arXiv subjects

Jordi Piñero

Publications and source records attributed to Jordi Piñero.

9 recordsLinked to original sources

arXiv2026

Information bounds production in replicator systems

Environmental fluctuations can shape replicator dynamics, with important consequences for both prebiotic and modern ecosystems. However, it remains unclear how simple replicators can acquire and use information about fluctuating environments, given that such information processing is often assumed to require sophisticated mechanisms for sensing and control. Here, we show that even simple replicator networks can increase productivity by exploiting environmental information in a functional way. Using a model of autocatalytic replicators in a flow reactor, we derive an information-theoretic decomposition of productivity, with separate contributions from environmental uncertainty, side information, and distribution mismatch. We derive optimal strategies and universal bounds on the benefit of information and compare our findings with existing work, including ``Kelly gambling'' in information theory. By applying our framework to a model of real-world molecular replicators, we demonstrate the benefits of internal memory and propose an experimental setup for detecting functional information in a minimal chemical system.

physics.bio-ph↗

arXiv2025

Neutral theory of cooperative dynamics

Mutualistic interactions are widespread in nature, from plant communities and microbiomes to human organizations. Along with competition for resources, cooperative interactions shape biodiversity and contribute to the robustness of complex ecosystems. We present a stochastic neutral theory of cooperator species. Our model shares with the classic neutral theory of biodiversity the assumption that all species are equivalent, but crucially differs in requiring cooperation between species for replication. With low migration, our model displays a bimodal species-abundance distribution, with a high-abundance mode associated with a core of cooperating species. This core is responsible for maintaining a diverse pool of long-lived species, which are present even at very small migration rates. We derive analytical expressions of the steady-state species abundance distribution, as well as scaling laws for diversity, number of species, and residence times. With high migration, our model recovers the results of classic neutral theory. We briefly discuss implications of our analysis for research on the microbiome, synthetic biology, and the origin of life.

q-bio.PE↗

arXiv2024

Universal bounds on optimization of free energy harvesting

Harvesting free energy from the environment is essential for the operation of many biological and artificial systems. We investigate the maximum rate of harvesting achievable by optimizing a set of reactions in a Markovian system, possibly given topological, kinetic, and thermodynamic constraints. We show that the maximum harvesting rate can be expressed as a variational principle, which we solve in closed-form for three physically meaningful regimes. Our approach is relevant for optimal design and for quantifying efficiency of existing reactions. Our results are illustrated on bacteriorhodopsin, a light-driven proton pump from Archae, which is found to be close to optimal under realistic conditions.

cond-mat.stat-mech↗

arXiv2023

Semantic Information in a model of Resource Gathering Agents

We explore the application of a new theory of Semantic Information to the well-motivated problem of a resource foraging agent. Semantic information is defined as the subset of correlations, measured via the transfer entropy, between agent $A$ and environment $E$ that is necessary for the agent to maintain its viability $V$. Viability, in turn, is endogenously defined as opposed to the use of exogenous quantities like utility functions. In our model, the forager's movements are determined by its ability to measure, via a sensor, the presence of an individual unit of resource, while the viability function is its expected lifetime. Through counterfactual interventions -- scrambling the correlations between agent and environment via noising the sensor -- we demonstrate the presence of a critical value of the noise parameter, $η_c$, above which the forager's expected lifetime is dramatically reduced. On the other hand, for $η< η_c$ there is little-to-no effect on its ability to survive. We refer to this boundary as the semantic threshold, quantifying the subset of agent-environment correlations that the agent actually needs to maintain its desired state of staying alive. Each bit of information affects the agent's ability to persist both above and below the semantic threshold. Modeling the viability curve and its semantic threshold via forager/environment parameters, we show how the correlations are instantiated. Our work provides a useful model for studies of established agents in terms of semantic information. It also shows that such semantic thresholds may prove useful for understanding the role information plays in allowing systems to become autonomous agents.

cond-mat.stat-mech↗

arXiv2022

Fixation and Fluctuations in Two-Species Cooperation

Cooperative interactions pervade in a broad range of many-body populations, such as ecological communities, social organizations, and economic webs. We investigate the dynamics of a population of two equivalent species A and B that are driven by cooperative and symmetric interactions between these species. For an isolated population, we determine the probability to reach fixation, where only one species remains, as a function of the initial concentrations of the two species, as well as the time to reach fixation. The latter scales exponentially with the population size. When members of each species migrate into the population at rate $λ$ and replace a randomly selected individual, surprisingly rich dynamics ensues. Ostensibly, the population reaches a steady state, but the steady-state population distribution undergoes a unimodal to trimodal transition as the migration rate decreases below a critical value $λ_c$. In the low-migration regime, $λ<λ_c$, the steady state is not truly steady, but instead strongly fluctuates between near-fixation states, where the population consists of mostly A's or of mostly B's. The characteristic time scale of these fluctuations diverges as $λ^{-1}$. Thus in spite of the cooperative interaction, a typical snapshot of the population will contain almost all A's or almost all B's.

q-bio.PE↗

arXiv2021

Exact edge landing probability for the bouncing coin toss and the three-sided die problem

Have you ever taken a disputed decision by tossing a coin and checking its landing side? This ancestral "heads or tails" practice is still widely used when facing undecided alternatives since it relies on the intuitive fairness of equiprobability. However, it critically disregards an interesting third outcome: the possibility of the coin coming at rest on its edge. Provided this evident yet elusive possibility, previous works have already focused on capturing all three landing probabilities of thick coins, but have only succeeded computationally as an exact and fully grounded analytical solution still evades the physics community. In this work we combine the classical equations of collisions with a statistical-mechanics approach to derive the exact analytical outcome probabilities of the partially inelastic coin toss. We validate the theoretical prediction by comparing it to previously reported simulations and experimental data; we discuss the moderate discrepancies arising at the highly inelastic regime; we describe the differences with previous, approximate models; and we finally propose the optimal geometry for the fair, cylindrical three-sided die based on the current results.

physics.class-ph↗

arXiv2019

Fixation in Fluctuating Populations

We investigate the dynamics of the voter model in which the population itself changes endogenously via the birth-death process. There are two species of voters, labeled A and B, and the population of each species can grow or shrink by the birth-death process at equal rates $b$. Individuals of opposite species also undergo voter model dynamics in which an AB pair can equiprobably become AA or BB with rate $v$---neutral evolution. In the limit $b/v\to\infty$, the distribution of consensus times varies as $t^{-3}$ and the probability that the population size equals $n$ at the moment of consensus varies as $n^{-3}$. As the birth/death rate $b$ is increased, fixation occurs more more quickly; that is, population fluctuations promote consensus.

q-bio.PE↗

arXiv2017

Nonequilibrium entropic bounds for Darwinian replicators

Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. Models are typically kinetic, based on standard replicator equations. On the other hand, the presence of thermodynamical constrains for these systems remain an open question. This is largely due to the lack of a general theory of out of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements in non-equilibrium physics, under the rubric of the extended second law of thermodynamics. The work presented here is twofold: firstly, we review this theoretical framework and provide a brief description of the three fundamental replicator types in prebiotic evolution: parabolic, malthusian and hyperbolic. Finally, we employ these previously mentioned techinques to explore how replicators are constrained by thermodynamics.

nlin.AO↗

arXiv2015

Field theory of molecular cooperators

It has been suggested that major transitions in evolution require the emergence of novelties, often associated to the cooperative behaviour of previously existing objects or agents. A key innovation involves the first cooperative interactions among molecules in a prebiotic biosphere. One of the simplest scenarios includes two molecular species capable of helping each other forming a catalytic loop or hypercycle. The second order kinetics of the hypercycle implies a hyperbolic growth dynamics, capable of overcoming some selection barriers associated to non-cooperative molecular systems. Moreover, it has been suggested that molecular replicators might have benefited from a limited diffusion associated to their attachment to surfaces: evolution and escape from extinction might have been tied to living on a surface. In this paper we propose a field theoretical model of the hypercycle involving reaction and diffusion through the use of a many-body Hamiltonian. This treatment allows a characterisation of the spatially correlated dynamics of the system, where the critical dimension is found to be $d_c=2$. We discuss the role of surface dynamics as a selective advantage for the system's survival.

nlin.AO↗