arXiv subjects

Giuseppe Gonnella

Publications and source records attributed to Giuseppe Gonnella.

At least 19 recordsLinked to original sources

arXiv2026

Phase Separation in a system of Brownian inertial rotors

We uncover an emergent phase separation in a system of inertial dumbbells put into persistent rotation by a constant applied torque, breaking chiral symmetry, while interacting with each other through repulsive hard-core interactions. We numerically determine the phase diagram of the model, showing that there exists a binodal and a spinodal region where the system separates into a dense liquid and an ordered phase, which we identify as hexatic. An analysis of the system pressure unveils that the mechanism underlying the phase separation is heavily controlled by inertia. Locally injected kinetic energy is steadily stored into the system in a way that depends on density and that, at large inertia, results in a hot dilute and cool dense state, leading to a generically unstable homogeneous phase. The interplay between dumbbells' arrangement into clusters and chiral forces produces a spontaneous rigid rotation of the clusters around their centers of mass.

cond-mat.soft↗

arXiv2026

Ordering and Defect Dynamics in Passive and Active Nematopolars

The coexistence of polar and nematic interactions, observed in a broad range of biological and synthetic active systems, gives rise to a rich phenomenology that continues to challenge our theoretical understanding of non-equilibrium collective behaviour. In this paper, we numerically investigate phase ordering and defect dynamics in a newly introduced minimal single-field model for dry nematopolar systems, where competing polar and nematic contributions enter the free energy, and activity is implemented through self-advection. At optimal balance, the system develops depolarization strings connecting half-integer defects and separating domains with opposite polarization, together with closed depolarization loops. We first characterize the elementary relaxation mechanisms of defect pairs and loops, showing that the interplay between polar and nematic alignment gives rise to non-monotonic string-mediated interactions, finite equilibrium separations and distinct loop-collapse pathways. Large-scale simulations from disordered states instead show dynamic scaling with a characteristic length growing as $\sim(t/\ln t)^{1/2}$, consistent with coarsening in systems with non-conserved order parameters and point-like defects. Upon introducing self-advection, sufficiently strong activity leads to the coexistence of positive integer and negative half-integer defects, which we term motility-induced charge symmetry breaking, and to saturation of the characteristic length scales, ultimately resulting in arrested coarsening. Overall, our results provide a simple unified framework for understanding the ordering and defect dynamics in biological and synthetic nematopolar systems.

cond-mat.soft↗

arXiv2026

Thinning-by-spinning: shear rheology of dense chiral fluids

We investigate the linear and nonlinear rheology of dense chiral fluids composed of self-spinning particles under external shear. Using particle-based simulations of a two-dimensional Lennard-Jones model with transverse interactions, we show that chirality acts as an intrinsic source of fluctuations and shear. In the solid regime, spinning fluidizes the system, weakening hexatic order. In the liquid regime, the viscosity is quantitatively described by a Green-Kubo relation upon replacing the temperature by a chirality-dependent effective temperature. Beyond linear response, flow curves collapse when expressed in terms of the ratio between imposed shear and spinning rates, revealing a thinning-by-spinning mechanism. At large forcing, this correspondence breaks down and a pronounced handedness asymmetry emerges: when transverse interactions oppose the imposed shear, stresses relax through the formation of string-like flow channels. Our results identify chirality as a generic mechanism for fluidization and provide a unified framework for understanding the rheology of dense chiral suspensions.

cond-mat.soft↗

arXiv2026

Role of mass fluctuations in the diffusion of clusters of Brownian particles with activity

Motivated by the anomalous diffusion observed in clusters of active Brownian particles (ABPs), where the center-of-mass diffusion coefficient scales as $D\sim N^{-1/2}$ with respect to the number $N$ of particles in the cluster, we derive a minimal theoretical framework starting from the single-particle Langevin equations. The model consists of two coupled stochastic equations: one for the cluster center-of-mass trajectory and one for the mass evolution $N(t)$, explicitly accounting for stochastic displacements induced by particle attachment and detachment. We specialize and validate the framework against ABP simulations of isolated clusters in stationary conditions, where $N(t)$ follows a Gaussian process with mean $N_0$, variance $\propto N_0^β$, and persistence time $\propto N_0^κ$. Analytical solution of the coupled equations yields the long-time diffusion coefficient as the sum of two contributions: a conventional term $\propto N_0^{-1}$) due to thermal noise plus summation of active forces, and a fluctuation-driven term $\propto N_0^{-δ}$ with $δ=2-2/d-β+κ$, where $d$ is the spatial dimension. We demonstrate that anomalous scaling emerges whenever the second term becomes dominant. The model predicts $D\sim N^{-α}$ with $α=0.63\pm0.06$, in good quantitative agreement with large-scale ABP simulations.

cond-mat.stat-mech↗

arXiv2026

Supercoiling DNA with a free end

In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is subjected to a constant torque. Even though the other end is free, and hence can spin and release torsional stress, we observe that the entire chain transitions between a swollen and a plectonemic phase as the torque increases beyond a critical threshold. In the plectonemic phase, we observe a non-linear twist profile in the steady state, resulting from the mutual interconversion between the injected twist and geometrical writhe, which distributes inhomogeneously along the chain. We also show that the non-equilibrium dynamics of twist accumulation is diffusive, and that writhe diffusion is negligible in this geometry, as plectonemes remain localised near the end that is being rotated. We discuss the feasibility of testing our results with single-molecule experiments.

cond-mat.soft↗

arXiv2025

Morphology, Polarization Patterns, Compression, and Entropy Production in Phase-Separating Active Dumbbell Systems

Polar patterns and topological defects are ubiquitous in active matter. In this paper, we study a paradigmatic polar active dumbbell system through numerical simulations, to clarify how polar patterns and defects emerge and shape evolution. We focus on the interplay between these patterns and morphology, domain growth, irreversibility, and compressibility, tuned by dumbbell rigidity and interaction strength. Our results show that, when separated through MIPS, dumbbells with softer interactions can slide one relative to each other and compress more easily, producing blurred hexatic patterns, polarization patterns extended across entire hexatically varied domains, and stronger compression effects. Analysis of isolated domains reveals the consistent presence of inward-pointing topological defects that drive cluster compression and generate non-trivial density profiles, whose magnitude and extension are ruled by the rigidity of the pairwise potential. Investigation of entropy production reveals instead that clusters hosting an aster (spiral) defect are characterized by a flat (increasing) entropy profile mirroring the underlying polarization structure, thus suggesting an alternative avenue to distinguish topological defects on thermodynamical grounds. Overall, our study highlights how interaction strength and defect-compression interplay affect cluster evolution in particle-based active models, and also provides connections with recent studies of continuum polar active field models.

cond-mat.soft↗

arXiv2025

Cluster size determines internal structure of transcription factories in human cells

Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observations indicate that these proteins tend to form macromolecular clusters, known as transcription factories, whose morphology and composition is still debated. While some microscopy experiments have revealed the presence of specialised factories, composed of similar TFs transcribing families of related genes, sequencing experiments suggest instead that mixed clusters may be prevalent, as a panoply of different TFs binds promiscuously the same chromatin region. The mechanisms underlying the formation of specialised or mixed factories remain elusive. With the aim of finding such mechanisms, here we develop a chromatin polymer model mimicking the chromatin binding-unbinding dynamics of different types of complexes of TFs. Surprisingly, both specialised (i.e., demixed) and mixed clusters spontaneously emerge, and which of the two types forms depends mainly on cluster size. The mechanism promoting mixing is the presence of non-specific interactions between chromatin and proteins, which become increasingly important as clusters become larger. This result, that we observe both in simple polymer models and more realistic ones for human chromosomes, reconciles the apparently contrasting experimental results obtained. Additionally, we show how the introduction of different types of TFs strongly affects the emergence of transcriptional networks, providing a pathway to investigate transcriptional changes following gene editing or naturally occurring mutations.

physics.bio-ph↗

arXiv2025

Arrested phase separation and chiral symmetry breaking in active dumbbells under shear

Through molecular dynamics simulations, we investigate the phase separation and aggregation dynamics of active dumbbell particles in two-dimensions subjected to shear. We find that the growth of the phase-separated region is arrested when shear is applied, with the average clusters size plateauing towards a value $R_s$ that remains constant over time. While activity enhances the resilience of clusters against shear-induced breakup, $R_s$ decreases with growing shear rate $\dotγ$, with an intermediate regime where $R_s\propto \dotγ^{-1}$. We find that clusters in the stationary state are progressively less polarized and increasingly elongated with increasing shear. At the same time, we find a breaking in chiral symmetry of both rotation direction and internal organization of clusters: typically, dumbbells point towards the cluster center with a small non-zero angle, such that the active torque opposes the shear torque, with cluster's angular velocity well captured by a simplified analytical model. We argue this conformation makes clusters more stable against shear.

cond-mat.soft↗

arXiv2025

Phase Separation Kinetics in a Polar Active Field Model

A milestone of phase separation kinetics is the emergence of universal power laws $\sim t^{1/z}$ governing the domain growth evolution. We investigate a phase-separating polar active model comprising a scalar density field with an advective coupling to a polarization field. Our analysis reveals a novel $\sim t^{0.6}$ regime, which agrees well with the accelerated growth recently observed in simulations of polar active particles. We provide analytical arguments to explain how advection facilitates the creation of topological defects and compresses the domains leading to faster growth. We also show that the $\sim t^{0.6}$ regime is robust to several model generalizations.

cond-mat.soft↗

arXiv2025

Transverse Self-Propulsion Enhances the Aggregation of Active Dumbbells

We investigate a two-dimensional system of active Brownian dumbbells using molecular dynamics simulations. In this model, each dumbbell is driven by an active force oriented perpendicular to the axis connecting its two constituent beads. We characterize the resulting phase behavior and find that, across all values of activity, the system undergoes phase separation between dilute and dense phases. The dense phase exhibits hexatic order, and for large enough activity, we observe a marked increase in local polarization, with dumbbells predominantly oriented towards the interior of the clusters. Compared to the case of axially self-propelled dumbbells, we find that the binodal region is enlarged towards lower densities at all activities. This shift arises because dumbbells with transverse propulsion can more easily form stable cluster cores, serving as nucleation seeds, and show a highly suppressed escaping rate from the cluster boundary. Finally, we observe that clusters exhibit spontaneous rotation, with the modulus of the angular velocity scaling as $ω\sim r_g^{-2}$, where $r_g$ is the cluster's radius of gyration. This contrasts with axially propelled dumbbells, where the scaling follows $ω\sim r_g^{-1}$. We develop a simplified analytical model to rationalize this scaling behavior.

cond-mat.soft↗

arXiv2024

Two-states Brownian particle in a Harmonic Potential

We study the behaviour of a Brownian particle in the overdamped regime in the presence of a harmonic potential, assuming its diffusion coefficient to randomly jump between two distinct values. In particular, we characterize the probability distribution of the particle position and provide detailed expressions for the mean square displacement and the kurtosis. We highlight non-Gaussian behaviour even within the long-term limit carried over with an excess of probability both in the central part and in the distribution's tails. Moreover, when one of the two diffusion coefficients assumes the value zero, we provide evidence that the probability distribution develops a cusp. Most of our results are analytical, and corroborated by numerical simulations.

cond-mat.stat-mech↗

arXiv2024

Work fluctuations for a confined Brownian particle: the role of initial conditions

We study the large fluctuations of the work injected by the random force into a Brownian particle under the action of a confining harmonic potential. In particular, we compute analytically the rate function for generic uncorrelated initial conditions, showing that, depending on the initial spread, it can exhibit no, one, or two singularities associated to the onset of linear tails. A dependence on the potential strength is observed for large initial spreads (entailing two singularities), which is lost for stationary initial conditions (giving one singularity) and concentrated initial values (no singularity). We discuss the mechanism responsible for the singularities of the rate function, identifying it as a big jump in the initial values. Analytical results are corroborated by numerical simulations.

cond-mat.stat-mech↗

arXiv2024

Entropy production of active Brownian particles going from liquid to hexatic and solid phases

Due to its inherent intertwinement with irreversibility, entropy production is a prime observable to monitor in systems of active particles. In this numerical study, entropy production in the liquid, hexatic and solid phases of a two-dimensional system of active Brownian particles is examined at both average and fluctuation level. The trends of averages as functions of density show no singularity and marked changes in their derivatives at the hexatic-solid transition. Distributions show instead peculiar tail structures interpreted by looking at microscopic configurations. Particles in regions of low local order generate tail values according to different dynamical mechanisms: they move towards empty regions or bounce back and forth into close neighbours. The tail structures are reproduced by a simple single-particle model including an intermittent harmonic potential.

cond-mat.soft↗

arXiv2024

3D active nematic disclinations behave as Majorana quasiparticles

Quasiparticles are low-energy excitations with important roles in condensed matter physics. An intriguing example is provided by Majorana fermions, quasiparticles which are identical to their antiparticles. Despite being implicated in neutrino oscillations and topological superconductivity, their experimental realisations remain scarce. Here we propose a purely classical realisation of Majorana fermions, in terms of 3-dimensional disclination lines in active nematics. Activity is required to overcome the elastic cost associated with these excitations, so they can appear in steady state. We combine topology and simulations to show that active nematics under confinement spontaneously create in their interior topologically charged disclination lines and loops, akin to Majorana quasiparticles with finite momentum. Within an elongated channel, we find a phenomenology similar to that of the Kitaev chain, as local Majorana-like excitations appear near surfaces, while a non-local system-spanning helical disclination line can arise along the centre. In unconfined active turbulence, Majorana-like charged loops are instead exceedingly rare, suggesting that boundaries are crucial to generate these quasiparticles, as in quantum condensed matter. We suggest that 3-dimensional active disclinations can be used to probe the physics of Majorana spinors at a much larger scale than traditionally considered, potentially facilitating the experimental observation of their dynamics.

cond-mat.soft↗

arXiv2024

Controlling flow patterns and topology in active emulsions

Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive small droplets are embedded in a larger active droplet. We find activity introduces a variety of rich and nontrivial nonequilibrium states in the system. First, a double emulsion with a single active droplet becomes self-motile, and there is a transition between translational and rotational motion: both of these regimes remain defect-free, hence topologically trivial. Second, a pair of particles nucleate one or more disclination loops, with conformational dynamics resembling a rotor or chaotic oscillator, accessed by tuning activity. In the first state a single, topologically charged, disclination loop powers the rotation. In the latter state, this disclination stretches and writhes in 3D, continuously undergoing recombination to yield an example of an active living polymer. These emulsions can be self-assembled in the lab, and provide a pathway to form flow and topology patterns in active matter in a controllable way, as opposed to bulk systems that typically yield active turbulence.

cond-mat.soft↗

arXiv2024

Growth regimes in three-dimensional phase separation of liquid-vapor systems

The liquid-vapor phase separation is investigated via lattice Boltzmann simulations in three dimensions. After expressing length and time scales in reduced physical units, we combined data from several large simulations (on $512^3$ nodes), with different values of viscosity, surface tension and temperature, to obtain a single curve of rescaled length $\hat{l}$ as a function of rescaled time $\hat{t}$. We find evidence of the existence of kinetic and inertial regimes with growth exponents $α_d=1/2$ and $α_i=2/3$ over several time decades, with a crossover from $α_d$ to $α_i$ at $\hat{t} \simeq 1$. This allows us to rule out the existence of a viscous regime with $α_v=1$ in three-dimensional liquid-vapor isothermal phase separation, differently from what happens in binary fluid mixtures. An in-depth analysis of the kinetics of the phase separation process, as well as a characterization of the morphology and the flow properties, are further presented in order to provide clues into the dynamics of the phase-separation process.

cond-mat.soft↗

arXiv2024

Ion channels in critical membranes: clustering, cooperativity, and memory effects

Much progress has been made in elucidating the inner workings of voltage-gated ion channels, but less understood is the influence of lipid rafts on gating kinetics. Here we propose that state-dependent channel affinity for different lipid species provides a unified explanation for the experimentally observed behaviors of clustering, cooperativity, and hysteresis. We develop models of diffusing lipids and channels engaged in Ising-like interactions to investigate the collective behaviors driven by raft formation in critical membranes close to the demixing transition. The model channels demonstrate lipid-mediated long-range interactions, activation curve steepening, and long-term memory in ionic currents. These behaviors likely play a role in channel-mediated cellular signaling and suggest a universal mechanism for self-organization of biomolecular assemblies.

cond-mat.soft↗

arXiv2023

Phase Coexistence and Edge Currents in the Chiral Lennard-Jones Fluid

We study a model chiral fluid in two dimensions composed of Brownian disks interacting via a Lennard-Jones potential and a non-conservative transverse force, mimicking colloids spinning at a rate $ω$. The system exhibits a phase separation between a chiral liquid and a dilute gas phase that can be characterized using a thermodynamic framework. We compute the equations of state and show that the surface tension controls interface corrections to the coexisting pressure predicted from the equal-area construction. Transverse forces increase surface tension and generate edge currents at the liquid-gas interface. The analysis of these currents shows that the rotational viscosity introduced in chiral hydrodynamics is consistent with microscopic bulk mechanical measurements. Chirality can also break the solid phase, giving rise to a dense fluid made of rotating hexatic patches. Our work paves the way for the development of the statistical mechanics of chiral particles assemblies.

cond-mat.soft↗