arXiv subjects

Juan J. Mazo

Publications and source records attributed to Juan J. Mazo.

6 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↗

arXiv2010

Thermal and mechanical properties of a DNA model with solvation barrier

We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the Principal Component Analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.

physics.bio-ph↗

arXiv2008

A model for hand-over-hand motion of molecular motors

A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the expected behavior is observed. We discuss different regimes of motion and efficiency depending of model parameters.

physics.bio-ph↗

arXiv1999

Ratchet potential for fluxons in Josephson-Junction arrays

We propose a simple configuration of a one-dimensional parallel array of Josephson junctions in which the pinning potential for trapped fluxons lacks inversion symmetry (ratchet potential). This sytem can be modelised by a set of non-linear pendula with alternating lengths and harmonic couplings. We show, by molecular dynamics simulations, that fluxons behave as single particles in which the predictions for overdamped thermal ratchet can be easily verified.

cond-mat↗

arXiv1996

Equilibrium properties of a Josephson junction ladder with screening effects

In this paper we calculate the ground state phase diagram of a Josephson Junction ladder when screening field effects are taken into account. We study the ground state configuration as a function of the external field, the penetration depth and the anisotropy of the ladder, using different approximations to the calculation of the induced fields. A series of tongues, characterized by the vortex density $ω$, is obtained. The vortex density of the ground state, as a function of the external field, is a Devil's staircase, with a plateau for every rational value of $ω$. The width of each of these steps depends strongly on the approximation made when calculating the inductance effect: if the self-inductance matrix is considered, the $ω=0$ phase tends to occupy all the diagram as the penetration depth decreases. If, instead, the whole inductance matrix is considered, the width of any step tends to a non-zero value in the limit of very low penetration depth. We have also analyzed the stability of some simple metastable phases: screening fields are shown to enlarge their stability range.

cond-mat↗

arXiv1995

Josephson Junction Ladders: Ground State and Relaxation Phenomena

This paper considers a Josephson Junction array with the geometry of a ladder and anisotropy in the Josephson couplings. The ground state problem for the ladder corresponds to the one for the one-dimensional chiral XY model in a two-fold anisotropy field, which allows of a rigorous characterization of the ground state phase diagram and the relevant elementary excitations for the system. The approach to equilibrium, which we study using Langevin dynamics, shows slow relaxation, typical of systems whose energy landscape in the configuration space consists of a wealthy of metastable states, dynamically disconnected.

cond-mat↗