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ORBi

Buffering variability in cell regulation motifs close to criticality Proverbio, Daniele ; Noronha Montanari, Arthur ; Skupin, Alexander et al in Physical Review. E. (2022) Bistable biological regulatory systems need to cope with stochastic noise to fine tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to ... [more ▼] Bistable biological regulatory systems need to cope with stochastic noise to fine tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative interactions buffer system variability, hampering noise-induced regime shifts. Our analysis also shows that, in the considered cooperativity range, impending regime shifts can be generically detected by statistical early warning signals from distributional data. Our generic framework, based on minimal models, can be used to extract robustness and variability properties of more complex models and empirical data close to criticality. Our generic framework, based on minimal models, can be used to extract robustness and variability properties of more complex models and empirical data close to criticality. [less ▲] Detailed reference viewed: 49 (1 UL)Statistical mechanics of active Ornstein-Uhlenbeck particles ; ; et al in Physical Review. E. (2021) We study the statistical properties of active Ornstein-Uhlenbeck particles (AOUPs). In this simplest of models, the Gaussian white noise of overdamped Brownian colloids is replaced by a Gaussian colored ... [more ▼] We study the statistical properties of active Ornstein-Uhlenbeck particles (AOUPs). In this simplest of models, the Gaussian white noise of overdamped Brownian colloids is replaced by a Gaussian colored noise. This suffices to grant this system the hallmark properties of active matter, while still allowing for analytical progress. We study in detail the steady-state distribution of AOUPs in the small persistence time limit and for spatially varying activity. At the collective level, we show AOUPs to experience motility-induced phase separation both in the presence of pairwise forces or due to quorum-sensing interactions. We characterize both the instability mechanism leading to phase separation and the resulting phase coexistence. We probe how, in the stationary state, AOUPs depart from their thermal equilibrium limit by investigating the emergence of ratchet currents and entropy production. In the small persistence time limit, we show how fluctuation-dissipation relations are recovered. Finally, we discuss how the emerging properties of AOUPs can be characterized from the dynamics of their collective modes. [less ▲] Detailed reference viewed: 38 (6 UL)Collective motion in large deviations of active particles ; Fodor, Etienne ; et al in Physical Review. E. (2021) We analyze collective motion that occurs during rare (large deviation) events in systems of active particles, both numerically and analytically. We discuss the associated dynamical phase transition to ... [more ▼] We analyze collective motion that occurs during rare (large deviation) events in systems of active particles, both numerically and analytically. We discuss the associated dynamical phase transition to collective motion, which occurs when the active work is biased towards larger values, and is associated with alignment of particles’ orientations. A finite biasing field is needed to induce spontaneous symmetry breaking, even in large systems. Particle alignment is computed exactly for a system of two particles. For many-particle systems, we analyze the symmetry breaking by an optimal-control representation of the biased dynamics, and we propose a fluctuating hydrodynamic theory that captures the emergence of polar order in the biased state. [less ▲] Detailed reference viewed: 35 (3 UL)Characterizing autonomous Maxwell demons ; Esposito, Massimiliano in Physical Review. E. (2021), 103(3), 032118 Detailed reference viewed: 115 (3 UL)Local detailed balance across scales: From diffusions to jump processes and beyond Falasco, Gianmaria ; Esposito, Massimiliano in Physical Review. E. (2021), 103 Detailed reference viewed: 125 (1 UL)Effective thermodynamics of two interacting underdamped Brownian particles Herpich, Tim ; ; Esposito, Massimiliano in Physical Review. E. (2020), 101 Detailed reference viewed: 159 (5 UL)Measurability of nonequilibrium thermodynamics in terms of the Hamiltonian of mean force ; Esposito, Massimiliano in Physical Review. E. (2020), 101(5), 050101 Detailed reference viewed: 47 (1 UL)Thermodynamic cycles with active matter ; ; Fodor, Etienne in Physical Review. E. (2020), 102(1), Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We ... [more ▼] Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We offer a consistent thermodynamic framework to characterize and optimize the performances of such cycles. Based on a minimal model, we put forward a protocol which extracts work by controlling only the properties of the confining walls at boundaries, and we rationalize the transitions between optimal cycles. We show that the corresponding power and efficiency are generally proportional, so that they reach their maximum values at the same cycle time in contrast with thermal cycles, and we provide a generic relation constraining the fluctuations of the power. [less ▲] Detailed reference viewed: 35 (3 UL)Chemical cloaking Avanzini, Francesco ; Falasco, Gianmaria ; Esposito, Massimiliano in Physical Review. E. (2020), 101(6), 060102 Detailed reference viewed: 46 (2 UL)Derivation of an exact, nonequilibrium framework for nucleation: Nucleation is a priori neither diffusive nor Markovian ; Meyer, Hugues ; et al in Physical Review. E. (2019), 100(5), 052140 We discuss the structure of the equation of motion that governs nucleation processes at first order phase transitions. From the underlying microscopic dynamics of a nucleating system, we derive by means ... [more ▼] We discuss the structure of the equation of motion that governs nucleation processes at first order phase transitions. From the underlying microscopic dynamics of a nucleating system, we derive by means of a nonequilibrium projection operator formalism the equation of motion for the size distribution of the nuclei. The equation is exact, ie, the derivation does not contain approximations. To assess the impact of memory, we express the equation of motion in a form that allows for direct comparison to the Markovian limit. As a numerical test, we have simulated crystal nucleation from a supersaturated melt of particles interacting via a Lennard-Jones potential. The simulation data show effects of non-Markovian dynamics. [less ▲] Detailed reference viewed: 147 (0 UL)Universality in driven Potts models Herpich, Tim ; Esposito, Massimiliano in Physical Review. E. (2019) Detailed reference viewed: 208 (8 UL)Non-Markovianity and negative entropy production rates ; Esposito, Massimiliano in Physical Review. E. (2019), 99(1), Detailed reference viewed: 101 (2 UL)Optimizing active work: Dynamical phase transitions, collective motion and jamming ; Fodor, Etienne ; et al in Physical Review. E. (2019), 99(2), Active work measures how far the local self-forcing of active particles translates into real motion. Using population Monte Carlo methods, we investigate large deviations in the active work for repulsive ... [more ▼] Active work measures how far the local self-forcing of active particles translates into real motion. Using population Monte Carlo methods, we investigate large deviations in the active work for repulsive active Brownian disks Minimizing the active work generically results in dynamical arrest; in contrast, despite the lack of aligning interactions, trajectories of high active work correspond to a collectively moving, aligned state. We use heuristic and analytic arguments to explain the origin of dynamical phase transitions separating the arrested, typical, and aligned regimes. [less ▲] Detailed reference viewed: 21 (3 UL)Landau-Zener Lindblad equation and work extraction from coherences ; Esposito, Massimiliano ; in Physical Review. E. (2019), 99(4), Detailed reference viewed: 80 (3 UL)Simulation study of the electrical tunneling network conductivity of suspensions of hard spherocylinders ; ; Rahm, Alexander et al in Physical Review. E. (2018), 98 Using Monte Carlo simulations, we investigate the electrical conductivity of networks of hard rods with aspect ratios 10 and 20 as a function of the volume fraction for two tunneling conductance models ... [more ▼] Using Monte Carlo simulations, we investigate the electrical conductivity of networks of hard rods with aspect ratios 10 and 20 as a function of the volume fraction for two tunneling conductance models. For a simple, orientationally independent tunneling model, we observe nonmonotonic behavior of the bulk conductivity as a function of volume fraction at the isotropic-nematic transition. However, this effect is lost if one allows for anisotropic tunneling. The relative conductivity enhancement increases exponentially with volume fraction in the nematic phase. Moreover, we observe that the orientational ordering of the rods in the nematic phase induces an anisotropy in the conductivity, i.e., enhanced values in the direction of the nematic director field. We also compute the mesh number of the Kirchhoff network, which turns out to be a simple alternative to the computationally expensive conductivity of large systems in order to get a qualitative estimate. [less ▲] Detailed reference viewed: 119 (4 UL)Vesicle dynamics in confined steady and harmonically modulated Poiseuille flows ; ; et al in Physical Review. E. (2018) Detailed reference viewed: 114 (1 UL)Non-Gaussian noise without memory in active matter Fodor, Etienne ; ; et al in Physical Review. E. (2018), 98(6), Modeling the dynamics of an individual active particle invariably involves an isotropic noisy self-propulsion component, in the form of run-and-tumble motion or variations around it. This nonequilibrium ... [more ▼] Modeling the dynamics of an individual active particle invariably involves an isotropic noisy self-propulsion component, in the form of run-and-tumble motion or variations around it. This nonequilibrium source of noise is neither white-there is persistence-nor Gaussian. While emerging collective behavior in active matter has hitherto been attributed to the persistent ingredient, we focus on the non-Gaussian ingredient of self-propulsion. We show that by itself, that is, without invoking any memory effect, it is able to generate particle accumulation close to boundaries and effective attraction between otherwise repulsive particles, a mechanism which generically leads to motility-induced phase separation in active matter. [less ▲] Detailed reference viewed: 28 (3 UL)Kinetics and thermodynamics of a driven open quantum system ; ; Esposito, Massimiliano in Physical Review. E. (2017), 96(5), Detailed reference viewed: 233 (5 UL)Active cage model of glassy dynamics Fodor, Etienne ; ; et al in Physical Review. E. (2016), 94(1), We build up a phenomenological picture in terms of the effective dynamics of a tracer confined in a cage experiencing random hops to capture some characteristics of glassy systems. This minimal ... [more ▼] We build up a phenomenological picture in terms of the effective dynamics of a tracer confined in a cage experiencing random hops to capture some characteristics of glassy systems. This minimal description exhibits scale invariance properties for the small-displacement distribution that echo experimental observations. We predict the existence of exponential tails as a crossover between two Gaussian regimes. Moreover, we demonstrate that the onset of glassy behavior is controlled only by two dimensionless numbers: the number of hops occurring during the relaxation of the particle within a local cage and the ratio of the hopping length to the cage size. [less ▲] Detailed reference viewed: 67 (1 UL)Fluctuating currents in stochastic thermodynamics. I. Gauge invariance of asymptotic statistics Wachtel, Artur ; ; in Physical Review. E. (2015), 92(4), 042132 Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the ... [more ▼] Stochastic thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from antisymmetric jump observables defined on the edges of the graph representing the network of states. The asymptotic statistics of such currents are characterized by scaled cumulants. In the present work, we use the algebraic and topological structure of Markovian models to prove a gauge invariance of the scaled cumulant-generating function. Exploiting this invariance yields an efficient algorithm for practical calculations of asymptotic averages and correlation integrals. We discuss how our approach generalizes the Schnakenberg decomposition of the average entropy-production rate, and how it unifies previous work. The application of our results to concrete models is presented in an accompanying publication. [less ▲] Detailed reference viewed: 112 (3 UL) |
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