arXiv subjects

Reinaldo García-García

Publications and source records attributed to Reinaldo García-García.

12 recordsLinked to original sources

arXiv2023

Branching processes with resetting as a model for cell division

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.

cond-mat.stat-mech↗

arXiv2021

Linking lineage and population observables in biological branching processes

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 are 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.

q-bio.PE↗

arXiv2021

Single-Trajectory Characterization of Active Swimmers in a Flow

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.

cond-mat.soft↗

arXiv2018

Heat leakage in equilibrium processes

The difference between the zero-mass limit of the heat exchanged with a thermal reservoir, and its value as determined from overdamped dynamics, is termed `heat leakage' or `hidden heat' in the Smoluchowski limit. If present, heat leakages are the sign of the unsuitability of the overdamped approximation for addressing thermodynamics. It is accepted that no hidden heat arises in an isothermal process driven by conservative forces. Here, we challenge that conclusion. The heat exchanged with a reservoir in any isothermal and quasistatic process connecting two equilibrium states, indeed exhibits hidden contributions. Our results imply that the overdamped dynamics misrepresents thermodynamics quite generally. Surprisingly, the hidden heat is described by an universal distribution in slow processes, easing the correction of the heat statistics in that context.

cond-mat.stat-mech↗

arXiv2018

Drift induced by dissipation

Active particles have become a subject of intense interest across several disciplines from animal behavior to granular physics. Usually the models of such particles contain an explicit internal driving. Here we propose a model with implicit driving in the sense that the behavior of our particle is fully dissipative at zero temperature but becomes active in the presence of seemingly innocent equilibrium fluctuations. The mechanism of activity is related to the breaking of the gradient structure in the chemo-mechanical coupling. We show that the thermodynamics of such active particles depends crucially on inertia and cannot be correctly captured in the standard Smoluchowski limit. To deal with stall conditions, we generalize the definition of Stokes efficiency, assessing the quality of active force generation. We propose a simple realization of the model in terms of an electric circuit capable of turning fluctuations into a directed current without an explicit source of voltage.

cond-mat.stat-mech↗

arXiv2018

On dissipation in crackling noise systems

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 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 nonequilibrium 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.

cond-mat.stat-mech↗

arXiv2016

Driven interfaces: from flow to creep through model reduction

The response of spatially extended systems to a force leading their steady state out of equilibrium is strongly affected by the presence of disorder. We focus on the mean velocity induced by a constant force applied on one-dimensional interfaces. In the absence of disorder, the velocity is linear in the force. In the presence of disorder, it is widely admitted, as well as experimentally and numerically verified, that the velocity presents a stretched exponential dependence in the force (the so-called 'creep law'), which is out of reach of linear response, or more generically of direct perturbative expansions at small force. In dimension one, there is no exact analytical derivation of such a law, even from a theoretical physical point of view. We propose an effective model with two degrees of freedom, constructed from the full spatially extended model, that captures many aspects of the creep phenomenology. It provides a justification of the creep law form of the velocity-force characteristics, in a quasistatic approximation. It allows, moreover, to capture the non-trivial effects of short-range correlations in the disorder, which govern the low-temperature asymptotics. It enables us to establish a phase diagram where the creep law manifests itself in the vicinity of the origin in the force--system-size--temperature coordinates. Conjointly, we characterise the crossover between the creep regime and a linear-response regime that arises due to finite system size.

cond-mat.stat-mech↗

arXiv2015

Thermodynamic inference based on coarse-grained data or noisy measurements

Fluctuation theorems have become an important tool in single molecule biophysics to measure free energy differences from non-equilibrium experiments. When significant coarse-graining or noise affect the measurements, the determination of the free energies becomes challenging. In order to address this thermodynamic inference problem, we propose improved estimators of free energy differences based on fluctuation theorems, which we test on a number of examples. The effect of the noise can be described by an effective temperature, which only depends on the signal to noise ratio, when the work is Gaussian distributed and uncorrelated with the error made on the work. The notion of effective temperature appears less useful for non-Gaussian work distributions or when the error is correlated with the work, but nevertheless, as we show, improved estimators can still be constructed for such cases. As an example of non-trivial correlations between the error and the work, we also consider measurements with delay, as described by linear Langevin equations.

cond-mat.stat-mech↗

arXiv2014

Symmetry for the duration of entropy-consuming intervals

We introduce the violation fraction $\upsilon$ as the cumulative fraction of time that a mesoscopic system spends consuming entropy at a single trajectory in phase space. We show that the fluctuations of this quantity are described in terms of a symmetry relation reminiscent of fluctuation theorems, which involve a function, $Φ$, which can be interpreted as an entropy associated to the fluctuations of the violation fraction. The function $Φ$, when evaluated for arbitrary stochastic realizations of the violation fraction, is odd upon the symmetry transformations which are relevant for the associated stochastic entropy production. This fact leads to a detailed fluctuation theorem for the probability density function of $Φ$. We study the steady-state limit of this symmetry in the paradigmatic case of a colloidal particle dragged by optical tweezers through an aqueous solution. Finally, we briefly discuss on possible applications of our results for the estimation of free-energy differences from single molecule experiments.

cond-mat.stat-mech↗

arXiv2014

Duration of local violations of the second law of thermodynamics along single trajectories in phase space

We define the {\it violation fraction} $ν$ as the cumulative fraction of time that the entropy change is negative during single realizations of processes in phase space. This quantity depends both on the number of degrees of freedom $N$ and the duration of the time interval $τ$. In the large-$τ$ and large-$N$ limit we show that, for ergodic and microreversible systems, the mean value of $ν$ scales as $\langleν(N,τ)\rangle\sim\big(τN^{\frac{1}{1+α}}\big)^{-1}$. The exponent $α$ is positive and generally depends on the protocol for the external driving forces, being $α=1$ for a constant drive. As an example, we study a nontrivial model where the fluctuations of the entropy production are non-Gaussian: an elastic line driven at a constant rate by an anharmonic trap. In this case we show that the scaling of $\langle ν\rangle$ with $N$ and $τ$ agrees with our result. Finally, we discuss how this scaling law may break down in the vicinity of a continuous phase transition.

cond-mat.stat-mech↗

arXiv2012

Non-adiabatic entropy production for non-Markov dynamics

We extend the definition of non-adiabatic entropy production given for Markovian systems in [M. Esposito and C. Van den Broeck, Phys. Rev. Lett. 104 090601, (2010)], to arbitrary non-Markov ergodic dynamics. We also introduce a notion of stability characterizing non-Markovianity. For stable non-Markovian systems, the non-adiabatic entropy production satisfies an integral fluctuation theorem, leading to the second law of thermodynamics for transitions between non-equilibrium steady-states. This quantity can also be written as a sum of products of generalized fluxes and forces, thus being suitable for thermodynamics. On the other hand, the generalized fluctuation-dissipation relation also holds, clarifying that the conditions for it to be satisfied are ergodicity and stability instead of Markovianity. We show that in spite of being counter-intuitive, the stability criterion introduced in this work may be violated in non-Markovian systems even if they are ergodic, leading to a violation of the fluctuation theorem and the generalized fluctuation-dissipation relation. Stability represents then a necessary condition for the above properties to hold and explains why the generalized fluctuation-dissipation relation has remained elusive in the study of non-Markov systems exhibiting non-equilibrium steady-states.

cond-mat.stat-mech↗

arXiv2012

Joint probability distributions and fluctuation theorems

We derive various exact results for Markovian systems that spontaneously relax to a non-equilibrium steady-state by using joint probability distributions symmetries of different entropy production decompositions. The analytical approach is applied to diverse problems such as the description of the fluctuations induced by experimental errors, for unveiling symmetries of correlation functions appearing in fluctuation-dissipation relations recently generalised to non-equilibrium steady-states, and also for mapping averages between different trajectory-based dynamical ensembles. Many known fluctuation theorems arise as special instances of our approach, for particular two-fold decompositions of the total entropy production. As a complement, we also briefly review and synthesise the variety of fluctuation theorems applying to stochastic dynamics of both, continuous systems described by a Langevin dynamics and discrete systems obeying a Markov dynamics, emphasising how these results emerge from distinct symmetries of the dynamical entropy of the trajectory followed by the system For Langevin dynamics, we embed the "dual dynamics" with a physical meaning, and for Markov systems we show how the fluctuation theorems translate into symmetries of modified evolution operators.

cond-mat.stat-mech↗