the presence of local particle density restrictions (finite prey carrying capacity), there exists an extinction threshold for the predator population. The accompanying continuous non-equilibrium phase transition is governed by the directed-percolation universality class. We employ field-theoretic methods based on the Doi-Peliti representation of the master equation for stochastic particle interaction models to (i) map the ensuing action in the vicinity of the absorbing state phase transition to Reggeon field theory, and (ii) to quantitatively address fluctuation-induced renormalizations of the population oscillation frequency, damping, and diffusion coefficients in the species coexistence phase., Comment: 14 pages, 6 figures, submitted to J. Phys C: Conf. Ser. (2011)

We numerically investigate the long-time behavior of the density-density auto-correlation function in driven lattice gases with particle exclusion and periodic boundary conditions in one, two, and three dimensions using precise Monte Carlo simulations. In the one-dimensional asymmetric exclusion process on a ring with half the lattice sites occupied, we find that correlations induce extremely slow relaxation to the asymptotic power law decay. We compare the crossover functions obtained from our simulations with various analytic results in the literature, and analyze the characteristic oscillations that occur in finite systems away from half-filling. As expected, in three dimensions correlations are weak and consequently the mean-field description is adequate. We also investigate the relaxation towards the nonequilibrium steady state in the two-time density-density auto-correlations, starting from strongly correlated initial conditions. We obtain simple aging scaling behavior in one, two, and three dimensions, with the expected power laws., Comment: 12 pages, 18 figures; to appear in Phys. Rev. E (2011)

We employ Monte Carlo simulations to numerically study the temporal evolution and transient oscillations of the population densities, the associated frequency power spectra, and the spatial correlation functions in the (quasi-)steady state in two-dimensional stochastic May--Leonard models of mobile individuals, allowing for particle exchanges with nearest-neighbors and hopping onto empty sites. We therefore consider a class of four-state three-species cyclic predator-prey models whose total particle number is not conserved. We demonstrate that quenched disorder in either the reaction or in the mobility rates hardly impacts the dynamical evolution, the emergence and structure of spiral patterns, or the mean extinction time in this system. We also show that direct particle pair exchange processes promote the formation of regular spiral structures. Moreover, upon increasing the rates of mobility, we observe a remarkable change in the extinction properties in the May--Leonard system (for small system sizes): (1) As the mobility rate exceeds a threshold that separates a species coexistence (quasi-)steady state from an absorbing state, the mean extinction time as function of system size N crosses over from a functional form ~ e^{cN} / N (where c is a constant) to a linear dependence; (2) the measured histogram of extinction times displays a corresponding crossover from an (approximately) exponential to a Gaussian distribution. The latter results are found to hold true also when the mobility rates are randomly distributed., Comment: 9 pages, 4 figures; to appear in Eur. Phys. J. B (2011)

We study the influence of spatially varying reaction rates on a spatial stochastic two-species Lotka-Volterra lattice model for predator-prey interactions using two-dimensional Monte Carlo simulations. The effects of this quenched randomness on population densities, transient oscillations, spatial correlations, and invasion fronts are investigated. We find that spatial variability in the predation rate results in more localized activity patches, which in turn causes a remarkable increase in the asymptotic population densities of both predators and prey, and accelerated front propagation., Comment: 4 pages, 3 figures, to appear in Phys. Rev. Lett

Many complex systems are characterized by intriguing spatio-temporal structures. Their mathematical description relies on the analysis of appropriate correlation functions. Functional integral techniques provide a unifying formalism that facilitates the computation of such correlation functions and moments, and furthermore allows a systematic development of perturbation expansions and other useful approximative schemes. It is explained how nonlinear stochastic processes may be mapped onto exponential probability distributions, whose weights are determined by continuum field theory actions. Such mappings are madeexplicit for (1) stochastic interacting particle systems whose kinetics is defined through a microscopic master equation; and (2) nonlinear Langevin stochastic differential equations which provide a mesoscopic description wherein a separation of time scales between the relevant degrees of freedom and background statistical noise is assumed. Several well-studied examples are introduced to illustrate the general methodology., Comment: Article for the Encyclopedia of Complexity and System Science, B. Meyers (Ed.), Springer-Verlag Berlin, 2008

We investigate the asymptotic properties of the large deviation function of the integrated particle current in systems, in or out of thermal equilibrium, whose dynamics exhibits anomalous diffusion. The physical systems covered by our study include mutually repelling particles with a drift, a driven lattice gas displaying a continuous nonequilibrium phase transition, and particles diffusing in a anisotropic random advective field. It is exemplified how renormalisation group techniques allow for a systematic determination of power laws in the corresponding current large deviation functions. We show that the latter are governed by known universal scaling exponents, specifically, the anomalous dimension of the noise correlators., Comment: 21 pages, 3 figures. Minor modifications. Accepted in Journal of Physics A

We consider a broad class of stochastic lattice predator-prey models, whose main features are overviewed. In particular, this article aims at drawing a picture of the influence of spatial fluctuations, which are not accounted for by the deterministic rate equations, on the properties of the stochastic models. Here, we outline the robust scenario obeyed by most of the lattice predator-prey models with an interaction "a' la Lotka-Volterra". We also show how a drastically different behavior can emerge as the result of a subtle interplay between long-range interactions and a nearest-neighbor exchange process., Comment: 5 pages, 2 figures. Proceedings paper of the workshop "Stochastic models in biological sciences" (May 29 - June 2, 2006 in Warsaw) for the Banach Center Publications

We study the general properties of stochastic two-species models for predator-prey competition and coexistence with Lotka-Volterra type interactions defined on a $d$-dimensional lattice. Introducing spatial degrees of freedom and allowing for stochastic fluctuations generically invalidates the classical, deterministic mean-field picture. Already within mean-field theory, however, spatial constraints, modeling locally limited resources, lead to the emergence of a continuous active-to-absorbing state phase transition. Field-theoretic arguments, supported by Monte Carlo simulation results, indicate that this transition, which represents an extinction threshold for the predator population, is governed by the directed percolation universality class. In the active state, where predators and prey coexist, the classical center singularities with associated population cycles are replaced by either nodes or foci. In the vicinity of the stable nodes, the system is characterized by essentially stationary localized clusters of predators in a sea of prey. Near the stable foci, however, the stochastic lattice Lotka-Volterra system displays complex, correlated spatio-temporal patterns of competing activity fronts. Correspondingly, the population densities in our numerical simulations turn out to oscillate irregularly in time, with amplitudes that tend to zero in the thermodynamic limit. Yet in finite systems these oscillatory fluctuations are quite persistent, and their features are determined by the intrinsic interaction rates rather than the initial conditions. We emphasize the robustness of this scenario with respect to various model perturbations., Comment: 19 pages, 11 figures, 2-column revtex4 format. Minor modifications. Accepted in the Journal of Statistical Physics. Movies corresponding to Figures 2 and 3 are available at http://www.phys.vt.edu/~tauber/PredatorPrey/movies/

It is explained how field-theoretic methods and the dynamic renormalisation group (RG) can be applied to study the universal scaling properties of systems that either undergo a continuous phase transition or display generic scale invariance, both near and far from thermal equilibrium. Part 1 introduces the response functional field theory representation of (nonlinear) Langevin equations. The RG is employed to compute the scaling exponents for several universality classes governing the critical dynamics near second-order phase transitions in equilibrium. The effects of reversible mode-coupling terms, quenching from random initial conditions to the critical point, and violating the detailed balance constraints are briefly discussed. It is shown how the same formalism can be applied to nonequilibrium systems such as driven diffusive lattice gases. Part 2 describes how the master equation for stochastic particle reaction processes can be mapped onto a field theory action. The RG is then used to analyse simple diffusion-limited annihilation reactions as well as generic continuous transitions from active to inactive, absorbing states, which are characterised by the power laws of (critical) directed percolation. Certain other important universality classes are mentioned, and some open issues are listed., Comment: 54 pages, 9 figures, Lecture Notes for Luxembourg Summer School "Ageing and the Glass Transition", submitted to Springer Lecture Notes in Physics (www.springeronline/com/series/5304/)

Including spatial structure and stochastic noise invalidates the classical Lotka-Volterra picture of stable regular population cycles emerging in models for predator-prey interactions. Growth-limiting terms for the prey induce a continuous extinction threshold for the predator population whose critical properties are in the directed percolation universality class. Here, we discuss the robustness of this scenario by considering an ecologically inspired stochastic lattice predator-prey model variant where the predation process includes next-nearest-neighbor interactions. We find that the corresponding stochastic model reproduces the above scenario in dimensions 1< d \leq 4, in contrast with mean-field theory which predicts a first-order phase transition. However, the mean-field features are recovered upon allowing for nearest-neighbor particle exchange processes, provided these are sufficiently fast., Comment: 5 pages, 4 figures, 2-column revtex4 format. Emphasis on the lattice predator-prey model with next-nearest-neighbor interaction (Rapid Communication in PRE)

We review the application of field-theoretic renormalization group (RG) methods to the study of fluctuations in reaction-diffusion problems. We first investigate the physical origin of universality in these systems, before comparing RG methods to other available analytic techniques, including exact solutions and Smoluchowski-type approximations. Starting from the microscopic reaction-diffusion master equation, we then pedagogically detail the mapping to a field theory for the single-species reaction k A -> l A (l < k). We employ this particularly simple but non-trivial system to introduce the field-theoretic RG tools, including the diagrammatic perturbation expansion, renormalization, and Callan-Symanzik RG flow equation. We demonstrate how these techniques permit the calculation of universal quantities such as density decay exponents and amplitudes via perturbative eps = d_c - d expansions with respect to the upper critical dimension d_c. With these basics established, we then provide an overview of more sophisticated applications to multiple species reactions, disorder effects, L'evy flights, persistence problems, and the influence of spatial boundaries. We also analyze field-theoretic approaches to nonequilibrium phase transitions separating active from absorbing states. We focus particularly on the generic directed percolation universality class, as well as on the most prominent exception to this class: even-offspring branching and annihilating random walks. Finally, we summarize the state of the field and present our perspective on outstanding problems for the future., Comment: 10 figures included

We review the field theory approach to percolation processes. Specifically, we focus on the so-called simple and general epidemic processes that display continuous non-equilibrium active to absorbing state phase transitions whose asymptotic features are governed respectively by the directed (DP) and dynamic isotropic percolation (dIP) universality classes. We discuss the construction of a field theory representation for these Markovian stochastic processes based on fundamental phenomenological considerations, as well as from a specific microscopic reaction-diffusion model realization. Subsequently we explain how dynamic renormalization group (RG) methods can be applied to obtain the universal properties near the critical point in an expansion about the upper critical dimensions d_c = 4 (DP) and 6 (dIP). We provide a detailed overview of results for critical exponents, scaling functions, crossover phenomena, finite-size scaling, and also briefly comment on the influence of long-range spreading, the presence of a boundary, multispecies generalizations, coupling of the order parameter to other conserved modes, and quenched disorder., Comment: 54 pages, figures included

We demonstrate that the `microscopic' field theory representation, directly derived from the corresponding master equation, fails to adequately capture the continuous nonequilibrium phase transition of the Pair Contact Process with Diffusion (PCPD). The ensuing renormalization group (RG) flow equations do not allow for a stable fixed point in the parameter region that is accessible by the physical initial conditions. There exists a stable RG fixed point outside this regime, but the resulting scaling exponents, in conjunction with the predicted particle anticorrelations at the critical point, would be in contradiction with the positivity of the equal-time mean-square particle number fluctuations. We conclude that a more coarse-grained effective field theory approach is required to elucidate the critical properties of the PCPD., Comment: revtex, 8 pages, 1 figure included

Receptor-ligand binding is a critical first step in signal transduction and the duration of the interaction can impact signal generation. In mammalian cells, clustering of receptors may be facilitated by heterogeneous zones of lipids, known as lipid rafts. In vitro experiments show that disruption of rafts significantly alters the dissociation of fibroblast growth factor-2 (FGF-2) from heparan sulfate proteoglycans, co-receptors for FGF-2. In this paper, we develop a continuum stochastic formalism in order to (i) study how rebinding affects the dissociation of ligands from a planar substrate, and (ii) address the question of how receptor clustering influences ligand rebinding. We find that clusters reduce the effective dissociation rate dramatically when the clusters are dense and the overall surface density of receptors is low. The effect is much less pronounced in the case of high receptor density and shows non-monotonic behavior with time. These predictions are verified via lattice Monte Carlo simulations. Comparison with experimental results suggests that the theory does not capture the complete biological system. We speculate that additional co-operative mechanisms might be present in order to increase ligand retention, and present one possible ``internal diffusion'' model., Comment: Expanded text and added figures, revised version to appear in Biophys. J

Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such as surface plasmon resonance (SPR). We present experimental results using SPR for the interaction of insulin-like growth factor-I (IGF-I) with one of its binding proteins, IGF binding protein-3 (IGFBP-3), and show that rebinding, even with the addition of soluble heparin in the dissociation phase, does not exhibit the expected exponential decay characteristic of a 1:1 binding reaction. We thus consider the effect of (multiple) rebinding events and, within a self-consistent mean-field approximation, we derive the complete mathematical form for the fraction of bound ligand as a function of time. We show that, except for very low surface coverage/association rate, this function is non-exponential at all times, indicating that multiple rebinding events strongly influence dissociation even at early times. We compare the mean-field results with numerical simulations and find good agreement, although deviations are measurable in certain cases. Our analysis of the IGF-I-IGFBP-3 data indicates that rebinding is prominent for this system and that the theoretical predictions fit the experimental data well. Our results provide a means for analyzing SPR biosensor data where rebinding is problematic and a methodology to do so is presented., Comment: minor errors in notation corrected, added figure, appendix and glossary, 37 pages, to appear in Eur. Biophys. J

This paper, which was concerned with a field-theoretic analysis of the PCPD by means of the renormalization group, has been withdrawn by the authors. We had found a nontrivial RG fixed point, but could not exclude the possibility that it was outside the basin attraction of the RG flow initial conditions. A benevolent, yet careful and critical reader, H.K. Janssen, kindly provided us with an argument showing that our fixed point actually led to unphysical consequences: Given the critical exponents we computed, the fluctuations of the total number of particles would be negative at large times close to the critical point. This renders our contribution inconsistent and thus invalid. Hence we have decided to withdraw our paper from the archive. A consistent analytical description of the PCPD unfortunately remains a challenge., Comment: This paper has been withdrawn by the authors

We investigate the critical dynamics of the $n$-component relaxational models C and D which incorporate the coupling of a nonconserved and conserved order parameter S, respectively, to the conserved energy density rho, under nonequilibrium conditions by means of the dynamical renormalization group. Detailed balance violations can be implemented isotropically by allowing for different effective temperatures for the heat baths coupling to the slow modes. In the case of model D with conserved order parameter, the energy density fluctuations can be integrated out. For model C with scalar order parameter, in equilibrium governed by strong dynamic scaling (z_S = z_rho), we find no genuine nonequilibrium fixed point. The nonequilibrium critical dynamics of model C with n = 1 thus follows the behavior of other systems with nonconserved order parameter wherein detailed balance becomes effectively restored at the phase transition. For n >= 4, the energy density decouples from the order parameter. However, for n = 2 and n = 3, in the weak dynamic scaling regime (z_S <= z_rho) entire lines of genuine nonequilibrium model C fixed points emerge to one-loop order, which are characterized by continuously varying critical exponents. Similarly, the nonequilibrium model C with spatially anisotropic noise and n < 4 allows for continuously varying exponents, yet with strong dynamic scaling. Subjecting model D to anisotropic nonequilibrium perturbations leads to genuinely different critical behavior with softening only in subsectors of momentum space and correspondingly anisotropic scaling exponents. Similar to the two-temperature model B the effective theory at criticality can be cast into an equilibrium model D dynamics, albeit incorporating long-range interactions of the uniaxial dipolar type., Comment: Revtex, 23 pages, 5 eps figures included (minor additions), to appear in Phys. Rev. E

The binding of basic fibroblast growth factor (FGF-2) to its cell surface receptor (CSR) and subsequent signal transduction is known to be enhanced by Heparan Sulfate Proteoglycans (HSPGs). HSPGs bind FGF-2 with low affinity and likely impact CSR-mediated signaling via stabilization of FGF-2-CSR complexes via association with both the ligand and the receptor. What is unknown is whether HSPG associates with CSR in the absence of FGF-2. In this paper, we determine conditions by which pre-association would impact CSR-FGF-2-HSPG triad formation assuming diffusion-limited surface reactions. Using mean-field rate equations, we show that (i) when [HSPG] is much higher than [CSR], the presence of pre-formed complexes does not affect the steady state of FGF-2 binding, and (ii) when the concentrations are comparable, the presence of pre-formed complexes substantially increases the steady state concentration of FGF-2 bound to CSR. These findings are supported by explicit cellular automaton simulations, which justify the mean-field treatment. We discuss the advantages of such a two-receptor system compared to a single receptor model, when the parameters are comparable. Further, we speculate that the observed high concentration of HSPG in intact cells ([HSPG] ~ 100[CSR]) provides a way to ensure that the binding levels of FGF-2 to its signaling receptor remains high, irrespective of the presence of pre-formed CSR-HSPG complexes on the cell surface, while allowing the cell to finely tune the response to FGF-2 via down-regulation of the signaling receptor., Comment: 32 pages, 9 figures included, submitted to J. Theor. Biol

We study the coupled two-species non-equilibrium reaction-controlled diffusion model introduced by Trimper et al. [Phys. Rev. E 62, 6071 (2000)] by means of detailed Monte Carlo simulations in one and two dimensions. Particles of type A may independently hop to an adjacent lattice site provided it is occupied by at least one B particle. The B particle species undergoes diffusion-limited reactions. In an active state with nonzero, essentially homogeneous B particle saturation density, the A species displays normal diffusion. In an inactive, absorbing phase with exponentially decaying B density, the A particles become localized. In situations with algebraic decay rho_B(t) ~ t^{-alpha_B}, as occuring either at a non-equilibrium continuous phase transition separating active and absorbing states, or in a power-law inactive phase, the A particles propagate subdiffusively with mean-square displacement ~ t^{1-alpha_A}. We find that within the accuracy of our simulation data, \alpha_A = \alpha_B as predicted by a simple mean-field approach. This remains true even in the presence of strong spatio-temporal fluctuations of the B density. However, in contrast with the mean-field results, our data yield a distinctly non-Gaussian A particle displacement distribution n_A(x,t) that obeys dynamic scaling and looks remarkably similar for the different processes investigated here. Fluctuations of effective diffusion rates cause a marked enhancement of n_A(x,t) at low displacements |x|, indicating a considerable fraction of practically localized A particles, as well as at large traversed distances., Comment: Revtex, 19 pages, 27 eps figures included

We investigate the dynamics of interacting magnetic flux lines driven by an external current in the presence of linear pinning centers, arranged either in a periodic square lattice or placed randomly in space, by means of three-dimensional Monte Carlo simulations. Compared to the non-interacting case, the repulsive forces between the vortices reduce the critical current J_c, as determined from the depinning threshold in the current-voltage (I-V) characteristics. Near the depinning current J_c, the voltage power spectrum S(w) reveals broad-band noise, characterized by a $1/w^a$ power law decay with a <= 2. At larger currents the flux lines move with an average velocity v_{cm}. For a periodic arrangement of columnar pins with a lattice constant $d$ and just above J_c, distinct peaks appear in the voltage noise spectrum S(w) at w ~ v_{cm}/d which we interpret as the signature of stick-slip flux line motion., Comment: Latex, 10 pages, four eps figures included

Many systems that can be described in terms of diffusion-limited `chemical' reactions display non-equilibrium continuous transitions separating active from inactive, absorbing states, where stochastic fluctuations cease entirely. Their critical properties can be analyzed via a path-integral representation of the corresponding classical master equation, and the dynamical renormalization group. An overview over the ensuing universality classes in single-species processes is given, and generalizations to reactions with multiple particle species are discussed as well. The generic case is represented by the processes A <-> A + A, and A -> 0, which map onto Reggeon field theory with the critical exponents of directed percolation (DP). For branching and annihilating random walks (BARW) A -> (m+1) A and A + A -> 0, the mean-field rate equation predicts an active state only. Yet BARW with odd m display a DP transition for d <= 2. For even offspring number m, the particle number parity is conserved locally. Below d_c' = 4/3, this leads to the emergence of an inactive phase that is characterized by the power laws of the pair annihilation process. The critical exponents at the transition are those of the `parity-conserving' (PC) universality class. For local processes without memory, competing pair or triplet annihilation and fission reactions k A -> (k - l) A, k A -> (k+m)A with k=2,3 appear to yield the only other universality classes not described by mean-field theory. In these reactions, site occupation number restrictions play a crucial role., Comment: 16 pages, talk given at 2003 German Physical Society Spring Meeting; four figures and style files included

We consider diffusion-limited reactions A_i + A_j -> 0 (1 <= i < j <= q) in d space dimensions. For q > 2 and d >= 2 we argue that the asymptotic density decay for such mutual annihilation processes with equal rates and initial densities is the same as for single-species pair annihilation A + A -> 0. In d = 1, however, particle segregation occurs for all q < oo. The total density decays according to a $q$ dependent power law, rho(t) ~ t^{-\alpha(q)}. Within a simplified version of the model \alpha(q) = (q-1) / 2q can be determined exactly. Our findings are supported through Monte Carlo simulations., Comment: 4 pages, revtex; two figures included

Many non-equilibrium systems display dynamic phase transitions from active to absorbing states, where fluctuations cease entirely. Based on a field theory representation of the master equation, the critical behavior can be analyzed by means of the renormalization group. The resulting universality classes for single-species systems are reviewed here. Generically, the critical exponents are those of directed percolation (Reggeon field theory), with critical dimension d_c = 4. Yet local particle number parity conservation in even-offspring branching and annihilating random walks implies an inactive phase (emerging below d_c' = 4/3) that is characterized by the power laws of the pair annihilation reaction, and leads to different critical exponents at the transition. For local processes without memory, the pair contact process with diffusion represents the only other non-trivial universality class. The consistent treatment of restricted site occupations and quenched random reaction rates are important open issues., Comment: 9 pages, latex; talk presented at RG02; Proc. to appear in Acta Physica Slovaca (style files included)

We study, by means of three-dimensional Monte Carlo simulations, the current-voltage (IV) characteristics and the voltage noise spectrum at low temperatures of driven magnetic flux lines interacting with randomly placed point or columnar defects, as well as with periodically arranged linear pinning centers. Near the depinning current J_c, the voltage noise spectrum S(w) universally follows a 1/w^a power law. For currents J > J_c, distinct peaks appear in S(w) which are considerably more pronounced for extended as compared to point defects, and reflect the spatial distribution of the correlated pinning centers., Comment: 8 pages, latex, Elsevier style file and figures included

Second-order phase transitions in a non-equilibrium liquid-gas model with reversible mode couplings, i.e., model H for binary-fluid critical dynamics, are studied using dynamic field theory and the renormalization group. The system is driven out of equilibrium either by considering different values for the noise strengths in the Langevin equations describing the evolution of the dynamic variables (effectively placing these at different temperatures), or more generally by allowing for anisotropic noise strengths, i.e., by constraining the dynamics to be at different temperatures in d_par- and d_perp-dimensional subspaces, respectively. In the first, case, we find one infrared-stable and one unstable renormalization group fixed point. At the stable fixed point, detailed balance is dynamically restored, with the two noise strengths becoming asymptotically equal. The ensuing critical behavior is that of the standard equilibrium model H. At the novel unstable fixed point, the temperature ratio for the dynamic variables is renormalized to infinity, resulting in an effective decoupling between the two modes. We compute the critical exponents at this new fixed point to one-loop order. For model H with spatially anisotropic noise, we observe a critical softening only in the d_perp-dimensional sector in wave vector space with lower noise temperature. The ensuing effective two-temperature model H does not have any stable fixed point in any physical dimension, at least to one-loop order. We obtain formal expressions for the novel critical exponents in a double expansion about the upper critical dimension d_c = 4 - d_par and with respect to d_par, i.e., about the equilibrium theory., Comment: 17 pages, revtex, one figure and EPJB style files included

We present an overview of the effects of detailed-balance violating perturbations on the universal static and dynamic scaling behavior near a critical point. It is demonstrated that the standard critical dynamics universality classes are generally quite robust: In systems with non-conserved order parameter, detailed balance is effectively restored at criticality. This also holds for models with conserved order parameter, and isotropic non-equilibrium perturbations. Genuinely novel features are found only for models with conserved order parameter and spatially anisotropic noise correlations., Comment: 4 pages, revtex, no figures

We study the effect of generic spatial anisotropies on the scaling behavior in the Kardar-Parisi-Zhang equation. In contrast to its "conserved" variants, anisotropic perturbations are found to be relevant in d > 2 dimensions, leading to rich phenomena that include novel universality classes and the possibility of first-order phase transitions and multicritical behavior. These results question the presumed scaling universality in the strong-coupling rough phase, and shed further light on the connection with generalized driven diffusive systems., Comment: 4 pages, revtex, 2 figures (eps files enclosed)