arXiv subjects

Alejandro Cuetos

Publications and source records attributed to Alejandro Cuetos.

18 recordsLinked to original sources

arXiv2026

A solvent-flux theory for nonequilibrium swelling dynamics of thermoresponsive microgels

Thermoresponsive microgels undergo large reversible size changes as temperature alters solvent quality. Predicting their nonequilibrium swelling and deswelling kinetics is challenging because polymer volume fraction, mechanical response, and solvent transport evolve during large volume changes. Here we develop a solvent-flux theory for the dynamics of a spherical microgel. The radius-change rate is driven by the osmotic-pressure imbalance across the particle boundary and resisted by water transport through the polymer network, yielding a nonlinear equation for the global swelling coordinate and a state- and temperature-dependent swelling diffusion coefficient, $D_{\mathrm{SW}}(\phi,T)$. In the linear-response regime, the theory recovers Tanaka--Fillmore exponential relaxation and the scaling $\tau_\mathrm{SW}\sim R_{\mathrm{eq}}^2\gamma/K_{\mathrm{eq}}$, while providing a microscopic interpretation of the polymer--solvent friction coefficient $\gamma$. Beyond this limit, the model retains quadratic size scaling while accounting for state-dependent transport and mechanics. For pNIPAM microgels, it predicts asymmetric pathways, with deswelling faster than swelling over the same temperature interval. Finite thermalization produces a crossover from a microgel-controlled to a thermalization-controlled regime, in which the apparent relaxation time grows linearly with the external thermalization time and hysteresis-like loops emerge in the radius--temperature plane. A stochastic extension based on the Smoluchowski equation predicts transient broadening of the radius distribution during collapse, with maximal fluctuations in the volume-transition region. The theory links solvent transport, nonlinear swelling dynamics, thermalization effects, and nonequilibrium size fluctuations in responsive microgels.

cond-mat.soft↗

arXiv2025

Diffusion of Tracer Particles in Early Growing Biofilms. A Computer Simulation Study

The diffusion of particles in complex media has gained significant interest due to its dual relevance: probing the viscoelastic properties of materials via microrheology and assessing the extent of particle displacement over time. In this work, we explore the early-stage diffusion of a tracer particle within a developing bacterial biofilm using implicit-solvent Brownian dynamics simulations. At these initial stages, bacterial colonies form two-dimensional structures that expand through cell growth and division. Employing an agent-based computational model (IbM), we analyse the passive diffusion of a spherical tracer within colonies of varying compaction levels. Our findings reveal that, at very short timescales, tracer diffusion follows a standard diffusive regime, modulated by colony ageing. However, at longer times, the dominant factor governing tracer motion is colony growth, which effectively confines the tracer within the expanding structure, except in cases where the microcolony is highly unstructured or the tracer is sufficiently small. Additionally, through MR techniques, we quantify the elastic and viscous moduli of the growing microcolony, offering insight into its evolving viscoelastic behavior.

cond-mat.soft↗

arXiv2025

Relevance of the Computational Models of Bacterial Interactions in the simulation of Biofilm Growth

This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based model, we have investigated the possibilities and limitations of modeling biofilm formation and growth using different models for interaction between bacteria, such as the Hertz model, Soft Repulsive Spherocylindrical (SRS) model, and attractive Kihara model. Our approach focuses on understanding how mechanical forces due to the interaction between cells, in addition to growth and diffusive parameters, influence the formation of complex bacterial communities. By comparing such force models, we evaluate their impact on the structural properties of bacterial microcolonies. The results indicate that, although the specific force model has some effect on biofilm properties, the intensity of the interaction between bacteria is the most important determinant. This study highlights the importance of properly selecting interaction strength in simulations to obtain realistic representations of biofilm growth, and suggests which adapted models of rod-shaped bacterial systems may offer a valid approach to study the dynamics of complex biofilms.

cond-mat.soft↗

arXiv2022

Dynamics in field-induced biaxial nematic liquid crystals of board-like particles

Biaxial nematic ($N_B$) liquid crystals have been indicated as promising candidates for the design of next-generation displays with novel electro-optical properties and faster switching times. While at the molecular scale their existence is still under debate, experimental evidence, supported by theory and simulation, has unambiguously proved that suitable colloidal particles can indeed form $N_B$ fluids under specific conditions. While this discovery has sparked a widespread interest in the characterisation of the phase behaviour of $N_B$ liquid crystals, significantly less attention has been devoted to the study of their transport properties. To bridge this gap, by Dynamic Monte Carlo simulations we have investigated the equilibrium dynamics of field-induced $N_B$ phases comprising monodisperse hard cuboids. In particular, we calculated the long-time self-diffusion coefficients of cuboids over a wide range of anisotropies, spanning prolate to oblate geometries. Additionally, we have compared these diffusivities with those that, upon switching the external field off, are measured in the thermodynamically-stable isotropic or uniaxial nematic phases at the same density. Our results indicate that while prolate cuboids diffuse significantly faster in biaxial nematics than in less ordered fluids, we do not observe such an increase with oblate cuboids at high packing fractions. We show that these changes are most likely due to the field-induced freezing of the axes perpendicular to the nematic director, along with a substantial increase in the ordering of the resulting $N_B$ phase.

cond-mat.soft↗

arXiv2022

Influence of homeostatic mechanisms of bacterial growth and division on structural properties of biofilms. A computer simulation study

Bacterial growth and division generally occur by the process known as binary fission, in which the cells grow polarly until they divide into two daughter cells. Although this process is affected by factors that introduce stochastic variability in both growth rate and daughter cell length, the fact is that the size distribution in bacterial communities, also known as biofilm, remains stable over time. This suggests the existence of homeostatic mechanisms that contribute to maintaining a stable size distribution. Those known as sizer and adder stand out among these mechanisms whose relevance is not entirely determined. In this work, computer simulations using an agent-based model, are used to study the effect of these homeostatic mechanisms on the geometrical and structural properties of the developing biofilm, focusing on the early stages of its development. Also, it was examined the effect of linear or exponential dependence with the time of cellular growth on these properties. From our study, we deduce that these mechanisms do not have a noticeable impact on the properties studied, which could be due to the importance that stochastic factors play in the cell division and growth process. In addition, we discuss how competition between cell growth and diffusion is a key aspect in explaining the structure and geometry of developing bacterial colonies.

cond-mat.soft↗

arXiv2021

Dynamics of Colloidal Cubes and Cuboids in Cylindrical Nanopores

Understanding how colloidal suspensions behave in confined environments has a striking relevance in practical applications. Despite the fact that the behaviour of colloids in the bulk is key to identify the main elements affecting their equilibrium and dynamics, it is only by studying their response under confinement that one can ponder the use of colloids in formulation technology. In particular, confining fluids of anisotropic particles in nanopores provides the opportunity to control their phase behaviour and stabilise a spectrum of morphologies that cannot form in the bulk. By properly selecting pore geometry, particle architecture and system packing, it is possible to tune thermodynamic, structural and dynamical properties for ad hoc applications. In the present contribution, we report Grand Canonical and Dynamic Monte Carlo simulations of suspensions of colloidal cubes and cuboids constrained into cylindrical nanopores of different size. We first study their phase behaviour, calculate the chemical potential vs density equation of state and characterise the effect of the pore walls on particle anchoring and layering. In particular, at large enough concentrations, we observe the formation of concentric nematic-like coronas of oblate or prolate particles surrounding an isotropic core, whose features resemble those typically detected in the bulk. We then analyse the main characteristics of their dynamics and discover that these are dramatically determined by the ability of particles to diffuse in the longitudinal and radial direction of the nanopore.

cond-mat.soft↗

arXiv2021

Microrheology of colloidal suspensions via Dynamic Monte Carlo simulations

Understanding the rheology of colloidal suspensions is crucial in the formulation of a wide selection of industry-relevant products. To characterise the viscoelastic behaviour of these soft materials, one can analyse the microscopic dynamics of colloidal tracers diffusing through the host fluid and generating local deformations and stresses. This technique, referred to as microrheology, links the bulk rheology of fluids to the microscopic dynamics at the particle scale. If tracers are subjected to external forces, rather than freely diffusing, it is called active microrheology. Motivated by the impact of microrheology in providing information on local structure in complex systems such as colloidal glasses, active matter or biological systems, we have extended the dynamic Monte Carlo (DMC) technique to investigate active microrheology in colloids. The original DMC framework, able to accurately describe the Brownian dynamics of colloids at equilibrium, is here reconsidered and expanded to describe the effects of an external force pulling a tracer embedded in isotropic colloidal suspensions at different densities. To this end, we studied the dynamics of a spherical tracer dragged by a constant external force through a bath of spherical and rod-like particles of comparable size. We could extract valuable details on its effective friction coefficient, being constant at small and large values of the external force, but otherwise displaying a nonlinear behaviour that indicates the occurrence of a force-thinning regime. Our DMC simulation results are in excellent quantitative agreement with past Langevin dynamics simulations and theoretical works for the bath of spherical colloids. The bath of rod-like particles is studied in the isotropic phase, and displays an example where DMC is more convenient than Brownian or Langevin dynamics, in this case in dealing with particle rotation.

cond-mat.soft↗

arXiv2021

Dynamics of Uniaxial-to-Biaxial Nematics Switching in Suspensions of Hard Cuboids

Field-induced reorientation of colloidal particles is especially relevant to manipulate the optical properties of a nanomaterial for target applications. We have recently shown that surprisingly feeble external stimuli are able to transform uniaxial nematic liquid crystals (LCs) of cuboidal particles into biaxial nematic LCs. In the light of these results, here we apply an external field that forces the reorientation of colloidal cuboids in nematic LCs and sparks a uniaxial-to-biaxial texture switching. By Dynamic Monte Carlo simulation, we investigate the unsteady-state reorientation dynamics at the particle scale when the field is applied (uniaxial-to-biaxial switching) and then removed (biaxial-to-uniaxial switching). We detect a strong correlation between the response time, being the time taken for the system to reorient, and particle anisotropy, which spans from rod-like to plate-like geometries. Interestingly, self-dual shaped cuboids, theoretically considered as the most suitable to promote phase biaxiality for being exactly in between prolate and oblate particles, exhibit surprisingly slow response times, especially if compared to prolate cuboids.

cond-mat.soft↗

arXiv2021

Polymer-induced microcolony compaction in early biofilms: a computer simulation study

Microscopic organisms, such as bacteria, have the ability of colonizing surfaces and developing biofilms that can determine diseases and infections. Most bacteria secrete a significant amount of extracellular polymer substances that are relevant for biofilm stabilization and growth. In this work, we apply computer simulation and perform experiments to investigate the impact of polymer size and concentration on early biofilm formation and growth. We observe as bacterial cells formed loose, disorganized clusters whenever the effect of diffusion exceeded that of cell growth and division. Addition of model polymeric molecules induced particle self-assembly and aggregation to form compact clusters in a polymer size- and concentration-dependent fashion. We also find that large polymer size or concentration lead to the development of intriguing stripe-like and dendritic colonies. The results obtained by Brownian dynamic simulation closely resemble the morphologies that we experimentally observe in biofilms of a Pseudomonas Putida strain with added polymers. The analysis of the Brownian dynamic simulation results suggests the existence of a threshold polymer concentration that distinguishes between two growth regimes. Below this threshold, the main force driving polymer-induced compaction is hindrance of bacterial cell diffusion, while collective effects play a minor role. Above this threshold, especially for large polymers, polymer-induced compaction is a collective phenomenon driven by depletion forces. Well above this concentration threshold, severely limited diffusion drives the formation of filaments and dendritic colonies.

physics.bio-ph↗

arXiv2020

Dynamic Monte Carlo Simulations of Inhomogeneous Colloidal Suspensions

The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is applicable to systems of spherical and/or anisotropic particles and to equilibrium or out-of-equilibrium processes. In this work, we present a theoretical and methodological framework to extend DMC to the study of heterogeneous systems, where the presence of an interface between coexisting phases introduces an additional element of complexity in determining the dynamic properties. In particular, we simulate a Lennard-Jones fluid at the liquid-vapor equilibrium and determine the diffusion coefficients in the bulk of each phase and across the interface. To test the validity of our DMC results, we also perform Brownian Dynamics simulations and unveil an excellent quantitative agreement between the two simulation techniques.

cond-mat.soft↗

arXiv2020

Self-assembly of Freely-rotating Polydisperse Cuboids: Unveiling the Boundaries of the Biaxial Nematic Phase

Colloidal cuboids have the potential to self-assemble into biaxial liquid crystal phases, which exhibit two independent optical axes. Over the last few decades, several theoretical works predicted the existence of a wide region of the phase diagram where the biaxial nematic phase would be stable, but imposed rather strong constraints on the particle rotational degrees of freedom. In this work, we employ molecular simulation to investigate the impact of size dispersity on the phase behaviour of freely-rotating hard cuboids, here modelled as self-dual-shaped nanoboards. This peculiar anisotropy, exactly in between oblate and prolate geometry, has been proposed as the most appropriate to promote phase biaxiality. We observe that size dispersity radically changes the phase behaviour of monodisperse systems and leads to the formation of the elusive biaxial nematic phase, being found in an large region of the packing fraction vs polydispersity phase diagram. Although our results confirm the tendencies reported in past experimental observations on colloidal dispersions of slightly prolate goethite particles, they cannot reproduce the direct isotropic-to-biaxial nematic phase transition observed in these experiments.

cond-mat.soft↗

arXiv2020

Dynamics of Hard Colloidal Cuboids in Nematic Liquid Crystals

We perform Dynamic Monte Carlo simulations to investigate the equilibrium dynamics of hard colloidal cuboids in oblate and prolate nematic liquid crystals. In particular, we characterise the particles' diffusion along the nematic director and perpendicularly to it, and observe a structural relaxation decay that strongly depend on the particle anisotropy. To assess the Gaussianity of their dynamics and eventual occurrence of collective motion, we calculate two- and four-point correlation functions that incorporate the instantaneous values of the diffusion coefficients parallel and perpendicular to the nematic director. Our simulation results highlight the occurrence of Fickian and Gaussian dynamics at short and long times, locate the minimum diffusivity at the self-dual shape, the particle geometry that would preferentially stabilise biaxial nematics, and exclude the existence of dynamically correlated particles.

cond-mat.soft↗

arXiv2019

Brownian dynamics simulations of oblate and prolate colloidal particles in nematic liquid crystals

It is well known that understanding the transport properties of liquid crystals (LCs) is crucial to optimise their performance in a number of technological applications. In this work, we analyse the effect of shape anisotropy on the diffusion of rod-like and disk-like particles by Brownian dynamics simulations. To this end, we compare the dynamics of prolate and oblate nematic LCs incorporating particles with the same infinite-dilution translational or rotational diffusion coefficients. Under these conditions, which are benchmarked against the standard case of identical aspect ratios, we observe that prolate particles display faster dynamics than oblate particles at short and long timescales. Nevertheless, when compared at identical infinite-dilution translational diffusion coefficients, oblate particles are faster than their prolate counterparts at short-to-intermediate timescales, which extend over almost three time decades. Both oblate and prolate particles exhibit an anisotropic diffusion with respect to the orientation of the nematic director. More specifically, prolate particles show a fast diffusion in the direction parallel to the nematic director, while their diffusion in the direction perpendicular to it is slower. By contrast, the diffusion of oblate particles is faster in the plane perpendicular to the nematic director. Finally, in the light of our recent study on the long-time Gaussian and Fickian diffusion in nematic LCs, we map the decay of the autocorrelation functions and their fluctuations over the timescales of our simulations to ponder the existence of mobile clusters of particles and the occurrence of collective motion.

cond-mat.soft↗

arXiv2018

Biaxial Nematics of Hard Cuboids in an External Field

We investigate the phase behavior of colloidal suspensions of board-like particles under the effect of an external field and assess the still disputed occurrence of the biaxial nematic (N$_\text{B}$) liquid crystal phase. The external field promotes the rearrangement of the initial isotropic (I) or uniaxial nematic (N$_\text{U}$) phase and the formation of the N$_\text{B}$ phase. In particular, very weak field strengths are sufficient to spark a direct I-N$_\text{B}$ or N$_\text{U}$-N$_\text{B}$ phase transition at the self-dual shape, where prolate and oblate particle geometries fuse into one. By contrast, forming the N$_\text{B}$ phase at any other geometry requires stronger fields and thus reduces the energy efficiency of the phase transformation. Our simulation results show that self-dual shaped board-like particles with moderate anisotropy are able to form N$_\text{B}$ liquid crystals under the effect of a surprisingly weak external stimulus and suggest a path to exploit low-energy uniaxial-to-biaxial order switching.

cond-mat.soft↗

arXiv2018

Is Fickian Yet Non-Gaussian Diffusion Ubiquitous?

Recent studies unveiled the Fickian yet non-Gaussian (FNG) dynamics of many soft matter systems and suggested this phenomenon as a general characteristic of the diffusion in complex fluids. In particular, it was shown that the distribution of particle displacements in Fickian diffusion is not necessarily Gaussian, and thus the Einstein and Smoluchowski theory describing the Brownian motion of individual objects in a fluid would not be applicable. In this Letter, we investigate whether the FNG dynamics so far reported in gels, granular materials, biological and active matter systems, is also a distinctive feature of colloidal liquid crystals. To this end, we perform Brownian Dynamics simulations of oblate and prolate colloidal particles in the nematic phase. We detect a normal and Gaussian dynamics at short and long time scales, whereas, at intermediate time scales, a non-Fickian and non-Gaussian dynamics is found. Additionally, we revisit the nature of the decay of the self-van Hove correlation function, $G_s(r,t)$, which is here approximated with an ellipsoidal, rather than spherical, Gaussian distribution. The new expression that we propose is able to correctly assess the Gaussian dynamics in inherently anisotropic systems, like liquid crystals, where the standard Gaussian approximation of $G_s(r,t)$ would fail.

cond-mat.soft↗

arXiv2018

Dynamic Monte Carlo algorithm for out-of-equilibrium processes in colloidal dispersions

Colloids have a striking relevance in a wide spectrum of industrial formulations, spanning from personal care products to protective paints. Their behaviour can be easily influenced by extremely weak forces, which disturb their thermodynamic equilibrium and dramatically determine their performance. Motivated by the impact of colloidal dispersions in fundamental science and formulation engineering, we have designed an efficient Dynamic Monte Carlo (DMC) approach to mimic their out-of-equilibrium dynamics. Our recent theory, which provided a rigorous method to reproduce the Brownian motion of colloids by MC simulations, is here generalised to reproduce the Brownian motion of colloidal particles during transitory unsteady states, when their thermodynamic equilibrium is significantly modified. To this end, we investigate monodisperse and bidisperse rod-like particles in the isotropic phase and apply an external field that forces their reorientation along a common direction and induces an isotropic-to-nematic phase transition. We also study the behaviour of the system once the external field is removed. Our simulations are in excellent quantitative agreement with Brownian Dynamics simulations when the DMC results are rescaled with a time-dependent acceptance ratio, which depends on the strength of the applied field. Further generalising our DMC algorithm to processes displaying significant density fluctuations, such as nucleation and growth, where the MC acceptance ratio is expected to depend on both time and space, is currently under investigation.

cond-mat.soft↗

arXiv2017

Monte Carlo simulation of binary mixtures of hard colloidal cuboids

We perform extensive Monte Carlo simulations to investigate the phase behaviour of colloidal suspensions of hard board-like particles (HBPs). While theories restricting particle orientation or ignoring higher ordered phases suggest the existence of a stable biaxial nematic phase, our recent simulation results on monodisperse systems indicate that this is not necessarily the case, even for particle shapes exactly in between prolate and oblate geometries, usually referred to as self-dual shape. Motivated by the potentially striking impact of incorporating biaxial ordering into display applications, we extend our investigation to bidisperse mixtures of short and long HBPs and analyse whether size dispersity can further enrich the phase behaviour of HBPs, eventually destabilise positionally ordered phases and thus favour the formation of the biaxial nematic phase. Not only do our results indicate that bidisperse mixtures of self-dual shaped HBPs cannot self-assemble into biaxial nematic phases, but they also show that these particles are not able to form uniaxial nematic phases either. This surprising behaviour is also observed in monodisperse systems. Additionally, bidisperse HBPs tend to phase separate in coexisting isotropic and smectic phases or, at relatively large pressures, in a smectic phase of mostly short HBPs and a smectic phase of mostly long HBPs. We conclude that limiting the particle orientational degrees of freedom or neglecting the presence of positionally ordered (smectic, columnar and crystal) phases can dramatically alter the phase behaviour of HBPs and unrealistically enlarge the region of stability of the biaxial nematic phase.

cond-mat.soft↗

arXiv2007

A Case Study of Sedimentation of Charged Colloids: The Primitive Model and the Effective One-Component Approach

Sedimentation-diffusion equilibrium density profiles of suspensions of charge-stabilized colloids are calculated theoretically and by Monte Carlo simulation, both for a one-component model of colloidal particles interacting through pairwise screened-Coulomb repulsions and for a three-component model of colloids, cations, and anions with unscreened-Coulomb interactions. We focus on a state point for which experimental measurements are available [C.P. Royall et al., J. Phys.: Cond. Matt. {\bf 17}, 2315 (2005)]. Despite the apparently different picture that emerges from the one- and three-component model (repelling colloids pushing each other to high altitude in the former, versus a self-generated electric field that pushes the colloids up in the latter), we find similar colloidal density profiles for both models from theory as well as simulation, thereby suggesting that these pictures represent different view points of the same phenomenon. The sedimentation profiles obtained from an effective one-component model by MC simulations and theory, together with MC simulations of the multi-component primitive model are consistent among themselves, but differ quantitatively from the results of a theoretical multi-component description at the Poisson-Boltzmann level. We find that for small and moderate colloid charge the Poisson-Boltzmann theory gives profiles in excellent agreement with the effective one-component theory if a smaller effective charge is used. We attribute this discrepancy to the poor treatment of correlations in the Poisson-Boltzmann theory.

cond-mat.soft↗