arXiv subjects

Chantal Valeriani

Publications and source records attributed to Chantal Valeriani.

At least 37 records · Page 2Linked to original sources

arXiv2025

Collective filament wrapping and nested spiral formation in active polydisperse systems

We investigate a two-dimensional polydisperse suspension of self-propelled semiflexible filaments and reveal a collective wrapping mechanism that is absent in monodisperse systems. At intermediate activity levels, long filaments coil around shorter ones, forming nested spiral structures stabilized by filament length disparity. These assemblies generalize the single-filament spiraling seen in active systems into cooperative, multi-filament configurations. As activity increases, the nested spirals undergo structural transitions: medium-length filaments unwind, longer filaments encapsulate shorter ones, and eventually all spiral structures dissolve. This reorganization is reflected in the dynamics, where van Hove distributions uncover coexisting confined and motile filament populations. Our findings identify filament length as a key control parameter for nonequilibrium self-assembly and establish inter-filament wrapping as a minimal mechanism for hierarchical organization in active matter. This mechanism provides a simple model for the cooperative confinement and structural hierarchy observed in both biological and synthetic active systems.

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arXiv2025

Numerical methods for unraveling inter-particle potentials in colloidal suspensions: A comparative study for two-dimensional suspensions

We compare three model-free numerical methods for inverting structural data to obtain interaction potentials, namely iterative Boltzmann inversion (IBI), test-particle insertion (TPI), and a machine-learning (ML) approach called ActiveNet. Three archetypal models of two-dimensional colloidal systems are used as test cases: Weeks--Chandler--Anderson short-ranged repulsion, the Lennard-Jones potential, and a repulsive shoulder interaction with two length scales. Additionally, data on an experimental suspension of colloidal spheres are acquired by optical microscopy and used to test the inversion methods. The methods have different merits. IBI is the only choice when the radial distribution function is known but particle coordinates are unavailable. TPI requires snapshots with particle positions and can extract both pair- and higher-body potentials without the need for simulation. The ML approach can only be used when particles can be tracked in time and it returns the force rather than the potential. However, it can unravel pair interactions from any one-body forces (such as drag or propulsion) and does not rely on equilibrium distributions for its derivation. Our results may serve as a guide when a numerical method is needed for application to experimental data, and as a reference for further development of the methodology itself.

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arXiv2025

Discovering dynamic laws from observations: the case of self-propelled, interacting colloids

Active matter spans a wide range of time and length scales, from groups of cells and synthetic self-propelled particles to schools of fish, flocks of birds, or even human crowds. The theoretical framework describing these systems has shown tremendous success at finding universal phenomenology. However, further progress is often burdened by the difficulty of determining the forces that control the dynamics of the individual elements within each system. Accessing this local information is key to understanding the physics dominating the system and to create the models that can explain the observed collective phenomena. In this work, we present a machine-learning model, a graph neural network, that uses the collective movement of the system to learn the active and two-body forces controlling the individual dynamics of the particles. We verify our approach using numerical simulations of active brownian particles, considering different interaction potentials and levels of activity. Finally, we apply our model to experiments of electrophoretic Janus particles, extracting the active and two-body forces that control the dynamics of the colloids. Due to this, we can uncover the physics dominating the behavior of the system. We extract an active force that depends on the electric field and also area fraction. We also discover a dependence of the two-body interaction with the electric field that leads us to propose that the dominant force between these colloids is a screened electrostatic interaction with a constant length scale. We expect that this methodology can open a new avenue for the study and modeling of experimental systems of active particles.

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arXiv2025

Interfacial Free Energy as the Key to the Pressure-Induced Deceleration of Ice Nucleation

The avoidance of water freezing is the holy grail in the cryopreservation of biological samples, food, and organs. Fast cooling rates are used to beat ice nucleation and avoid cell damage. This strategy can be enhanced by applying high pressures to decrease the nucleation rate, but the physics behind this procedure has not been fully understood yet. We perform computer experiments to investigate ice nucleation at high pressures consisting in embedding ice seeds in supercooled water. We find that the slowing down of the nucleation rate is mainly due to an increase of the ice I-water interfacial free energy with pressure. Our work also clarifies the molecular mechanism of ice nucleation for a wide pressure range. This study is not only relevant to cryopreservation, but also to water amorphization and climate change modeling.

cond-mat.stat-mech↗

arXiv2024

Active Polymer Behavior in Two Dimensions: A Comparative Analysis of Tangential and Push-Pull Models

In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers. These models serve as valuable frameworks for understanding self-organization in biological polymers and synthetic materials. At low activity, all models exhibit similar behaviors. Differences emerge in the intermediate range as activity increases, though at higher activity levels, their behaviors converge. Importantly, adjusting for differences in mean active force reveals nearly identical behavior across models. Our results highlight the importance of force definitions in active polymer simulations and provide insights into phase transitions across varying filament configurations.

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arXiv2024

Sedimentation and structure of squirmer suspensions under gravity

The effect of gravity on the collective motion of living microswimmers, such as bacteria and micro-algae, is pivotal to unravel not only bio-convection patterns but also the settling of bacterial biofilms on solid surfaces. In this work, we investigate suspensions of microswimmers under the influence of a gravitational field and hydrodynamics, simulated via dissipative particle dynamics (DPD) coarse-grained model. We first study the collective sedimentation of passive colloids and microswimmers of the puller and pusher types upon increasing the imposed gravitational field and compare with previous results. Once sedimentation occurs, we observe that, as the gravitational field increases, the bottom layer undergoes a transition to an ordered state compatible with a hexagonal crystal. In comparison with passive colloids, both pullers and pushers easily rearrange at the bottom layer to anneal defects. Specifically, pullers are better than pushers in preserving the hexagonal order of the bottom mono-layer at high gravitational fields.

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arXiv2024

Self-Assembly of Active Bivalent Patchy Particles

In the present work, with the intent of exploring the out-of-equilibrium polymerization of active patchy particles in linear chains, we study a suspension of active bivalent Brownian particles (ABBPs). At all studied temperatures and densities, ABBPs self-assemble in aggregating chains, as opposed to the uniformly space-distributed chains observed in the corresponding passive systems. The main effect of activity, other than inducing chain aggregation, is to reduce the chain length and favor alignment of the propulsion vectors in the bonding process. At low activities, attraction dominates over activity in the bonding process, leading self-assembly to occur randomly regardless of the particle orientations.Interestingly, we find that at the lowest temperature, as density increases, chains aggregate forming a novel state: MISP, i.e., Motility-Induced Spirals, where spirals are characterised by a finite angular velocity. On the contrary, at the highest temperature, density and activity, chains aggregate forming a different novel state (a spinning crystalline cluster) characterized by a compact and hexagonal ordered structure, both translating and rotating. The rotation arises from an effective torque generated by the presence of competing domains where particles self-propel in the same direction.

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arXiv2024

Anomalous behaviour of transport properties in a supercooled water-glycerol mixture

Glycerol acts as a natural cryoprotectant by depressing the temperature of ice nucleation and slowing down the dynamics of water mixtures. In this work we characterize dynamics -- diffusion, viscosity, and hydrogen-bond dynamics -- as well as density anomaly and structure of water mixtures with 1\% to 50\% w/w glycerol at low temperatures via molecular dynamics simulations using all-atom and coarse-grained models. Simulations reveal distinct violations of the Stokes-Einsten relation in the low temperature regime for water and glycerol. Deviations are positive for water at all concentrations, and positive for glycerol in very dilute solutions but turning negative in concentrated ones. The all-atom and coarse-grained models reveal an unexpected crossover in the dynamics of the 1% and 10 % w/w glycerol at the lowest simulated temperatures. This crossover manifests in the diffusion coefficients of water and glycerol, as well as in the viscosity and lifetime of hydrogen-bonds in water. We interpret that the crossover originates on the opposing dependence with glycerol concentration of the two factors controlling the solution's slow-down: the increase in tetrahedrally coordinated water and the dynamics and clustering of the glycerol molecules. We anticipate that this dynamic crossover will also occur for solution of water with other polyols.

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arXiv2024

Re-entrant percolation in active Brownian hard disks

Non-equilibrium clustering and percolation are investigated in an archetypal model of two-dimensional active matter using dynamic simulations of self-propelled Brownian repulsive particles. We concentrate on the single-phase region up to moderate levels of activity, before motility-induced phase separation (MIPS) sets in. Weak activity promotes cluster formation and lowers the percolation threshold. However, driving the system further out of equilibrium partly reverses this effect, resulting in a minimum in the critical density for the formation of system-spanning clusters and introducing re-entrant percolation as a function of activity in the pre-MIPS regime. This non-monotonic behaviour arises from competition between activity-induced effective attraction (which eventually leads to MIPS) and activity-driven cluster breakup. Using an adapted iterative Boltzmann inversion method, we derive effective potentials to map weakly active cases onto a passive (equilibrium) model with conservative attraction, which can be characterised by Monte Carlo simulations. While the active and passive systems have practically identical radial distribution functions, we find decisive differences in higher-order structural correlations, to which the percolation threshold is highly sensitive. For sufficiently strong activity, no passive pairwise potential can reproduce the radial distribution function of the active system.

cond-mat.stat-mech↗

arXiv2024

Collective motion of energy depot active disks

In the present work we have studied collectives of active disks with an energy depot, moving in the two-dimensional plane and interacting via excluded volume. The energy depot accounts for the extraction of energy taking place at the level of each particle in order to perform self-propulsion, included in an underdampled Langevin dynamics. We show that this model undergoes a flocking transition, exhibiting some of the key features of the Vicsek model, namely, band formation and giant number fluctuations. Large density bands disappear as the activity is further increased, eventually reaching a homogeneous polar state. We unravel an effective alignment interaction at the level of two-particle collisions that can be controlled by activity and gives rise to flocking at large scales.

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arXiv2024

Tangentially Active Polymers in Cylindrical Channels

We present an analytical and computational study characterizing the structural and dynamical properties of an active filament confined in cylindrical channels. We first outline the effects of the interplay between confinement and polar self-propulsion on the conformation of the chains. We observe that the scaling of the polymer size in the channel, quantified by the end-to-end distance, shows different anomalous behaviours at different confinement and activity conditions. Interestingly, we show that the universal relation, describing the ratio between the end-to-end distance of passive polymer chains in cylindrical channels and in bulk is broken by activity. Finally, we show that the long-time diffusion coefficient under confinement can be rationalised by an analytical model, that takes into account the presence of the channel and the elongated nature of the polymer.

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arXiv2023

The carnivorous plant Genlisea harnesses active particle dynamics to prey on microfauna

Carnivory in plants is an unusual trait that has arisen multiple times, independently, throughout evolutionary history. Plants in the genus Genlisea are carnivorous, and feed on microorganisms that live in soil using modified subterranean leaf structures (rhizophylls). A surprisingly broad array of microfauna has been observed in the plants' digestive chambers, including ciliates, amoebae and soil mites. Here we show, through experiments and simulations, that Genlisea exploit active matter physics to 'rectify' bacterial swimming and establish a local flux of bacteria through the structured environment of the rhizophyll towards the plant's digestion vesicle. In contrast, macromolecular digestion products are free to diffuse away from the digestion vesicle and establish a concentration gradient of carbon sources to draw larger microorganisms further inside the plant. Our experiments and simulations show that this mechanism is likely to be a localised one, and that no large-scale efflux of digested matter is present.

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arXiv2023

Non-monotonous translocation time of polymers across pores

Polymers confined in corrugated channels, i.e. channels of varying amplitude, display {multiple local maxima and minima of the diffusion coefficient upon increasing their degree of polymerization $N$}. We propose a theoretical effective free energy for linear polymers based on a Fick-Jacobs approach. We validate the predictions against numerical data, obtaining quantitative agreement for {the effective free energy, the diffusion coefficient and the Mean First Passage Time}. Finally, we employ the effective free energy to compute the polymer lengths $N_{min}$ at which the diffusion coefficient presents a minimum: we find a scaling expression that we rationalize with a blob model. Our results could be useful to design porous adsorbers, that separate polymers of different sizes without the action of an external flow.

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arXiv2023

Rheology of Pseudomonas fluorescens biofilms: from experiments to predictive DPD mesoscopic modelling

Bacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria crosslinked to a selfproduced network of extracellular polymeric substances (EPS) embedded in water. Structural principles for numerical modelling aim at describing mesoscopic viscoelasticity without loosing detail on the underlying interactions existing in wide regimes of deformation under hydrodynamic stress. Here we approach the computational challenge to model bacterial biofilms for predictive mechanics in silico under variable stress conditions. Up-to-date models are not entirely satisfactory due to the plethora of parameters required to make them functioning under the effects of stress. As guided by the structural depiction gained in a previous work with Pseudomonas fluorescens (Jara et al. Front. Microbiol. (2021)), we propose a mechanical modeling by means of Dissipative Particle Dynamics (DPD), which captures the essentials of the topological and compositional interactions between bacteria particles and crosslinked EPS-embedding under imposed shear. The P. fluorescens biofilms have been modeled under mechanical stress mimicking shear stresses as undergone in vitro. The predictive capacity for mechanical features in DPD-simulated biofilms has been investigated by varying the externally imposed field of shear strain at variable amplitude and frequency. The parametric map of essential biofilm ingredients has been explored by making the rheological responses to emerge among conservative mesoscopic interactions and frictional dissipation in the underlying microscale. The proposed coarse grained DPD simulation qualitatively catches the rheology of the P. fluorescens biofilm over several decades of dynamic scaling.

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arXiv2023

Minimal numerical ingredients describe chemical microswimmers's 3D motion

The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore, developing a minimal (and more general) model capable of capturing the overall dynamics of these autonomous particles is highly desirable. In the presented work, we demonstrate that a coarse-grained dissipative particle-hydrodynamics model is capable of describing the behaviour of various chemical microswimmer systems. Specifically, we show how a competing balance between hydrodynamic interactions experienced by a squirmer in the presence of a substrate, gravity, and mass and shape asymmetries can reproduce a range of dynamics seen in different experimental systems. We hope that our general model will inspire further synthetic work where various modes of swimmer motion can be encoded via shape and mass during fabrication, helping to realise the still outstanding goal of microswimmers capable of complex 3-D behaviour

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arXiv2023

Self-organized states of solutions of active ring polymers in bulk and under confinement

In the presented work we study, by means of numerical simulations, the behaviour of a suspension of active ring polymers in the bulk and under lateral confinement. When changing the separation between the confining planes and the polymers' density, we detect the emergence of a self-organised dynamical state, characterised by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. This system represents a peculiar case at the crossing point between polymer, liquid crystals and active matter physics, where the interplay between activity, topology and confinement leads to a spontaneous segregation of a one component solution.

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arXiv2023

Colloidal Hard Spheres: Triumphs, Challenges and Mysteries

The simplicity of hard spheres as a model system is deceptive. Although the particles interact solely through volume exclusion, that nevertheless suffices for a wealth of static and dynamical phenomena to emerge, making the model an important target for achieving a comprehensive understanding of matter. In addition, while real colloidal suspensions are typically governed by complex interactions, Pusey and Van Megen [Nature 320 340--342 (1986)] demonstrated that suitably tuned suspensions result in hard-sphere like behavior, thus bringing a valuable experimental complement to the celebrated theoretical model. Colloidal hard spheres are thus both a material in their own right and a platform upon which phenomena exhibited by simple materials can be explored in great detail. These various purposes enable a particular synergy between experiment, theory and computer simulation. Here we review the extensive body of work on hard spheres, ranging from their equilibrium properties such as phase behavior, interfaces and confinement to some of the non--equilibrium phenomena they exhibit such as sedimentation, glass formation and nucleation.

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arXiv2022

Rheology of Pseudomonas fluorescens biofilms: from experiments to DPD mesoscopic modelling

The presence of bacterial biofilms in clinical and industrial settings is a major issue worldwide. A biofilm is a viscoelastic matrix, composed of bacteria producing a network of Extracellular Polymeric Substances (EPS) to which bacteria crosslink. Modelling of complex biofilms is relevant to provide accurate descriptions and predictions that include parameters as hydrodynamics, dynamics of the bacterial population and solute mass transport. However, up-to-date numerical modelling, even at a coarse-grained level, is not satisfactorily. In this work, we present a numerical coarse-grain model of a bacterial biofilm, consisting of bacteria immersed in an aqueous matrix of a polymer network, that allows to study rheological properties of a biofilm. We study its viscoelastic modulus, varying topology and composition (such as the number of crosslinks between EPS polymers, the number of bacteria and the amount of solvent), and compare the numerical results with experimental rheological data of Pseudomonas fluorescens biofilms grown under static and shaking conditions, as previously described by Jara et al, Frontiers in Microbiology (2021).

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