arXiv subjects

Stefano Bo

Publications and source records attributed to Stefano Bo.

29 records · Page 2Linked to original sources

arXiv2017

Experimental Realization of a Minimal Microscopic Heat Engine

Microscopic heat engines are microscale systems that convert energy flows between heat reservoirs into work or systematic motion. We have experimentally realized a minimal microscopic heat engine. It consists of a colloidal Brownian particle optically trapped in an elliptical potential well and simultaneously coupled to two heat baths at different temperatures acting along perpendicular directions. For a generic arrangement of the principal directions of the baths and the potential, the symmetry of the system is broken, such that the heat flow drives a systematic gyrating motion of the particle around the potential minimum. Using the experimentally measured trajectories, we quantify the gyrating motion of the particle, the resulting torque that it exerts on the potential, and the associated heat flow between the heat baths. We find excellent agreement between the experimental results and the theoretical predictions.

cond-mat.stat-mech↗

arXiv2017

Driven anisotropic diffusion at boundaries: noise rectification and particle sorting

We study the diffusive dynamics of a Brownian particle in proximity of a flat surface under non-equilibrium conditions, which are created by an anisotropic thermal environment with different temperatures being active along distinct spatial directions. By presenting the exact time-dependent solution of the Fokker-Planck equation for this problem, we demonstrate that the interplay between anisotropic diffusion and hard-core interaction with the plain wall rectifies the thermal fluctuations and induces directed particle transport parallel to the surface, without any deterministic forces being applied in that direction. Based on current micromanipulation technologies, we suggest a concrete experimental set-up to observe this novel noise-induced transport mechanism. We furthermore show that it is sensitive to particle characteristics, such that this set-up can be used for sorting particles of different size.

cond-mat.stat-mech↗

arXiv2017

On the role of extrinsic noise in microRNA-mediated bimodal gene expression

Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions of gene expression levels, where the modes of the distribution often correspond to different physiological states of the system. We theoretically address the presence of bimodal phenotypes in the context of microRNA (miRNA)-mediated regulation. MiRNAs are small noncoding RNA molecules that downregulate the expression of their target mRNAs. The nature of this interaction is titrative and induces a threshold effect: below a given target transcription rate no mRNAs are free and available for translation. We investigate the effect of extrinsic noise on the system by introducing a fluctuating miRNA-transcription rate. We find that the presence of extrinsic noise favours the presence of bimodal target distributions which can be observed for a wider range of parameters compared to the case with intrinsic noise only and for lower miRNA-target interaction strength. Our results suggest that combining threshold-inducing interactions with extrinsic noise provides a simple and robust mechanism for obtaining bimodal populations not requiring fine tuning. We furthermore characterise the protein distributions dependence on protein half-life.

q-bio.MN↗

arXiv2016

Multiple-scale stochastic processes: decimation, averaging and beyond

The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This has provided fruitful applications for established stochastic methods and motivated further developments. These systems often involve processes taking place on widely separated time scales. For an efficient modeling one usually focuses on the slower degrees of freedom and it is of great importance to accurately eliminate the fast variables in a controlled fashion, carefully accounting for their net effect on the slower dynamics. This procedure in general requires to perform two different operations: decimation and coarse-graining. We introduce the asymptotic methods that form the basis of this procedure and discuss their application to a series of physical, biological and chemical examples. We then turn our attention to functionals of the stochastic trajectories such as residence times, counting statistics, fluxes, entropy production, etc. which have been increasingly studied in recent years. For such functionals, the elimination of the fast degrees of freedom can present additional difficulties and naive procedures can lead to blatantly inconsistent results. Homogenization techniques for functionals are less covered in the literature and we will pedagogically present them here, as natural extensions of the ones employed for the trajectories. We will also discuss recent applications of these techniques to the thermodynamics of small systems and their interpretation in terms of information-theoretic concepts.

cond-mat.stat-mech↗

arXiv2016

Diffusion of a Brownian ellipsoid in a force field

We calculate the effective long-term convective velocity and dispersive motion of an ellipsoidal Brownian particle in three dimensions when it is subjected to a constant external force. This long-term motion results as a "net" average behavior from the particle rotation and translation on short time scales. Accordingly, we apply a systematic multi-scale technique to derive the effective equations of motion valid on long times. We verify our theoretical results by comparing them to numerical simulations.

cond-mat.stat-mech↗

arXiv2015

Detecting concentration changes with cooperative receptors

Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed as a Neyman-Pearson detector. Within this framework, we investigate the role of receptor cooperativity in improving the cell's ability to detect changes. We find that cooperativity decreases the probability of missing an occurred change. This becomes especially beneficial when difficult detections have to be made. Concerning the influence of cooperativity on how fast a desired detection power is achieved, we find in general that there is an optimal value at finite levels of cooperation, even though easy discrimination tasks can be performed more rapidly by noncooperative receptors.

q-bio.QM↗

arXiv2015

Thermodynamic limits to information harvesting by sensory systems

In view of the relation between information and thermodynamics we investigate how much information about an external protocol can be stored in the memory of a stochastic measurement device given an energy budget. We consider a layered device with a memory component storing information about the external environment by monitoring the history of a sensory part coupled to the environment. We derive an integral fluctuation theorem for the entropy production and a measure of the information accumulated in the memory device. Its most immediate consequence is that the amount of information is bounded by the average thermodynamic entropy produced by the process. At equilibrium no entropy is produced and therefore the memory device does not add any information about the environment to the sensory component. Consequently, if the system operates at equilibrium the addition of a memory component is superfluous. Such device can be used to model the sensing process of a cell measuring the external concentration of a chemical compound and encoding the measurement in the amount of phosphorylated cytoplasmic proteins.

q-bio.QM↗

arXiv2014

Adaptation and irreversibility in microevolution

Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting selection changes stochastically. We derive the effective genotype and fitness dynamics on the slower time-scales at which the relevant genetic modifications take place. We find that, despite the fast environmental switches, the population manages to adapt on the fast time-scales yielding a finite positive contribution to the fitness. However, such contribution is balanced by the continuous loss in fitness due to the varying selection so that the statistics of the global fitness can be described neglecting the details of the fast environmental process. The occurrence of adaptation on fast time-scales would be undetectable if one were to consider only the effective genotype and fitness dynamics on the slow time-scales. We therefore propose an experimental observable to detect it.

q-bio.PE↗

arXiv2013

Optimal stochastic transport in inhomogeneous thermal environments

We consider optimization of the average entropy production in inhomogeneous temperature environments within the framework of stochastic thermodynamics. For systems modeled by Langevin equations (e.g. a colloidal particle in a heat bath) it has been recently shown that a space dependent temperature breaks the time reversal symmetry of the fast velocity degrees of freedom resulting in an anomalous contribution to the entropy production of the overdamped dynamics. We show that optimization of entropy production is determined by an auxiliary deterministic problem describing motion on a curved manifold in a potential. The "anomalous contribution" to entropy plays the role of the potential and the inverse of the diffusion tensor is the metric. We also find that entropy production is not minimized by adiabatically slow, quasi-static protocols but there is a finite optimal duration for the transport process. As an example we discuss the case of a linearly space dependent diffusion coefficient.

cond-mat.stat-mech↗

arXiv2012

Entropic anomaly and maximal efficiency of microscopic heat engines

The efficiency of microscopic heat engines in a thermally heterogenous environment is considered. We show that, as a consequence of the recently discovered entropic anomaly, quasi-static engines, whose efficiency is maximal in a fluid at uniform temperature, have in fact vanishing efficiency in presence of temperature gradients. For slow cycles the efficiency falls off as the inverse of the period. The maximum efficiency is reached at a finite value of the cycle period that is inversely proportional to the square root of the gradient intensity. The relative loss in maximal efficiency with respect to the thermally homogeneous case grows as the square root of the gradient. As an illustration of these general results, we construct an explicit, analytically solvable example of a Carnot stochastic engine. In this thought experiment, a Brownian particle is confined by a harmonic trap and immersed in a fluid with a linear temperature profile. This example may serve as a template for the design of real experiments in which the effect of the entropic anomaly can be measured.

cond-mat.stat-mech↗

arXiv2012

Anomalous thermodynamics at the micro-scale

Particle motion at the micro-scale is an incessant tug-of-war between thermal fluctuations and applied forces on one side, and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting inertia - the overdamped approximation - gives an excellent effective description of the actual particle mechanics. In sharp contrast with this result, here we show that the overdamped approximation dramatically fails when thermodynamic quantities such as the entropy production in the environment is considered, in presence of temperature gradients. In the limit of vanishingly small, yet finite inertia, we find that the entropy production is dominated by a contribution that is anomalous, i.e. has no counterpart in the overdamped approximation. This phenomenon, that we call entropic anomaly, is due to a symmetry-breaking that occurs when moving to the small, finite inertia limit. Strong production of anomalous entropy is traced back to intense sweeps down the temperature gradient.

cond-mat.stat-mech↗