Buffering variability in cell regulation motifs close to criticality

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 ▲]

Collective motion in large deviations of active particles

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 ▲]

Local detailed balance across scales: From diffusions to jump processes and beyond

in Physical Review. E. (2021), 103

Thermodynamic cycles with active matter

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 ▲]

Measurability of nonequilibrium thermodynamics in terms of the Hamiltonian of mean force

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

Universality in driven Potts models

in Physical Review. E. (2019)

Non-Markovianity and negative entropy production rates

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

Simulation study of the electrical tunneling network conductivity of suspensions of hard spherocylinders

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 ▲]

Non-Gaussian noise without memory in active matter

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 ▲]

Active cage model of glassy dynamics

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 ▲]