arXiv subjects

Davide Breoni

Publications and source records attributed to Davide Breoni.

13 recordsLinked to original sources

arXiv2026

Coarse-grained simulations of dsDNA polycatenanes and network formation in annular nanochannels with topoisomerase II

We numerically investigate the behavior of a system of initially unlinked nicked dsDNA rings confined into an annular square nanochannel in the presence of TopoII. Channel confinement can enhance the catenation likelihood by bringing highly bent regions from different rings in close proximity, while at the same time reducing the emergence of knots. The annular channel topology simplifies the characterization of the system by removing periodic boundary conditions and can lead to the formation of circular catenanes.We characterize the equilibrium and dynamical properties of the steady-state system, including the amount of catenation and the topologies explored by the system, under different parameters of the model and for different levels of confinement. We argue that a similar setup could allow for a direct comparison between experiments and simulations under well characterized and controlled conditions, thus providing a way to select and tune computational models of TopoII, as well as provide a way to obtain dsDNA interlocked materials in a controlled fashion.

cond-mat.soft↗

arXiv2026

Active embracement enables autonomous tweezing in active star polymers

The capacity for autonomous structural reconfiguration is a defining trait of living systems, yet it remains elusive in artificial active matter. Here, we report the discovery of active embracement, a non-equilibrium phenomenon where active star polymers, comprising a central core and self-propelled monomeric arms, transition from open configurations to tightly collapsed, ``hugging'' states. By combining polymer experiments using connected vibrobots with simulations, we demonstrate that internal self-propulsion fundamentally overrides the steric repulsion that keeps passive polymers dispersed. This active drive enables a suite of behaviors unattainable in equilibrium systems: individual star polymers undergo a globular-like self-collapse, multiple star polymers mutually intertwine and mutually embrace, and can spontaneously embrace and capture surrounding passive particles. Our findings reveal that active embracement is a distinct kinetic phase that allows star polymers to function as autonomous tweezers. By bridging the gap between macroscopic robotic collectives and microscopic polymer physics, this work provides a versatile blueprint for the design of smart materials capable of targeted cargo capture and self-directed assembly in complex environments.

cond-mat.soft↗

arXiv2026

Controlling microalgae populations by phototactic memory

Understanding how microorganisms navigate in complex environments is a central question in active matter and biological physics. Phototaxis - the ability to use light as a navigation cue - is a widespread strategy in motile microalgae to optimise photosynthesis and avoid light-induced stress. The microalga Chlamydomonas reinhardtii is a model system for studying this behaviour, where navigation is classically attributed to a photosensitive organelle named eyespot. While this mechanism enables cells to sense the direction of incoming light, their response to light intensity gradients remains less understood. Here we show that structured light landscapes can guide microalgae populations and localise them in defined spatial regions. By analysing single-cell trajectories, we find that cells actively steer relative to the local light gradient, and a comparison with a minimal theoretical model shows that a short-time memory of light exposure acting on the transition between positive and negative phototaxis is necessary to reproduce the observed accumulation. At longer times, we observe a gradual decrease in cell number density within the trapping region, consistent with phototactic adaptation. Beyond controlling population dynamics, our results reveal new aspects of phototactic behaviour, highlighting gradient-aligned steering together with temporal integration as central mechanisms for navigation in structured environments.

cond-mat.soft↗

arXiv2025

The effects of solvent quality and core wetting on the circularization of star polymers

We simulate the formation of cyclical arms in star polymers, focusing on the effects of solvent quality on their resulting linking complexity and gyration radius. We find that polymers circularized in bad solvent present a higher degree of linking among arms with respect to those circularized in good solvent. When both are transported to good solvent, this results in a smaller gyration radius of the former with respect to the latter. This effect is magnified when the polymers present a sufficiently small number of arms (or functionality $f$): in this case, in bad solvent, all arms tend to clump together on one side of the central core, due to circularization, and can hence all interact with each other. Instead, when $f$ is large enough, the whole surface of the core is wetted by the arms, whose distribution becomes radially symmetric. This hinders interactions between faraway arms and reduces the probability of inter-arm linking. Interestingly, we find that both the critical $f_c$ at which the clump transition happens and the minimal arm length $n_c$ for which the transition appears depend on the core size: the grafting density of the arms must be larger than a certain constant $\rho_g^c$, while their length must be sufficient to stretch for, at least, half of the core's circumference.

cond-mat.soft↗

arXiv2025

Effects of knotting on the collapse of active ring polymers

We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of polymerization. We find that topology has a significant effect on the polymer size at which the collapse takes place, with twist knots collapsing earlier than torus knots. Increasing knot complexity further accentuates this difference, as the collapse point of torus knots grows linearly with the minimum crossing number of the knot while that of twist knots shrinks, eventually canceling the actively stretched regime altogether. This behavior is a consequence of the ordered configuration of torus knots in their stretched active state, featuring an effective alignment for non-neighboring bonds which increases with the minimal crossing number. Twist knots do not feature ordered configurations or bond alignment, increasing the likelihood of collisions, leading to collapse. These results show that topology yields a degree of control on the properties of active ring polymers, and can be used to tune them. At the same time, they suggest that activity might introduce a bias for torus knots, as complex twist knots cannot be formed in extended active polymers.

cond-mat.soft↗

arXiv2024

Conformation and topology of cyclical star polymers

We study the conformation and topological properties of cyclical star polymers with $f$ ring arms, each made of $n$ beads. We find that the conformational properties of unlinked cyclical star polymers are compatible to those of linear star polymers with $2f$ arms made of $n/2$ beads each. This compatibility vanishes when the topology of the star, measured as the degree of linking between arms, changes. In fact, when links are allowed we notice that the gyration radius decreases as a function of the absolute linking number $\vert Lk \vert$ of the arms, regardless of the protocol that is employed to introduce said links. Furthermore, the internal structure of the macromolecules, as highlighted by the radial density function, changes qualitatively for large values of $\vert Lk \vert$.

cond-mat.soft↗

arXiv2024

Dynamical clustering and wetting phenomena in inertial active matter

Dynamical clustering represents a characteristic feature of active matter consisting of self-propelled agents that convert energy from the environment into mechanical motion. At the micron scale, typical of overdamped dynamics, particles with opposite motility block each other and show transient dynamical arrest that can induce cluster nucleation and motility-induced phase separation. However, for macroscopic agents, inertia plays a leading role, and clustering is strongly affected by bounce-back effects during collisions that could inhibit cluster growth. Here we present an experiment on the clustering of active granular particles, in which inertia can be systematically tuned. A plethora of new phenomena impacted severely by inertia is presented. Clusters display an inertia-induced transition from liquid-like to crystal-like inner structures that is accompanied by the suppression of cluster nucleation at system boundaries due to particle inertia. In contrast to microswimmers, where active particles wet the boundary by primarily forming clusters attached to the container walls, in an underdamped inertial active system, walls do not favor cluster formation and effectively annihilate motility-induced wetting phenomena.

cond-mat.soft↗

arXiv2023

Giant Activity-Induced Stress Plateau in Entangled Polymer Solutions

We study the viscoelastic properties of highly entangled, flexible, self-propelled polymers using Brownian dynamics simulations. Our results show that the active motion of the polymer increases the height of the stress plateau by orders of magnitude due to the emergence of grip forces at entanglement points. Identifying the activity-induced energy of a single polymer and the ratio of polymer length to self-propulsion velocity as relevant energy and time scales, we find the stress autocorrelation functions collapse across P\'eclet numbers. We predict that the long-time viscosity scales with polymer length squared $\sim L^2$, in contrast to equilibrium counterparts $\sim L^3$. These insights offer prospects for designing new materials with activity-responsive mechanical properties.

cond-mat.soft↗

arXiv2023

Patchy landscapes promote stability of small groups

Group formation and coordination are fundamental characteristics of living systems, essential for performing tasks and ensuring survival. Interactions between individuals play a key role in group formation, and the impact of resource distributions is a vibrant area of research. Using active particles in a tuneable optical environment as a model system, we demonstrate that heterogeneous energy source distributions result in smaller, more stable groups with reduced individual exchange between clusters compared to homogeneous conditions. Reduced group sizes can be beneficial to optimise resources in heterogeneous environments and to control information flow within populations. Devoid of biological complications, our system provides insights into the importance of patchy landscapes in ecological dynamics and holds implications for refining swarm intelligence algorithms and enhancing crowd control techniques.

cond-mat.soft↗

arXiv2022

A one-dimensional three-state run-and-tumble model with a `cell cycle'

We study a one-dimensional three-state run-and-tumble model motivated by the bacterium Caulobacter crescentus which displays a cell cycle between two non-proliferation mobile phase and a proliferating sedentary phase. Our model implements kinetic transitions between the two mobile and one sedentary states described in terms of their number densities, where mobility is allowed with different running speeds in forward and backward direction. We start by analyzing the stationary states of the system and compute the mean and squared-displacements for the distribution of all cells, as well as for the number density of settled cells. The latter displays a surprising super-ballistic scaling ~t^3 at early times. Including repulsive and attractive interactions between the mobile cell populations and the settled cells, we explore the stability of the system and then employ numerical methods to study structure formation in the fully nonlinear system. We find traveling waves of bacteria, whose occurrence is quantified in a nonequilibrium state diagram.

cond-mat.soft↗

arXiv2021

Brownian particles driven by spatially periodic noise

We discuss the dynamics of a Brownian particle under the influence of a spatially periodic noise strength in one dimension using analytical theory and computer simulations. In the absence of a deterministic force, the Langevin equation can be integrated formally exactly. We determine the short- and long-time behaviour of the mean displacement (MD) and mean-squared displacement (MSD). In particular we find a very slow dynamics for the mean displacement, scaling as $t^{-1/2}$ with time $t$. Placed under an additional external periodic force near the critical tilt value we compute the stationary current obtained from the corresponding Fokker-Planck equation and identify an essential singularity if the minimum of the noise strength is zero. Finally, in order to further elucidate the effect of the random periodic driving on the diffusion process, we introduce a phase factor in the spatial noise with respect to the external periodic force and identify the value of the phase shift for which the random force exerts its strongest effect on the long-time drift velocity and diffusion coefficient.

cond-mat.stat-mech↗

arXiv2021

Active noise-driven particles under space-dependent friction in one dimension

We study a Langevin equation describing the stochastic motion of a particle in one dimension with coordinate $x$, which is simultaneously exposed to a space-dependent friction coefficient $\gamma(x)$, a confining potential $U(x)$ and non-equilibrium (i.e., active) noise. Specifically, we consider frictions $\gamma(x)=\gamma_0 + \gamma_1 | x |^p$ and potentials $U(x) \propto | x |^n$ with exponents $p = 1,2$ and $n = 0, 1, 2$. We provide analytical and numerical results for the particle dynamics for short times and the stationary probability density functions (PDFs) for long times. The short-time behaviour displays diffusive and ballistic regimes while the stationary PDFs display unique characteristic features depending on the exponent values $(p, n)$. The PDFs interpolate between Laplacian, Gaussian and bimodal distributions, whereby a change between these different behaviours can be achieved by a tuning of the friction strengths ratio $\gamma_0/\gamma_1$. Our model is relevant for molecular motors moving on a one-dimensional track and can also be realized for confined self-propelled colloidal particles.

cond-mat.soft↗

arXiv2020

Active Brownian and inertial particles in disordered environments: short-time expansion of the mean-square displacement

We consider an active Brownian particle moving in a disordered two-dimensional energy or motility landscape. The averaged mean-square-displacement (MSD) of the particle is calculated analytically within a systematic short-time expansion. As a result, for overdamped particles, both an external random force field and disorder in the self-propulsion speed induce ballistic behaviour adding to the ballistic regime of an active particle with sharp self-propulsion speed. Spatial correlations in the force and motility landscape contribute only to the cubic and higher order powers in time for the MSD. Finally, for inertial particles two superballistic regimes are found where the scaling exponent of the MSD with time is $\alpha=3$ and $\alpha=4$. We confirm our theoretical predictions by computer simulations. Moreover they are verifiable in experiments on self-propelled colloids in random environments.

cond-mat.soft↗