arXiv subjects

M. Hidalgo-Soria

Publications and source records attributed to M. Hidalgo-Soria.

5 recordsLinked to original sources

arXiv2026

Telomeres in Lamin-A Depleted Cells Exhibit Directed Motion and Dynamic Coherence

Investigating the dynamics of chromatin loci and the factors that influence them provides valuable insights into the organization and functionality of the genome within the cell nucleus. We control the expression of Lamin-A, an important organizer of chromatin and nuclear structure. By simultaneously tracking hundreds of telomeres in Lamin-A knocked-out (KO) and wild-type (WT) nuclei, we find that telomere motion in Lamin-A depleted cells is both faster and more directed on micrometer scales, comparable to the size of chromosome territories. In contrast, telomere trajectories in WT cells exhibit pronounced anti-persistent behavior, consistent with caging by the surrounding chromatin environment. We further observe correlated motion between distinct telomeres in both WT and KO cells, with significantly stronger correlations in the KO case, indicating enhanced collective behavior. These correlations reflect cross-correlations among different loci rather than temporal correlations along individual trajectories. Together, these findings highlight the central role of Lamin-A in regulating both local confinement and collective telomere dynamics.

physics.bio-ph↗

arXiv2021

Cusp of non-Gaussian density of particles for a diffusing diffusivity model

We study a two state ``jumping diffusivity'' model for a Brownian process alternating between two different diffusion constants, $D_{+}>D_{-}$, with random waiting times in both states whose distribution is rather general. In the limit of long measurement times Gaussian behavior with an effective diffusion coefficient is recovered. We show that for equilibrium initial conditions and when the limit of the diffusion coefficient $D_-\to0$ is taken, the short time behavior leads to a cusp, namely a non - analytical behavior, in the distribution of the displacements $P(x,t)$ for $x\longrightarrow 0$. Visually this cusp, or tent-like shape, resembles similar behavior found in many experiments of diffusing particles in disordered environments, such as glassy systems and intracellular media. This general result depends only on the existence of finite mean values of the waiting times at the different states of the model. Gaussian statistics in the long time limit is achieved due to ergodicity and convergence of the distribution of the temporal occupation fraction in state $D_{+}$ to a $δ$-function. The short time behavior of the same quantity converges to a uniform distribution, which leads to the non - analyticity in $P(x,t)$. We demonstrate how super - statistical framework is a zeroth order short time expansion of $P(x,t)$, in the number of transitions, that does not yield the cusp like shape. The latter, considered as the key feature of experiments in the field, is found with the first correction in perturbation theory.

cond-mat.stat-mech↗

arXiv2020

The Hitchhiker model for Laplace diffusion processes in the cell environment

Aggregation and fragmentation of single molecules in the cell environment lead to a spectrum of diffusivities and to statistical laws of movement very different from typical Brownian motion. Current models of intracellular transport do not explain at a microscopical level the emergence of theses deviations. Employing a many body approach, which we call the Hitchhiker model, we elucidate how the widely observed exponential tails in the particle spreading, i.e. the Laplace distribution and the modulations of the diffusivities, are controlled by size fluctuations of single molecules. By means of numerical simulations Laplace distributions are obtained whether we track one molecule or many molecules in parallel. However, we show that the diffusivity varies significantly depending on which tracking protocol is applied. Using a renewal process in the space of sizes, we quantify to what extent the average diffusivity in the single molecule technique is decreased compared with the ensemble average.

cond-mat.stat-mech↗

arXiv2016

Scarce defects induce anomalous deterministic diffusion

We introduce a simple model of deterministic particles in weakly disordered media which exhibits a transition from normal to anomalous diffusion. The model consists of a set of non-interacting overdamped particles moving on a disordered potential. The disordered potential can be thought as a substrate having some "defects" scattered along a one-dimensional line. The distance between two contiguous defects is assumed to have a heavy-tailed distribution with a given exponent $α$, which means that the defects along the substrate are scarce if $α$ is small. We prove that this system exhibits a transition from normal to anomalous diffusion when the distribution exponent $α$ decreases, i.e., when the defects become scarcer. Thus we identify three distinct scenarios: a normal diffusive phase for $α>2$, a superdiffusive phase for $1/2<α\leq 2$, and a subdiffusive phase for $α\leq 1/2$. We also prove that the particle current is finite for all the values of $α$, which means that the transport is normal independently of the diffusion regime (normal, subdiffusive, or superdiffusive). We give analytical expressions for the effective diffusion coefficient for the normal diffusive phase and analytical expressions for the diffusion exponent in the case of anomalous diffusion. We test all these predictions by means of numerical simulations.

cond-mat.dis-nn↗

arXiv2015

Non-linear irreversible thermodynamics of single-molecule experiments

Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external constraints, we are able to calculate the entropy production and the general non-linear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events, and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.

physics.bio-ph↗