arXiv subjects

Luis Dinis

Publications and source records attributed to Luis Dinis.

9 recordsLinked to original sources

arXiv2026

Evolutionary adaptation through bet-hedging in finite populations under fluctuating environments

Natural populations evolve under fluctuating environments and limited resources, yet it is unclear how these factors jointly shape adaptation. Here, we introduce a minimal stochastic model of a population undergoing a birth-death process in a randomly switching environment, where individuals inherit phenotypic strategies that determine the distribution of phenotypes across generations. First, we confirm that environmental variability can favor phenotypic diversity (bet-hedging), and that the strategy maximizing the average growth rate generally differs from the one minimizing extinction risk. We then demonstrate that evolution drives populations toward strategies that balance these competing objectives. Furthermore, we show that population size modulates this evolutionary outcome: large populations converge to the growth-maximizing strategy, whereas smaller ones evolve toward more resilient strategies. Finally, we provide a simple heuristic approximation that captures these results, clarifying the interplay between growth, extinction, and mutation.

q-bio.PE↗

arXiv2024

Extinction in agent-based and collective models of bet-hedging

Bet-hedging is a phenotype diversification strategy that combines a fast-growing vulnerable phenotype with a slow-growing resistant phenotype. In environments switching between favorable and unfavorable conditions, bet-hedging optimizes growth and reduces fluctuations over a long time, which is expected to reduce extinction risk. Here, we address directly how bet-hedging can reduce extinction probability in an agent-based model. An agent-based model is appropriate for studying extinction due to the low number of individuals close to extinction. We also show that the agent-based model converges to the collective model behavior for populations of $100$ individuals or more. However, the collective model provides relevant qualitative insight even for low populations. The collective model provides expressions for extinction that stress the relevance of the population number, showing that a factor four increase in the total population has a greater effect than a change of strategy from maximum growth to minimal extinction. This work provides further insight into the impact of finite population effects on the bet-hedging strategy's success.

q-bio.PE↗

arXiv2021

Self-adaptation of Pseudomonas fluorescens biofilms to hydrodynamic stress

In some conditions, bacteria self-organise into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed on polysaccharides, DNA, proteins and lipids. It is known that bacteria change their colony/matrix ratio in the presence of external stimuli such as hydrodynamic stress. However, little is still known about the molecular mechanisms driving this self-adaptation. In this work, we monitor structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress. Our measurements show that the hydrodynamic stress concomitantly increases the cell density population and the matrix production. At short growth timescales, the matrix mediates a weak cell-cell attractive interaction due to the depletion forces originated by the polymer constituents. Using a population dynamics model, we conclude that hydrodynamic stress causes a faster diffusion of nutrients and a higher incorporation of planktonic bacteria to the already formed microcolonies. This results in the formation of more mechanically stable biofilms due to an increase of the number of crosslinks, as shown by computer simulations. The mechanical stability also lies on a change in the chemical compositions of the matrix, which becomes enriched in carbohydrates, known to display adhering properties. Overall, we demonstrate that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.

cond-mat.soft↗

arXiv2016

Reversible feedback confinement

We present a feedback protocol that is able to confine a system to a single micro-state without heat dissipation. The protocol adjusts the Hamiltonian of the system in such a way that the Bayesian posterior distribution after measurement is in equilibrium. As a result, the whole process satisfies feedback reversibility -- the process is indistinguishable from its time reversal -- and assures the lowest possible dissipation for confinement. In spite of the whole process being reversible it can surprisingly be implemented in finite time. We illustrate the idea with a Brownian particle in a harmonic trap with increasing stiffness and present a general theory of reversible feedback confinement for systems with discrete states.

cond-mat.stat-mech↗

arXiv2015

Non-sinusoidal current and current reversals in a gating ratchet

In this work, the ratchet dynamics of Brownian particles driven by an external sinusoidal (harmonic) force is investigated. The gating ratchet effect is observed when another harmonic is used to modulate the spatially symmetric potential in which the particles move. For small amplitudes of the harmonics, it is shown that the current (average velocity) of particles exhibits a sinusoidal shape as a function of a precise combination of the phases of both harmonics. By increasing the amplitudes of the harmonics beyond the small-limit regime, departures from the sinusoidal behavior are observed and current reversals can also be induced. These current reversals persist even for the overdamped dynamics of the particles.

cond-mat.stat-mech↗

arXiv2014

Brownian Carnot engine

The Carnot cycle imposes a fundamental upper limit to the efficiency of a macroscopic motor operating between two thermal baths. However, this bound needs to be reinterpreted at microscopic scales, where molecular bio-motors and some artificial micro-engines operate. As described by stochastic thermodynamics, energy transfers in microscopic systems are random and thermal fluctuations induce transient decreases of entropy, allowing for possible violations of the Carnot limit. Despite its potential relevance for the development of a thermodynamics of small systems, an experimental study of microscopic Carnot engines is still lacking. Here we report on an experimental realization of a Carnot engine with a single optically trapped Brownian particle as working substance. We present an exhaustive study of the energetics of the engine and analyze the fluctuations of the finite-time efficiency, showing that the Carnot bound can be surpassed for a small number of non-equilibrium cycles. As its macroscopic counterpart, the energetics of our Carnot device exhibits basic properties that one would expect to observe in any microscopic energy transducer operating with baths at different temperatures. Our results characterize the sources of irreversibility in the engine and the statistical properties of the efficiency -an insight that could inspire novel strategies in the design of efficient nano-motors.

cond-mat.stat-mech↗

arXiv2014

Adiabatic processes realized with a trapped Brownian particle

We experimentally realize quasistatic adiabatic processes using a single optically-trapped micro- sphere immersed in water whose effective temperature is controlled by an external random electric field. A full energetic characterization of adiabatic processes that preserve either the position dis- tribution or the full phase space volume is presented. We show that only in the latter case the exchanged heat and the change in the entropy of the particle vanish when averaging over many repetitions. We provide analytical expressions for the distributions of the fluctuating heat and en- tropy, which we verify experimentally. We show that the heat distribution is asymmetric for any non-isothermal quasistatic process. Moreover, the shape of the distribution of the system entropy change in the adiabatic processes depends significantly on the number of degrees of freedom that are considered for the calculation of system entropy.

cond-mat.stat-mech↗

arXiv2014

Measuring kinetic energy changes in the mesoscale with low acquisition rates

We describe a new technique to estimate the mean square velocity of a Brownian particle from time series of the position of the particle sampled at frequencies several orders of magnitude smaller than the momentum relaxation frequency. We apply our technique to determine the mean square velocity of single optically trapped polystyrene microspheres immersed in water. The velocity is increased applying a noisy electric field that mimics a higher kinetic temperature. Therefore, we are able to measure the average kinetic energy change in isothermal and non-isothermal quasistatic processes. Moreover, we show that the dependence of the mean square time-averaged velocity on the sampling frequency can be used to quantify properties of the electrophoretic mobility of a charged colloid. Our method could be applied to detect temperature gradients in inhomogeneous media and to characterize the complete thermodynamics of microscopic heat engines.

cond-mat.stat-mech↗

arXiv2002

Optimal strategies in collective Parrondo games

We present a modification of the so-called Parrondo's paradox where one is allowed to choose in each turn the game that a large number of individuals play. It turns out that, by choosing the game which gives the highest average earnings at each step, one ends up with systematic loses, whereas a periodic or random sequence of choices yields a steadily increase of the capital. An explanation of this behavior is given by noting that the short-range maximization of the returns is "killing the goose that laid the golden eggs". A continuous model displaying similar features is analyzed using dynamic programming techniques from control theory.

cond-mat.stat-mech↗