arXiv subjects

C. Valeriani

Publications and source records attributed to C. Valeriani.

At least 19 recordsLinked to original sources

arXiv2026

Tunable mesoscopic numerical model for bacterial biofilms

We present a tunable mesoscale model to provide a basis for future rheological calculations of of bacterial biofilms, explicitly incorporating reversible crosslinking within the extracellular polymeric substance (EPS) matrix. Using a Dissipative Particle Dynamics framework combined with a Gillespie-inspired algorithm, bonds between polymers and bacteria dynamically form and break, capturing the intrinsically evolving nature of the network. We show that biofilm structure is governed by a competition between polymer-polymer and polymer-bacteria crosslinks, controlled by binding energy, linker availability, and bond stiffness and provide a minimal model that helps to understand the competition between both species.

physics.comp-ph↗

arXiv2024

Coil-to-globule collapse of active polymers: a Rouse perspective

We derive an effective Rouse model for tangentially active polymers, characterized by a constant active force tangent to their backbone. In particular, we show that, once extended to account for finite bending rigidity, such active Rouse model captures the reduction in the gyration radius, or coil-to-globule-like transition, that has been observed numerically in the literature for such active filaments. Interestingly, our analysis identifies the proper definition of the Peclet number, that allows to collapse all numerical data onto a master curve.

cond-mat.soft↗

arXiv2021

Self-assembly of active amphiphilic Janus particles

In this article, we study the phenomenology of a two dimensional dilute suspension of active amphiphilic Janus particles. We analyze how the morphology of the aggregates emerging from their self-assembly depends on the strength and the direction of the active forces. We systematically explore and contrast the phenomenologies resulting from particles with a range of attractive patch coverages. Finally, we illustrate how the geometry of the colloids and the directionality of their interactions can be used to control the physical properties of the assembled active aggregates and suggest possible strategies to exploit self-propulsion as a tunable driving force for self-assembly.

cond-mat.soft↗

arXiv2021

An active approach to colloidal self-assembly

In this review we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and suggest possible strategies on how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise for the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.

cond-mat.soft↗

arXiv2015

Anomalous dynamics of an elastic membrane in an active fluid

Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance to bending and the self-propulsion strength of the active components in solution. We show how flexible membranes tend to collapse into multi-folded states, whereas stiff membranes oscillates between an extended configuration and a singly folded state. This study provides a simple example of how to exploit the random motion of active particles to perform mechanical work at the micro-scale.

cond-mat.soft↗

arXiv2014

Homogeneous ice nucleation evaluated for several water models

In this work, we evaluate by means of computer simulations the rate for ice homogeneous nucleation for several water models such as TIP4P, TIP4P/2005,TIP4P/ICE, and mW (following the same procedure as in Sanz et al. [J. Am. Chem. Soc.135, 15008 (2013)]) in a broad temperature range. We estimate the ice-liquid interfacial free-energy, and conclude that for all water models γ decreases as the temperature decreases. Extrapolating our results to the melting temperature, we obtain a value of the interfacial free-energy between 25 and 32 mN/m in reasonable agreement with the reported experimental values. Moreover, we observe that the values of γ depend on the chosen water model and this is a key factor when numerically evaluating nucleation rates, given that the kinetic prefactor is quite similar for all water models with the exception of the mW (due to the absence of hydrogens). Somewhat surprisingly the estimates of the nucleation rates found in this work for TIP4P/2005 are slightly higher than those of the mW model, even though the former has explicit hydrogens. Our results suggest that it may be possible to observe in computer simulations spontaneous crystallization of TIP4P/2005 at about 60 K below the melting point.

cond-mat.stat-mech↗

arXiv2014

The role of particle shape in active depletion

Using numerical simulations, we study how a solution of small active disks, acting as depletants, induces effective interactions on large passive colloids. Specifically, we analyze how the range, strength, and sign of these interactions are crucially dependent on the shape of the colloids. Our findings indicate that while colloidal rods experience a long-ranged predominantly attractive interaction, colloidal disks feel a purely repulsive force that is short-ranged in nature and grows in strength with the size ratio between the colloids and active depletants. For colloidal rods, simple scaling arguments are proposed to characterize the strength of these induced interactions.

cond-mat.soft↗

arXiv2014

Curvature Induced Activation of a Passive Tracer in an Active Bath

We use numerical simulations to study the motion of a large asymmetric tracer immersed in a low density suspension of self-propelled nanoparticles in two dimensions. Specifically, we analyze how the curvature of the tracer affects its translational and rotational motion in an active environment. We find that even very small amounts of curvature are sufficient for the active bath to impart directed motion to the tracer which results in its effective activation. We propose simple scaling arguments to characterize this induced activity in terms of the curvature of the tracer and the strength of the self-propelling force. Our results suggest new ways of controlling the transport properties of passive tracers in an active medium by carefully tailoring their geometry.

cond-mat.soft↗

arXiv2014

Anomalous Thermomechanical Properties of a Self-propelled Colloidal Fluid

We use numerical simulations to compute the equation of state of a suspension of spherical, self-propelled nanoparticles. We study in detail the effect of excluded volume interactions and confinement as a function of the system temperature, concentration and strength of the propulsion. We find a striking non-monotonic dependence of the pressure with the temperature, and provide simple scaling arguments to predict and explain the occurrence of such an anomalous behavior. We conclude the paper by explicitly showing how our results have an important implications for the effective forces exerted by fluids of self-propelled particles on passive, larger components.

cond-mat.soft↗

arXiv2014

Living clusters and crystals from low density suspensions of active colloids

Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move towards each other as a result of active agents (e.g. by molecular motors). In both cases fluid-like `living' clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behaviour onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.

cond-mat.soft↗

arXiv2013

Homogeneous ice nucleation at moderate supercooling from molecular simulation

Among all the freezing transitions, that of water into ice is probably the most relevant to biology, physics, geology or atmospheric science. In this work we investigate homogeneous ice nucleation by means of computer simulations. We evaluate the size of the critical cluster and the nucleation rate for temperatures ranging between 15K and 35K below melting. We use the TIP4P/2005 and the TIP4P/Ice water models. Both give similar results when compared at the same temperature difference with the model's melting temperature. The size of the critical cluster varies from $\sim$8000 molecules (radius$ = 4$nm) at 15K below melting to $\sim$600 molecules (radius$ = 1.7$nm) at 35K below melting. We use Classical Nucleation Theory (CNT) to estimate the ice-water interfacial free energy and the nucleation free energy barrier. We obtain an interfacial free energy of 29(3)mN/m from an extrapolation of our results to the melting temperature. This value is in good agreement both with experimental measurements and with previous estimates from computer simulations of TIP4P-like models. Moreover, we obtain estimates of the nucleation rate from simulations of the critical cluster at the barrier top. The values we get for both models agree within statistical error with experimental measurements. At temperatures higher than 20K below melting we get nucleation rates slower than the appearance of a critical cluster in all the water of the hydrosphere in the age of the universe. Therefore, our simulations predict that water freezing above this temperature must necessarily be heterogeneous.

cond-mat.soft↗

arXiv2013

Homogeneous bubble nucleation in water at negative pressure: A Voronoi polyhedra analysis

We investigate vapor bubble nucleation in metastable TIP4P/2005 water at negative pressure via the Mean First Passage Time (MFPT) method using the volume of the largest bubble as a local order parameter. We identify the bubbles in the system by means of a Voronoi-based analysis of the Molecular Dynamics trajectories. By comparing the features of the tessellation of liquid water at ambient conditions to those of the same system with an empty cavity we are able to discriminate vapor (or interfacial) molecules from the bulk ones. This information is used to follow the time evolution of the largest bubble until the system cavitates at 280 K above and below the spinodal line. At the pressure above the spinodal line, the MFPT curve shows the expected shape for a moderately metastable liquid from which we estimate the bubble nucleation rate and the size of the critical cluster. The nucleation rate estimated using Classical Nucleation Theory turns out to be about 8 order of magnitude lower than the one we compute by means of MFPT. The behavior at the pressure below the spinodal line, where the liquid is thermodynamically unstable, is remarkably different, the MFPT curve being a monotonous function without any inflection point.

cond-mat.stat-mech↗

arXiv2012

Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS

In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs: GROMACS and LAMMPS. The obtained results are compared with the results obtained from Monte Carlo. Good agreement between the different programs and methodologies was found. The procedure to perform the free energy calculations for the solid phase in the Molecular Dynamic programs is described. Since these programs allow to study any continuous intermolecular potential (when given in a tabulated form) this work shows that for isotropic potentials (describing for instance atomic solids or colloidal particles) free energy calculations can be performed on a routinely basis using GROMACS and/or LAMMPS.

cond-mat.soft↗

arXiv2012

Calculation of the melting point of alkali halides by means of computer simulations

In this manuscript we study the liquid-solid coexistence of NaCl-type alkali halides, described by interaction potentials such as Tosi-Fumi (TF), Smith-Dang (SD) and Joung-Cheatham (JC), and compute their melting temperature (Tm) at 1 bar via three independent routes: 1) liquid/solid direct coexistence, 2) free-energy calculations and 3) Hamiltonian Gibbs-Duhem integration. The melting points obtained by the three routes are consistent with each other. The calculated Tm of the Tosi-Fumi model of NaCl is in good agreement with the experimental value as well as with other numerical calculations. However, the other two models considered for NaCl, SD and JC, overestimate the melting temperature of NaCl by more than 200 K. We have also computed the melting temperature of other alkali halides using the Tosi-Fumi interaction potential and observed that the predictions are not always as close to the experimental values as they are for NaCl. It seems that there is still room for improvement in the area of force-fields for alkaline halides, given that so far most models are still unable to describe a simple yet important property such as the melting point.

cond-mat.stat-mech↗

arXiv2012

Phase separation and rotor self-assembly in active particle suspensions

Adding a non-adsorbing polymer to passive colloids induces an attraction between the particles via the `depletion' mechanism. High enough polymer concentrations lead to phase separation. We combine experiments, theory and simulations to demonstrate that using active colloids (such as motile bacteria) dramatically changes the physics of such mixtures. First, significantly stronger inter-particle attraction is needed to cause phase separation. Secondly, the finite size aggregates formed at lower inter-particle attraction show unidirectional rotation. These micro-rotors demonstrate the self assembly of functional structures using active particles. The angular speed of the rotating clusters scales approximately as the inverse of their size, which may be understood theoretically by assuming that the torques exerted by the outermost bacteria in a cluster add up randomly. Our simulations suggest that both the suppression of phase separation and the self assembly of rotors are generic features of aggregating swimmers, and should therefore occur in a variety of biological and synthetic active particle systems.

cond-mat.soft↗

arXiv2011

Irreducible finite-size effects in surface free energies from crystal-nucleation data

In this Letter we report a simulation study in which we compare the solid-liquid interfacial free energy of NaCl at coexistence, with the value that follows from the height of the homogeneous nucleation barrier. We find that the two estimates differ by more than 100%. Similar, although smaller discrepancies are found for crystals of hard-sphere colloids and of Lennard-Jones ("argon") particles. We consider a variety of possible causes for this discrepancy and are forced to conclude that it is due to a finite-size effect that cannot be corrected for by any simple thermodynamic procedure. Importantly, we find that the surface free energies that follow from real nucleation experiments should be subject to large finite size effects. Taking this in to account, we obtain quantitative agreement between the simulation data and the surface free energy of NaCl that follows from nucleation experiments. Our finding suggests that most published solid-liquid surface free energies derived from nucleation experiments will have to be revised.

cond-mat.mtrl-sci↗

arXiv2010

Non-equilibrium dynamics of an active colloidal "chucker"

We report Monte Carlo simulations of the dynamics of a "chucker": a colloidal particle which emits smaller solute particles from its surface, isotropically and at a constant rate k_c. We find that the diffusion constant of the chucker increases for small k_c, as recently predicted theoretically. At large k_c the chucker diffuses more slowly due to crowding effects. We compare our simulation results to those of a "point particle" Langevin dynamics scheme in which the solute concentration field is calculated analytically, and in which hydrodynamic effects can be included albeit in an approximate way. By simulating the dragging of a chucker, we obtain an estimate of its apparent mobility coefficient which violates the fluctuation-dissipation theorem. We also characterise the probability density profile for a chucker which sediments onto a surface which either repels or absorbs the solute particles, and find that the steady state distributions are very different in the two cases. Our simulations are inspired by the biological example of exopolysaccharide-producing bacteria, as well as by recent experimental, simulation and theoretical work on phoretic colloidal "swimmers".

cond-mat.soft↗

arXiv2009

Crystallization of hard-sphere glasses

We study by molecular dynamics the interplay between arrest and crystallization in hard spheres. For state points in the plane of volume fraction ($0.54 \leq phi \leq 0.63$) and polydispersity ($0 \leq s \leq 0.085$), we delineate states that spontaneously crystallize from those that do not. For noncrystallizing (or precrystallization) samples we find isodiffusivity lines consistent with an ideal glass transition at $ϕ_g \approx 0.585$, independent of $s$. Despite this, for $s<0.05$, crystallization occurs at $ϕ> ϕ_g$. This happens on time scales for which the system is aging, and a diffusive regime in the mean square displacement is not reached; by those criteria, the system is a glass. Hence, contrary to a widespread assumption in the colloid literature, the occurrence of spontaneous crystallization within a bulk amorphous state does not prove that this state was an ergodic fluid rather than a glass.

cond-mat.soft↗