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See detailTopological origin of the protein folding transition
di Cairano, Loris UL; Capelli, Riccardo; Bel-Hadj-Aissa, Ghofrane et al

in Physical Review. E. (2022), 106

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See detailBuffering variability in cell regulation motifs close to criticality
Proverbio, Daniele UL; Noronha Montanari, Arthur UL; Skupin, Alexander UL 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 ▲]

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See detailStatistical mechanics of active Ornstein-Uhlenbeck particles
Martin, David; O’Byrne, Jérémy; Cates, Michael E. 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 ▲]

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See detailCollective motion in large deviations of active particles
Keta, Yann-Edwin; Fodor, Etienne UL; van Wijland, Frédéric 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 ▲]

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See detailCharacterizing autonomous Maxwell demons
Freitas, Nahuel; Esposito, Massimiliano UL

in Physical Review. E. (2021), 103(3), 032118

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See detailEffective thermodynamics of two interacting underdamped Brownian particles
Herpich, Tim UL; Shayanfard, Kamran; Esposito, Massimiliano UL

in Physical Review. E. (2020), 101

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See detailThermodynamic cycles with active matter
Ekeh, Timothy; Cates, Michael E.; Fodor, Etienne UL

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 ▲]

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See detailChemical cloaking
Avanzini, Francesco UL; Falasco, Gianmaria UL; Esposito, Massimiliano UL

in Physical Review. E. (2020), 101(6), 060102

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See detailMeasurability of nonequilibrium thermodynamics in terms of the Hamiltonian of mean force
Strasberg, Philipp; Esposito, Massimiliano UL

in Physical Review. E. (2020), 101(5), 050101

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See detailDerivation of an exact, nonequilibrium framework for nucleation: Nucleation is a priori neither diffusive nor Markovian
Kuhnhold, Anja; Meyer, Hugues UL; Amati, Graziano 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 ▲]

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See detailUniversality in driven Potts models
Herpich, Tim UL; Esposito, Massimiliano UL

in Physical Review. E. (2019)

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See detailLandau-Zener Lindblad equation and work extraction from coherences
Thingna, J.; Esposito, Massimiliano UL; Barra, F.

in Physical Review. E. (2019), 99(4),

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See detailNon-Markovianity and negative entropy production rates
Strasberg, P.; Esposito, Massimiliano UL

in Physical Review. E. (2019), 99(1),

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See detailOptimizing active work: Dynamical phase transitions, collective motion and jamming
Nemoto, Takahiro; Fodor, Etienne UL; Cates, Michael E. 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 ▲]

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See detailSimulation study of the electrical tunneling network conductivity of suspensions of hard spherocylinders
Atashpendar, Arshia; Arora, Sarthak; Rahm, Alexander UL 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 ▲]

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See detailVesicle dynamics in confined steady and harmonically modulated Poiseuille flows
Boujja, Z.; Misbah, C.; Ez-Zahraouy, H. et al

in Physical Review. E. (2018)

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See detailNon-Gaussian noise without memory in active matter
Fodor, Etienne UL; Hayakawa, Hisao; Tailleur, Julien 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 ▲]

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See detailKinetics and thermodynamics of a driven open quantum system
Thingna, J.; Barra, F.; Esposito, Massimiliano UL

in Physical Review. E. (2017), 96(5),

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See detailActive cage model of glassy dynamics
Fodor, Etienne UL; Hayakawa, Hisao; Visco, Paolo 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 ▲]

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