arXiv subjects

David Mukamel

Publications and source records attributed to David Mukamel.

At least 55 records · Page 3Linked to original sources

arXiv2011

Diffusion in a logarithmic potential: scaling and selection in the approach to equilibrium

The equation which describes a particle diffusing in a logarithmic potential arises in diverse physical problems such as momentum diffusion of atoms in optical traps, condensation processes, and denaturation of DNA molecules. A detailed study of the approach of such systems to equilibrium via a scaling analysis is carried out, revealing three surprising features: (i) the solution is given by two distinct scaling forms, corresponding to a diffusive (x ~ \sqrt{t}) and a subdiffusive (x >> \sqrt{t}) length scales, respectively; (ii) the scaling exponents and scaling functions corresponding to both regimes are selected by the initial condition; and (iii) this dependence on the initial condition manifests a "phase transition" from a regime in which the scaling solution depends on the initial condition to a regime in which it is independent of it. The selection mechanism which is found has many similarities to the marginal stability mechanism which has been widely studied in the context of fronts propagating into unstable states. The general scaling forms are presented and their practical and theoretical applications are discussed.

cond-mat.stat-mech↗

arXiv2011

Approach to equilibrium of diffusion in a logarithmic potential

The late-time distribution function P(x,t) of a particle diffusing in a one-dimensional logarithmic potential is calculated for arbitrary initial conditions. We find a scaling solution with three surprising features: (i) the solution is given by two distinct scaling forms, corresponding to a diffusive (x ~ t^(1/2)) and a subdiffusive (x ~ t^γ with a given γ < 1/2) length scale, respectively, (ii) the overall scaling function is selected by the initial condition, and (iii) depending on the tail of the initial condition, the scaling exponent which characterizes the scaling function is found to exhibit a transition from a continuously varying to a fixed value.

cond-mat.stat-mech↗

arXiv2011

Denaturation of Circular DNA: Supercoil Mechanism

The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double stranded helix, released by a loop denaturation, is absorbed by \emph{supercoils}. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent $c$. However the first order transition displayed by the PS model for $c>2$ in linear DNA is replaced by a continuous transition with arbitrarily high order as $c$ approaches 2, while the second-order transition found in the linear case in the regime $1<c\le2$ disappears. In addition, our analysis reveals that melting under fixed linking number is a \emph{condensation transition}, where the condensate is a macroscopic loop which appears above the critical temperature.

cond-mat.stat-mech↗

arXiv2011

Phase diagram of the ABC model with nonequal densities

The ABC model is a driven diffusive exclusion model, composed of three species of particles that hop on a ring with local asymmetric rates. In the weak asymmetry limit, where the asymmetry vanishes with the length of the system, the model exhibits a phase transition between a homogenous state and a phase separated state. We derive the exact solution for the density profiles of the three species in the hydrodynamic limit for arbitrary average densities. The solution yields the complete phase diagram of the model and allows the study of the nature of the first order phase transition found for average densities that deviate significantly from the equal densities point.

cond-mat.stat-mech↗

arXiv2011

Long-range steady state density profiles induced by localized drive

We show that the presence of a localized drive in an otherwise diffusive system results in steady-state density and current profiles that decay algebraically to their global average value, away from the drive in two or higher dimensions. An analogy to an electrostatic problem is established, whereby the density profile induced by a driving bond maps onto the electrostatic potential due to an electric dipole located along the bond. The dipole strength is proportional to the drive, and is determined self-consistently by solving the electrostatic problem. The profile resulting from a localized configuration of more than one driving bond can be straightforwardly determined by the superposition principle of electrostatics. This picture is shown to hold even in the presence of exclusion interaction between particles.

cond-mat.stat-mech↗

arXiv2011

Quasistationarity in a model of classical spins with long-range interactions

Systems with long-range interactions, while relaxing towards equilibrium, sometimes get trapped in long-lived non-Boltzmann quasistationary states (QSS) which have lifetimes that grow algebraically with the system size. Such states have been observed in models of globally coupled particles that move under Hamiltonian dynamics either on a unit circle or on a unit spherical surface. Here, we address the ubiquity of QSS in long-range systems by considering a different dynamical setting. Thus, we consider an anisotropic Heisenberg model consisting of classical Heisenberg spins with mean-field interactions and evolving under classical spin dynamics. Our analysis of the corresponding Vlasov equation for time evolution of the phase space distribution shows that in a certain energy interval, relaxation of a class of initial states occurs over a timescale which grows algebraically with the system size. We support these findings by extensive numerical simulations. This work further supports the generality of occurrence of QSS in long-range systems evolving under Hamiltonian dynamics.

cond-mat.stat-mech↗

arXiv2010

Thermodynamics and dynamics of systems with long-range interactions

Thermodynamic and dynamical properties of systems with long-range pairwise interactions (LRI), which decay as $1/r^{d+σ}$ at large distances $r$ in $d$ dimensions, are reviewed. Two broad classes of such systems are discussed. (i) Systems with a slow decay of the interactions, termed "strong" LRI, where the energy is super-extensive. These systems are characterized by unusual properties such as inequivalence of ensembles, negative specific heat, slow decay of correlations, anomalous diffusion and ergodicity breaking. (ii) Systems with faster decay of the interaction potential, where the energy is additive, thus resulting in less dramatic effects. These interactions affect the thermodynamic behavior of systems near phase transitions, where long-range correlations are naturally present. Long-range correlations are often present in systems driven out of equilibrium when the dynamics involves conserved quantities. Steady state properties of driven systems with local dynamics are considered within the framework outlined above.

cond-mat.stat-mech↗

arXiv2010

Relaxation dynamics of stochastic long-range interacting systems

Long-range interacting systems, while relaxing towards equilibrium, may get trapped in nonequilibrium quasistationary states (QSS) for a time which diverges algebraically with the system size. These intriguing non-Boltzmann states have been observed under deterministic Hamiltonian evolution of a paradigmatic system, the Hamiltonian Mean-Field (HMF) model. We study here the robustness of QSS with respect to stochastic processes beyond deterministic dynamics within a microcanonical ensemble. To this end, we generalize the HMF model by allowing for stochastic three-particle collision dynamics in addition to the deterministic ones. By analyzing the resulting Boltzmann equation for the phase space density, we demonstrate that in the presence of stochasticity, QSS occur only as a crossover phenomenon over a finite time determined by the strength of the stochastic process. In particular, we argue that the relaxation time to equilibrium does not scale algebraically with the system size. We propose a scaling form for the relaxation time which is in very good agreement with results of extensive numerical simulations. The broader validity of these results is tested on a different stochastic HMF model involving microcanonical Monte Carlo dynamical moves.

cond-mat.stat-mech↗

arXiv2010

Slow relaxation in long-range interacting systems with stochastic dynamics

Quasistationary states are long-lived nonequilibrium states, observed in some systems with long-range interactions under deterministic Hamiltonian evolution. These intriguing non-Boltzmann states relax to equilibrium over times which diverge algebraically with the system size. To test the robustness of this phenomenon to non-deterministic dynamical processes, we have generalized the paradigmatic model exhibiting such a behavior, the Hamiltonian Mean-Field model, to include energy-conserving stochastic processes. Analysis, based on the Boltzmann equation, a scaling approach and numerical studies, demonstrates that in the long time limit, the system relaxes to the equilibrium state on timescales which do not diverge algebraically with the system size. Thus, quasistationarity takes place only as a crossover phenomenon on times determined by the strength of the stochastic process.

cond-mat.stat-mech↗

arXiv2010

Statistical mechanics of collisionless relaxation in a noninteracting system

We introduce a model of uncoupled pendula, which mimics the dynamical behavior of the Hamiltonian Mean Field (HMF) model. This model has become a paradigm for long-range interactions, like Coulomb or dipolar forces. As in the HMF model, this simplified integrable model is found to obey the Vlasov equation and to exhibit Quasi Stationary States (QSS), which arise after a "collisionless" relaxation process. Both the magnetization and the single particle distribution function in these QSS can be predicted using Lynden-Bell's theory. The existence of an extra conserved quantity for this model, the energy distribution function, allows us to understand the origin of some discrepancies of the theory with numerical experiments. It also suggests us an improvement of Lynden-Bell's theory, which we fully implement for the zero field case.

cond-mat.stat-mech↗

arXiv2010

Epidemic spreading in evolving networks

A model for epidemic spreading on rewiring networks is introduced and analyzed for the case of scale free steady state networks. It is found that contrary to what one would have naively expected, the rewiring process typically tends to suppress epidemic spreading. In particular it is found that as in static networks, rewiring networks with degree distribution exponent $γ>3$ exhibit a threshold in the infection rate below which epidemics die out in the steady state. However the threshold is higher in the rewiring case. For $2<γ\leq 3$ no such threshold exists, but for small infection rate the steady state density of infected nodes (prevalence) is smaller for rewiring networks.

physics.soc-ph↗

arXiv2009

Robustness of spontaneous symmetry breaking in a bridge model

A simple two-species asymmetric exclusion model in one dimension with bulk and boundary exchanges of particles is investigated for the existence of spontaneous symmetry breaking. The model is a generalization of the bridge model for which earlier studies have confirmed the existence of symmetry-broken phases, and the motivation here is to check the robustness of the observed symmetry breaking with respect to additional dynamical moves, in particular, the boundary exchange of the two species of particles. Our analysis, based on general considerations, mean-field approximation and numerical simulations, shows that the symmetry breaking in the bridge model is sustained for a range of values of the boundary exchange rate. Moreover, the mechanism through which symmetry is broken is similar to that in the bridge model. Our analysis allows us to plot the complete phase diagram of the model, demarcating regions of symmetric and symmetry-broken phases.

cond-mat.stat-mech↗

arXiv2009

Condensation in Temporally Correlated Zero-Range Dynamics

Condensation phenomena in non-equilibrium systems have been modeled by the zero-range process, which is a model of particles hopping between boxes with Markovian dynamics. In many cases, memory effects in the dynamics cannot be neglected. In an attempt to understand the possible impact of temporal correlations on the condensate, we introduce and study a process with non-Markovian zero-range dynamics. We find that memory effects have significant impact on the condensation scenario. Specifically, two main results are found: (1) In mean-field dynamics, the steady state corresponds to that of a Markovian ZRP, but with modified hopping rates which can affect condensation, and (2) for nearest-neighbor hopping in one dimension, the condensate occupies two adjacent sites on the lattice and drifts with a finite velocity. The validity of these results in a more general context is discussed.

cond-mat.stat-mech↗

arXiv2009

Notes on the Statistical Mechanics of Systems with Long-Range Interactions

Thermodynamic and dynamical properties of systems with long range pairwise interactions (LRI) which decay as 1/r^{d+σ} at large distances r in $d$ dimensions are reviewed in these Notes. Two broad classes of such systems are identified: (a) systems with a slow decay of the interactions, termed "strong" LRI, where the energy is super-extensive. These systems are characterized by unusual properties such as inequivalence of ensembles, negative specific heat, slow decay of correlations and ergodicity breaking. And (b) systems with faster decay of the interaction potential where the energy is additive, thus resulting in less dramatic effects. These interaction affect the thermodynamic behavior of systems near phase transitions, where long range correlations are naturally present. Long range correlations are often present in systems driven out of equilibrium when the dynamics involves conserved quantities. Steady state properties of driven systems are considered within the framework outlined above.

cond-mat.stat-mech↗

arXiv2008

Statistical Mechanics of systems with long range interactions

Recent theoretical studies of statistical mechanical properties of systems with long range interactions are briefly reviewed. In these systems the interaction potential decays with a rate slower than 1/r^d at large distances r in d dimensions. As a result, these systems are non-additive and they display unusual thermodynamic and dynamical properties which are not present in systems with short range interactions. In particular, the various statistical mechanical ensembles are not equivalent and the microcanonical specific heat may be negative. Long range interactions may also result in breaking of ergodicity, making the maximal entropy state inaccessible from some regions of phase space. In addition, in many cases long range interactions result in slow relaxation processes, with time scales which diverge in the thermodynamic limit. Various models which have been found to exhibit these features are discussed.

cond-mat.stat-mech↗

arXiv2008

Spontaneous symmetry breaking in a bridge model fed by junctions

We introduce a class of 1D models mimicking a single-lane bridge with two junctions and two particle species driven in opposite directions. The model exhibits spontaneous symmetry breaking (SSB) for a range of injection/extraction rates. In this phase the steady state currents of the two species are not equal. Moreover there is a co-existence region in which the symmetry broken phase co-exists with a symmetric phase. Along a path in which the extraction rate is varied, keeping the injection rate fixed and large, hysteresis takes place. The mean field phase diagram is calculated and supporting Monte-Carlo simulations are presented. One of the transition lines exhibits a kink, a feature which cannot exist in transition lines of equilibrium phase transitions.

cond-mat.stat-mech↗

arXiv2008

A possible mechanism for self coordination of bi-directional traffic across nuclear pores

Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bi-directional traffic occurring in a narrow channel can easily lead to jamming. How then is passage between the nucleus and cytoplasm maintained under the varying conditions that arise during the lifetime of the cell? Here, we address this question using computer simulations in which the behaviour of the ensemble of transporting cargoes is analyzed under different conditions. We suggest that traffic can exist in two distinct modes, depending on concentration of cargoes and dissociation rates of the transport receptor-cargo complexes from the pores. In one mode, which prevails when dissociation is quick and cargo concentration is low, transport in either direction proceeds uninterrupted by the other direction. The result is that overall-traffic-direction fluctuates rapidly and unsystematically between import and export. Remarkably, when cargo concentrations are high and dissociation is slow, another mode takes over in which traffic proceeds in one direction for a certain extent of time, after which it flips direction for another period. The switch between this, more regulated, mode of transport and the other, quickly fluctuating state, does not require an active gating mechanism but rather occurs spontaneously through the dynamics of the transported particles themselves. The determining factor for the behaviour of traffic is found to be the exit rate from the pore channel, which is directly related to the activity of the Ran system that controls the loading and release of cargo in the appropriate cellular compartment.

physics.bio-ph↗

arXiv2008

Dynamics of DNA Melting

The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time asymptotic behavior of the autocorrelation function is expressed in terms of the entropy exponent, c, of a loop. The validity of the scaling argument is tested using a microscopic model of an isolated loop and a toy model of interacting loops. This suggests a method for measuring the entropy exponent using single-molecule experiments such as florescence correlation spectroscopy.

cond-mat.stat-mech↗