Journals

Magazine:
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
ISSN:
1751-8113

Year:
2022
Vol:
55
N°:
7
Pp:
074001

We study the stochastic thermodynamics of cell growth and division using a theoretical framework based on branching processes with resetting. Cell division may be split into two sub-processes: branching, by which a given cell gives birth to an identical copy of itself, and resetting, by which some properties of the daughter cells (such as their size or age) are reset to new values following division. We derive the first and second laws of stochastic thermodynamics for this process, and identify separate contributions due to branching and resetting. We apply our framework to well-known models of cell size control, such as the sizer, the timer, and the adder. We show that the entropy production of resetting is negative and that of branching is positive for these models in the regime of exponential growth of the colony. This property suggests an analogy between our model for cell growth and division and heat engines, and the introduction of a thermodynamic efficiency, which quantifies the conversion of one form of entropy production to another.

Authors:
Junot, G.; Clement, E.; Auradou, H.; et al.

Magazine:
PHYSICAL REVIEW E
ISSN:
2470-0045

Year:
2021
Vol:
103
N°:
3
Pp:
032608

We develop a maximum likelihood method to infer relevant physical properties of elongated active particles. Using individual trajectories of advected swimmers as input, we are able to accurately determine their rotational diffusion coefficients and an effective measure of their aspect ratio, also providing reliable estimators for the uncertainties of such quantities. We validate our theoretical construction using numerically generated active trajectories upon no flow, simple shear, and Poiseuille flow, with excellent results. Being designed to rely on single-particle data, our method eases applications in experimental conditions where swimmers exhibit a strong morphological diversity. We briefly discuss some of such ongoing experimental applications, specifically, in the characterization of swimming E. coli in a flow.

Magazine:
PHYSICAL REVIEW E
ISSN:
2470-0045

Year:
2019
Vol:
100
N°:
4
Pp:
042608

To account for the possibility of an externally driven cabs in active systems, we develop a model of a guided active drift which relies on the presence of an external guiding field and a vectorial coupling between the mechanical degrees of freedom and a chemical reaction. To characterize the ability of guided active particles to carry position, we generalize the notion of Stokes efficiency extending it to the case of stall conditions. To show the generality of the proposed mechanism, we discuss guided electric circuits capable of turning fluctuations into a directed current without a source of voltage.

Magazine:
PHYSICAL REVIEW E
ISSN:
2470-0045

Year:
2019
Vol:
99
N°:
4
Pp:
042413

Using a population dynamics inspired by an ensemble of growing cells, a set of fluctuation theorems linking observables measured at the lineage and population levels is derived. One of these relations implies specific inequalities comparing the population doubling time with the mean generation time at the lineage or population levels. While these inequalities have been derived before for age-controlled models with negligible mother-daughter correlations, we show that they also hold for a broad class of size-controlled models. We discuss the implications of this result for the interpretation of a recent experiment in which the growth of bacteria strains has been probed at the single-cell level.

Authors:
Barbot, A.; Lerbinger, M.; Hernandez-Garcia, A.; et al.

Magazine:
PHYSICAL REVIEW E
ISSN:
2470-0045

Year:
2018
Vol:
97
N°:
3
Pp:
033001

We develop and extend a method presented by Patinet, Vandembroucq, and Falk [Phys. Rev. Lett. 117, 045501 (2016)] to compute the local yield stresses at the atomic scale in model two-dimensional Lennard-Jones glasses produced via differing quench protocols. This technique allows us to sample the plastic rearrangements in a nonperturbative manner for different loading directions on a well-controlled length scale. Plastic activity upon shearing correlates strongly with the locations of low yield stresses in the quenched states. This correlation is higher in more structurally relaxed systems. The distribution of local yield stresses is also shown to strongly depend on the quench protocol: the more relaxed the glass, the higher the local plastic thresholds. Analysis of the magnitude of local plastic relaxations reveals that stress drops follow exponential distributions, justifying the hypothesis of an average characteristic amplitude often conjectured in mesoscopic or continuum models. The amplitude of the local plastic rearrangements increases on average with the yield stress, regardless of the system preparation. The local yield stress varies with the shear orientation tested and strongly correlates with the plastic rearrangement locations when the system is sheared correspondingly. It is thus argued that plastic rearrangements are the consequence of shear transformation zones encoded in the glass structure that possess weak slip planes along different orientations.

Magazine:
EPL
ISSN:
0295-5075

Year:
2018
Vol:
121
N°:
2
Pp:
26001

We consider the amount of energy dissipated during individual avalanches at the depinning transition of disordered and athermal elastic systems. Analytical progress is possible in the case of the Alessandro-Beatrice-Bertotti-Montorsi (ABBM) model for Barkhausen noise, due to an exact mapping between the energy released in an avalanche and the area below a Brownian path until its first zero-crossing. Scaling arguments and examination of an extended mean-field model with internal structure show that dissipation relates to a critical exponent recently found in a study of the rounding of the depinning transition in the presence of activated dynamics. A new numerical method to compute the dynamic exponent at depinning in terms of blocked and marginally stable configurations is proposed, and a kind of "dissipative anomaly" ¿with potentially important consequences for non-equilibrium statistical mechanics¿ is discussed. We conclude that for depinning systems the size of an avalanche does not constitute by itself a univocal measure of the energy dissipated.

National and Regional

**degree scroll:**
Passive criticality mediated by subject active and live

**Code from transcript:**
PID2021-129066NA-I00

**researcher principal: **
Reinaldo García García

**Funder:**
STATE RESEARCH AGENCY

**Call for proposals:**
2021 AEI Generation Projects of the. knowledge

**Start date: **
01/09/2022

**End date:**
31/08/2025

**Amount granted:**
78.650,00€

**Other funds:**
ERDF funds