arXiv subjects

C. S. Dias

Publications and source records attributed to C. S. Dias.

At least 19 recordsLinked to original sources

arXiv2025

Rigid m-percolation in limited-valence gels

Determining the onset of rigidity in gels is a fundamental challenge with significant practical implications across different applications. Limited-valence, or patchy-particle systems have proven to be a valuable model to study the relationship between microscopic interactions and macroscopic mechanical properties. It has been suggested that the emergence of rigidity coincides with the formation of an infinitely spanning cluster of particles with at least three bonds. This work explores this hypothesis, its implications, and its broader applicability across a range of system parameters, by associating the emergence of rigidity with m-percolation transition for m=3. The properties of m-percolation are developed using a mean-field theoretical approach validated with numerical simulations, and used to build phase and rigidity diagrams for different particle valences of both single-component systems and binary mixtures of patchy particles. The difference between connectivity and rigidity percolation thresholds is found to reduce with increasing valence, providing an explanation for the challenges encountered in experimental attempts to distinguish isotropic connectivity percolation from the onset of rigidity. For binary mixtures, we found a robust minimum average valence, below which the gel is never rigid.

cond-mat.soft↗

arXiv2024

Convolutional Neural Network analysis of optical texture patterns in liquid-crystal skyrmions

Liquid crystals are known for their optical birefringence, a property that gives rise to intricate patterns and colors when viewed in a microscope between crossed polarisers. Resulting images are rich in geometric patterns and serve as valuable fingerprints of the liquid crystal's intrinsic properties. By using machine learning techniques, it is possible to extract from the images information about, e.g., liquid crystal elastic constants, the scalar order parameter, local orientation of the director, etc. Machine learning can also be employed to identify phase transitions and classify different liquid crystalline phases and topological defects. In addition to well studied singular defects such as point or line disclinations, liquid crystals can also host non-singular solitonic defects such as skyrmions, hopfions, and torons. The solitons, with their localised and stable configurations, offer an alternative view into material properties and behaviour of liquid crystals. In this study, we demonstrate that the optical signatures of skyrmions can be utilised effectively in machine learning to predict important system parameters. Our method focuses specifically on the skyrmion-localised regions, reducing significantly the computational cost. By training convolutional neural networks on simulated polarised optical microscopy images of liquid crystal skyrmions, we showcase the ability of trained networks to accurately predict several selected parameters such as the free energy, cholesteric pitch, and strength of applied electric fields. This study highlights the importance of localized topologically arrested order parameter configurations for materials characterisation research empowered by state-of-the-art data science methods, and may pave the way for the development of advanced skyrmion-based applications.

cond-mat.soft↗

arXiv2023

Structural criterion for the onset of rigidity in a colloidal gel

Identifying the necessary conditions for the onset of rigidity in a gel remains a challenge. It has been suggested that local particle coordination could be used to establish such conditions, but rigid gels occur for various coordination numbers. Combining simulations, oscillatory rheology, and a percolation analysis, for particles where the valence can be controlled, we find that the onset of rigidity coincides with the percolation of particles with three or more bonds, which arises after the connectivity percolation. We show that the rigidity results from an interplay of bonding and non-bonding interactions, providing insight into low-valence colloidal gel rigidity.

cond-mat.soft↗

arXiv2022

Percolation in binary mixtures of linkers and particles: chaining {\it {vs}} branching

Equilibrium gels of colloidal particles can be realized through the introduction of a second species, a linker that mediates the bonds between the colloids. A gel forming binary mixture whose linkers can self-assemble into linear chains while still promoting the aggregation of particles is considered in this work. The particles are patchy particles with $f_C$ patches of type $C$ and the linkers are patchy particles with $2$ patches of type $A$ and $f_B$ patches of type B. The bonds between patches of type $A$ ($AA$ bonds) promote the formation of linear chains of linkers. Two different ways (model A and model B) of bonding the linkers to the particles - or inducing branching - are studied. In model A, there is a competition between chaining and branching, since the bonding between linkers and particles is done through $AC$ bonds only. In model B linkers aggregate to particles through bonds $BC$ only, making chaining and branching independent. The percolation behaviour of these two models is studied in detail, employing a generalized Flory-Stockmayer theory and Monte Carlo simulations. The self-assembly of linkers into chains reduces the fraction of particles needed for percolation to occur (models A and B) and induces percolation when the fraction of particles is high (model B). Percolation by heating and percolation loops in temperature composition diagrams are obtained when the formation of chains is energetically favourable, by increasing the entropic gain of branching (model A). Chaining and branching are found to follow a model dependent relation at percolation, which shows that, for the same composition, longer chains require less branching for percolation to occur.

cond-mat.soft↗

arXiv2022

Effect of anisotropy on the formation of active particle films

Active colloids belong to a class of non-equilibrium systems where energy uptake, conversion and dissipation occurs at the level of individual colloidal particles, which can lead to particles self-propelled motion and surprising collective behavior. Examples include coexistence of vapor and liquid-like steady states for active particles with repulsive interactions only, phenomena known as motility induced phase transition. Similarly to motile unicellular organisms, active colloids tend to accumulate at confining surfaces forming dense adsorbed films. In this work, we study the structure and dynamics of aggregates of self-propelled particle near confining solid surfaces, focusing on the effects of the particle anisotropic interactions. We performed Langevin dynamics simulations of two complementary models for active particles: ellipsoidal particles interacting through Gay-Berne potential, and rod-like particles composed of several repulsive Lennard-Jones beads. We observe a non-monotonic behavior of the structure of clusters formed along the confining surface as a function of the particle aspect ratio, with a film spreading when particles are near spherical, compact clusters with hedgehog-like particle orientation for more elongated active particles, and a complex dynamical behavior for intermediate aspect ratio. The stabilization time of cluster formation along the confining surface also displays a non-monotonic dependence on the aspect ratio, with a local minimum at intermediate values. Additionally, we demonstrate that the hedgehog-like aggregates formed by Gay-Berne ellipsoids exhibit higher structural stability as compared to the ones formed by purely repulsive active rods, which are stable due to the particle activity only.

cond-mat.soft↗

arXiv2021

Molecular Dynamics Simulations of Active Matter using LAMMPS

LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main advantage is the optimization of the methods, mainly for parallel computing. The main disadvantage is that, due to the complexity of the code, it ha long learning curve. One purpose of these notes is to shorten that curve for researchers are starting to use LAMMPS to simulate soft active matter. In these notes, we first discuss some Molecular Dynamics methods implemented in LAMMPS. We present an hands-on introduction to first-time users and we finish with an advanced hands-on section, where we implement and test Active Brownian particles simulations.

cond-mat.soft↗

arXiv2020

Smoluchowski equations for linker-mediated irreversible aggregation

In order to study linker-mediated aggregation of colloidal particles with limited valence, we combine kinetic Monte Carlo simulations and an approximate theory based on the Smoluchowski equations. We found that aggregation depends strongly on two parameters, the ratio of the number of linkers and particles and the ratio of their diffusion coefficients. These control parameters are absent in single-species aggregation and provide a much greater variety and control of the resulting structures. We show that aggregation is non-trivial when two time scales of aggregation are present. Our aggregation dynamics theory is in qualitative and quantitative agreement with kinetic Monte Carlo simulations. Our results show how the optimal aggregation may be tuned through the ratio of the linkers and particles and that of the diffusion coefficients.

cond-mat.soft↗

arXiv2020

How to design cell-mediated self-assembled colloidal scaffolds

A critical step in tissue engineering is the design and synthesis of 3D biocompatible matrices (scaffolds) to support and guide the proliferation of cells and tissue growth. Most existing techniques rely on the processing of scaffolds under controlled conditions and then implanting them \textit{in vivo}, with questions related to biocompatibility and the implantation process that are still challenging. As an alternative, it was proposed to assemble the scaffolds \textit{in loco} through the self-organization of colloidal particles mediated by cells. In this study, we combine experiments, particle-based simulations, and mean-field calculations to show that, in general, the size of the self-assembled scaffold scales with the cell-to-particle ratio. However, we found an optimal value of this ratio, for which the size of the scaffold is maximal when cell-cell adhesion is suppressed. These results suggest that the size and structure of the self-assembled scaffolds may be designed by tuning the adhesion between cells in the colloidal suspension.

cond-mat.soft↗

arXiv2020

Optimal Number of Faces for Fast Self-Folding Kirigami

We study the spontaneous folding of a 2D template of microscopic panels into a 3D pyramid, driven by thermal fluctuations. Combining numerical simulations and analytical calculations, we find that the total folding time is a non-monotonic function of the number of faces, with a minimum for five faces. The motion of each face is consistent with a Brownian process and folding occurs through a sequence of irreversible binding events that close edges between pairs of faces. The first edge closing is well-described by a first-passage process in 2D, with a characteristic time that decays with the number of faces. By contrast, the subsequent edge closings are all first-passage processes in 1D and so the time of the last one grows logarithmically with the number of faces. It is the interplay between these two different sets of events that explains the non-monotonic behavior. Implications in the self-folding of more complex structures are discussed.

cond-mat.soft↗

arXiv2019

Optimal number of linkers per monomer in linker-mediated aggregation

We study the dynamics of diffusion-limited irreversible aggregation of monomers, where bonds are mediated by linkers. We combine kinetic Monte Carlo simulations of a lattice model with a mean-field theory to study the dynamics when the diffusion of aggregates is negligible and only monomers diffuse. We find two values of the number of linkers per monomer which maximize the size of the largest aggregate. We explain the existence of the two maxima based on the distribution of linkers per monomer. This observation is well described by a simple mean-field model. We also show that a relevant parameter is the ratio of the diffusion coefficients of monomers and linkers. In particular, when this ratio is close to ten, the two maxima merge at a single maximum.

cond-mat.soft↗

arXiv2018

Crossover from three- to six-fold symmetry of colloidal aggregates in circular traps

At sufficiently low temperatures and high densities, repulsive spherical particles in two-dimensions (2d) form close-packed structures with six-fold symmetry. By contrast, when the interparticle interaction has an attractive anisotropic component, the structure may exhibit the symmetry of the interaction. We consider a suspension of spherical particles interacting through an isotropic repulsive potential and a three-fold symmetric attractive interaction, confined in circular potential traps in 2d. We find that, due to the competition between the interparticle and the external potentials, the particles self-organize into structures with three- or six-fold symmetry, depending on the width of the traps. For intermediate trap widths, a core-shell structure is formed, where the core has six-fold symmetry and the shell is three-fold symmetric. When the width of the trap changes periodically in time, the symmetry of the colloidal structure also changes, but it does not necessarily follow that of the corresponding static trap.

cond-mat.soft↗

arXiv2018

Dynamics of a network fluid within the liquid-gas coexistence region

Low-density networks of molecules or colloids are formed at low temperatures when the interparticle interactions are valence limited. Prototypical examples are networks of patchy particles, where the limited valence results from highly directional pairwise interactions. We combine extensive Langevin simulations and Wertheim's theory of association to study these networks. We find a scale-free (relaxation) dynamics within the liquid-gas coexistence region, which differs from that usually observed for isotropic particles. While for isotropic particles the relaxation dynamics is driven by surface tension (coarsening), when the valence is limited, the slow relaxation proceeds through the formation of an intermediate non-equilibrium gel via a geometrical percolation transition in the Random Percolation universality class.

cond-mat.soft↗

arXiv2017

Dynamics of patchy particles in and out of equilibrium

We combine particle-based simulations, mean-field rate equations, and Wertheim's theory to study the dynamics of patchy particles in and out of equilibrium, at different temperatures and densities. We consider an initial random distribution of non-overlapping three-patch particles, with no bonds, and analyze the time evolution of the breaking and bonding rates of a single bond. We find that the asymptotic (equilibrium) dynamics differs from the initial (out of equilibrium) one. These differences are expected to depend on the initial conditions, temperature, and density.

cond-mat.soft↗

arXiv2017

Dynamics of Network Fluids

Network fluids are structured fluids consisting of chains and branches. They are characterized by unusual physical properties, such as, exotic bulk phase diagrams, interfacial roughening and wetting transitions, and equilibrium and nonequilibrium gels. Here, we provide an overview of a selection of their equilibrium and dynamical properties. Recent research efforts towards bridging equilibrium and non-equilibrium studies are discussed, as well as several open questions.

cond-mat.soft↗

arXiv2016

Nonequilibrium self-organization of colloidal particles on substrates: adsorption, relaxation, and annealing

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate (mesoscopic) structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. Here we discuss the self-organization of functionalized colloids (also known as patchy colloids) on attractive substrates. We review our recent results on the adsorption and relaxation and explore the use of annealing cycles to overcome kinetic barriers and drive the relaxation towards the targeted structures.

cond-mat.soft↗

arXiv2015

Relaxation dynamics of functionalized colloids on attractive substrates

Particle-based simulations are performed to study the post-relaxation dynamics of functionalized (patchy) colloids adsorbed on an attractive substrate. Kinetically arrested structures that depend on the number of adsorbed particles and the strength of the particle-particle and particle-substrate interactions are identified. The radial distribution function is characterized by a sequence of peaks, with relative intensities that depend on the number of adsorbed particles. The first-layer coverage is a non-monotonic function of the number of particles, with an optimal value around one layer of adsorbed particles. The initial relaxation towards these structures is characterized by a fast (exponential) and a slow (power-law) dynamics. The fast relaxation timescale is a linearly increasing function of the number of adsorbed particles in the submonolayer regime, but it saturates for more than one adsorbed layer. The slow dynamics exhibits two characteristic exponents, depending on the surface coverage.

cond-mat.soft↗

arXiv2014

Effect of the number of patches on the growth of networks of patchy colloids on substrates

We investigate numerically the irreversible aggregation of patchy spherical colloids on a flat substrate. We consider $n$-patch particles and characterize the dependence of the irreversible aggregation kinetics on $n$. For all values of $n$, considered in this study, the growing interface of the aggregate is in the Kardar-Parisi-Zhang universality class, although the bulk structure exhibits a rich dependence on $n$. In particular, the bulk density varies with $n$ and the network is more ordered for particles with fewer patches. Preferred orientations of the bonds are also observed for networks of particles with low $n$.

cond-mat.soft↗

arXiv2014

Kinetic interfaces of patchy particles

We study the irreversible adsorption of patchy particles on substrates in the limit of advective mass transport. Recent numerical results show that the interface roughening depends strongly on the particle attributes, such as, patch-patch correlations, bond flexibility, and strength of the interactions, uncovering new absorbing phase transitions. Here, we revisit these results and discuss in detail the transitions. In particular, we present new evidence that the tricritical point, observed in systems of particles with flexible patches, is in the tricritical directed percolation universality class. A scaling analysis of the time evolution of the correlation length for the aggregation of patchy particles with distinct bonding energies confirms that the critical regime is in the Kardar-Parisi-Zhang with quenched disorder universality class.

cond-mat.stat-mech↗