arXiv subjects

Rodrigo Soto

Publications and source records attributed to Rodrigo Soto.

At least 37 records · Page 2Linked to original sources

arXiv2023

Accumulation and depletion of E. coli in surfaces mediated by curvature

Can topography be used to control bacteria accumulation? We address this question in the model system of smooth-swimming and run-and-tumble \textit{Escherichia coli} swimming near a sinusoidal surface, and show that the accumulation of bacteria is determined by the characteristic curvature of the surface. For low curvatures, cells swim along the surface due to steric alignment and are ejected from the surface when they reach the peak of the sinusoid. Increasing curvature enhances this effect and reduces the density of bacteria in the curved surface. However, for curvatures larger than $κ^*\approx 0.3 μm^{-1}$, bacteria become trapped in the valleys, where they can remain for long periods of time. Minimal simulations considering only steric interactions with the surface reproduce these results and give insights into the physical mechanisms defining the critical curvature, which is found to scale with the inverse of the bacterial length. We show that for curvatures larger than $κ^*$, the otherwise stable alignment with the wall becomes unstable while the stable orientation is now perpendicular to the wall, thus predicting accurately the onset of trapping at the valleys.

cond-mat.soft↗

arXiv2023

Mixtures of self-propelled particles interacting with asymmetric obstacles

In the presence of an obstacle, active particles condensate into a surface "wetting" layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of "fast" and "slow" active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion "diversity", defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter. Finally, rectification alters particle evaporation and absorption by the layer, making the density of the dilute phase increase with the global density. Therefore, the steady state violates the lever rule, a result which is valid even for systems of identical particles.

cond-mat.soft↗

arXiv2023

Wetting dynamics by mixtures of fast and slow self-propelled particles

We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of "fast" and "slow" self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Non-monotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.

cond-mat.soft↗

arXiv2021

Diversity of self-propulsion speeds reduces motility-induced clustering in confined active matter

Self-propelled swimmers such as bacteria agglomerate into clusters as a result of their persistent motion. In 1D, those clusters do not coalesce macroscopically and the stationary cluster size distribution (CSD) takes an exponential form. We develop a minimal lattice model for active particles in narrow channels to study how clustering is affected by the interplay between self-propulsion speed diversity and confinement. A mixture of run-and-tumble particles with a distribution of self-propulsion speeds is simulated in 1D. Particles can swap positions at rates proportional to their relative self-propulsion speed. Without swapping, we find that the average cluster size $L_\text{c}$ decreases with diversity and follows a non-arithmetic power mean of the single-component $L_\text{c}$'s, unlike the case of tumbling-rate diversity previously studied. Effectively, the mixture is thus equivalent to a system of identical particles whose self-propulsion speed is the harmonic mean self-propulsion speed of the mixture. With swapping, particles escape more quickly from clusters. As a consequence, $L_\text{c}$ decreases with swapping rates and depends less strongly on diversity. We derive a dynamical equilibrium theory for the CSDs of binary and fully polydisperse systems. Similarly to the clustering behaviour of one-component models, our qualitative results for mixtures are expected to be universal across active matter. Using literature experimental values for the self-propulsion speed diversity of unicellular swimmers known as choanoflagellates, which naturally differentiate into slower and faster cells, we predict that the error in estimating their $L_\text{c}$ via one-component models which use the conventional arithmetic mean self-propulsion speed is around $30\%$.

cond-mat.soft↗

arXiv2021

Modelling of active contraction pulses in epithelial cells using the vertex model

Several models have been proposed to describe the dynamics of epithelial tissues undergoing morphogenetic changes driven by apical constriction pulses, which differ in where the constriction is applied, either at the perimeter or medial regions. To help discriminate between these models, using the vertex model for epithelial dynamics, we analysed the impact of where the constriction is applied on the final geometry of the active cell that is reducing its apical size. We find that medial activity, characterised by a reduction in the reference area in the vertex model, induces symmetry breaking and generates anisotropic cell shapes, while isotropic cell shapes and larger contractions occur when the reference perimeter in the model is reduced. When plasticity is included, sufficiently slow processes of medial contractile activity, compared with typical apical constriction pulses, can also achieve significant cell contraction. Finally, we apply the model to describe the active apical contractile pulses observed during cellular mitotic events within the epithelial enveloping cell layer in the developing annual killifish Austrolebias nigripinnis, being able to quantitatively describe the temporal evolution of cell shape changes when perimeter activity and area plasticity are included. A global fit of all parameters of the vertex model is provided.

cond-mat.soft↗

arXiv2021

Navier--Stokes transport coefficients for a model of a confined quasi-two-dimensional granular binary mixture

The Navier--Stokes transport coefficients for a model of a confined quasi-two-dimensional granular binary mixture of inelastic hard spheres are determined from the Boltzmann kinetic equation. A normal or hydrodynamic solution to the Boltzmann equation is obtained via the Chapman--Enskog method for states near the local version of the homogeneous time-dependent state. The mass, momentum, and heat fluxes are determined to first order in the spatial gradients of the hydrodynamic fields, and the associated transport coefficients are identified. As expected, they are given in terms of the solutions of a set of coupled linear integral equations. In addition, in contrast to previous results obtained for low-density granular mixtures, there are also nonzero contributions to the first-order approximations to the partial temperatures $T_i^{(1)}$ and the cooling rate $ζ^{(1)}$. Explicit forms for the diffusion transport coefficients, the shear viscosity coefficient, and the quantities $T_i^{(1)}$ and $ζ^{(1)}$ are obtained by assuming the steady-state conditions and by considering the leading terms in a Sonine polynomial expansion. The above transport coefficients are given in terms of the coefficients of restitution, concentration, and the masses and diameters of the components of the mixture. The results apply in principle for arbitrary degree of inelasticity and are not limited to specific values of concentration, mass and/or size ratios. As a simple application of these results, the violation of the Onsager reciprocal relations for a confined granular mixture is quantified in terms of the parameter space of the problem.

cond-mat.soft↗

arXiv2020

Stability of the homogeneous steady state for a model of a confined quasi-two-dimensional granular fluid

A linear stability analysis of the hydrodynamic equations of a model for confined quasi-two-dimensional granular gases is carried out. The stability analysis is performed around the homogeneous steady state (HSS) reached eventually by the system after a transient regime. In contrast to previous studies (which considered dilute or quasielastic systems), our analysis is based on the results obtained from the inelastic Enskog kinetic equation, which takes into account the (nonlinear) dependence of the transport coefficients and the cooling rate on dissipation and applies to moderate densities. As in earlier studies, the analysis shows that the HSS is linearly stable with respect to long enough wavelength excitations.

cond-mat.stat-mech↗

arXiv2020

Active mixtures in a narrow channel: Motility diversity changes cluster sizes

The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e. polydispersity in motility parameters) and confinement. A mixture of run-and-tumble particles with a distribution of tumbling rates (denoted generically by $α$) is considered on a 1D lattice. Particles facing each other cross at constant rate, rendering the lattice quasi-1D. To isolate the role of diversity, the global average $α$ stays fixed. For a binary mixture with no particle crossing, the average cluster size ($L_\text{c}$) increases with the diversity as lower-$α$ particles trap higher-$α$ ones for longer. At finite crossing rate, particles escape from the clusters sooner, making $L_\text{c}$ smaller and the diversity less important, even though crossing can enhance demixing of particle types between the cluster and gas phases. If the crossing rate is increased further, the clusters become controlled by particle crossing. We also consider an experiment-based continuous distribution of tumbling rates, revealing similar physics. Using parameters fitted from experiments with Escherichia coli bacteria, we predict that the error in estimating $L_\text{c}$ without accounting for polydispersity is around $60\%$. We discuss how to find a binary system with the same CSD as the fully polydisperse mixture. An effective theory is developed and shown to give accurate expressions for the CSD, the effective $α$, and the average fraction of mobile particles. We give reasons why our qualitative results are expected to be valid for other active matter models and discuss the changes that would result from polydispersity in the active speed rather than in the tumbling rate.

cond-mat.soft↗

arXiv2020

Energy nonequipartition in a collisional model of a confined quasi-two-dimensional granular mixture

A collisional model of a confined quasi-two-dimensional granular mixture is considered to analyze homogeneous steady states. The model includes an effective mechanism to transfer the kinetic energy injected by vibration in the vertical direction to the horizontal degrees of freedom of grains. The set of Enskog kinetic equations for the velocity distribution functions of each component is derived first to analyze the homogeneous state. As in the one-component case, an exact scaling solution is found where the time dependence of the distribution functions occurs entirely through the granular temperature $T$. As expected, the kinetic partial temperatures $T_i$ of each component are different and hence, energy equipartition is broken down. In the steady state, explicit expressions for the temperature $T$ and the ratio of partial kinetic temperatures $T_i/T_j$ are obtained by considering Maxwellian distributions defined at the partial temperatures $T_i$. The (scaled) granular temperature and the temperature ratios are given in terms of the coefficients of restitution, the solid volume fraction, the (scaled) parameters of the collisional model, and the ratios of mass, concentration, and diameters. In the case of a binary mixture, the theoretical predictions are exhaustively compared with both direct simulation Monte Carlo and molecular dynamics simulations with a good agreement. The deviations are identified to be originated in the non-Gaussianity of the velocity distributions and on microsegregation patterns, which induce spatial correlations not captured in the Enskog theory.

cond-mat.stat-mech↗

arXiv2020

Vertex model instabilities for tissues subject to cellular activity or applied stresses

The vertex model is widely used to describe the dynamics of epithelial tissues, because of its simplicity and versatility and the direct inclusion of biophysical parameters. Here, it is shown that quite generally, when cells modify their equilibrium perimeter due to their activity, or the tissue is subject to external stresses, the tissue becomes unstable with deformations that couple pure-shear or deviatoric modes, with rotation and expansion modes. For short times, these instabilities deform cells increasing their ellipticity while, at longer times, cells become non-convex, indicating that the vertex model ceases to be a valid description for tissues under these conditions. The agreement between the analytic calculations performed for a regular hexagonal tissue and the simulations of disordered tissues is excellent due to the homogenization of the tissue at long wavelengths.

cond-mat.soft↗

arXiv2020

Run-and-tumble bacteria slowly approaching the diffusive regime

The run-and-tumble (RT) dynamics followed by bacterial swimmers gives rise first to a ballistic motion due to their persistence, and later, through consecutive tumbles, to a diffusive process. Here we investigate how long it takes for a dilute swimmer suspension to reach the diffusive regime as well as what is the amplitude of the deviations from the diffusive dynamics. A linear time dependence of the mean-squared displacement (MSD) is insufficient to characterize diffusion and thus we also focus on the excess kurtosis of the displacement distribution. Four swimming strategies are considered: (i) the conventional RT model with complete reorientation after tumbling, (ii) the case of partial reorientation, characterized by a distribution of tumbling angles, (iii) a run-and-reverse model with rotational diffusion, and (iv) a RT particle where the tumbling rate depends on the stochastic concentration of an internal protein. By analyzing the associated kinetic equations for the probability density function and simulating the models, we find that for models (ii), (iii), and (iv) the relaxation to diffusion can take much longer than the mean time between tumble events, evidencing the existence of large tails in the particle displacements. Moreover, the excess kurtosis can assume large positive values. In model (ii) it is possible for some distributions of tumbling angles that the MSD reaches a linear time dependence but, still, the dynamics remains non-Gaussian for long times. This is also the case in model (iii) for small rotational diffusivity. For all models, the long-time diffusion coefficients are also obtained. The theoretical approach, which relies on eigenvalue and angular Fourier expansions of the van Hove function, is in excellent agreement with the simulations.

cond-mat.soft↗

arXiv2019

Bacteria driving droplets

We confine a dense suspension of motile \textit{Escherichia coli} inside a spherical droplet in a water-in-oil emulsion, creating a "bacterially" propelled droplet. We show that droplets move in a persistent random walk, with a persistence time $τ\sim 0.3\, {\rm s}$, a long-time diffusion coefficient $D\sim 0.5\, μ{\rm m}^2/{\rm s}$, and an average instantaneous speed $V\sim 1.5\, μ{\rm m/s}$ when the bacterial suspension is at the maximum studied concentration. Several droplets are analyzed, varying the drop radius and bacterial concentration. We show that the persistence time, diffusion coefficient and average speed increase with the bacterial concentration inside the drop, but are largely independent of the droplet size. By measuring the turbulent-like motion of the bacteria inside the drop, we demonstrate that the mean velocity of the bacteria near the bottom of the drop, which is separated from a glass substrate by a thin lubrication oil film, is antiparallel to the instantaneous velocity of the drop. This suggests that the driving mechanism is a slippery rolling of the drop over the substrate, caused by the collective motion of the bacteria. Our results show that microscopic organisms can transfer useful mechanical energy to their confining environment, opening the way to the assembly of mesoscopic motors composed of microswimmers.

cond-mat.soft↗

arXiv2019

3D spatial exploration by E. coli echoes motor temporal variability

Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection spreading and the microbiota organization in guts or in soils. Most theoretical approaches for modeling bacterial transport rely on their run-and-tumble motion. For Escherichia coli, the run time distribution was reported to follow a Poisson process with a single characteristic time related to the rotational switching of the flagellar motors. However, direct measurements on flagellar motors show heavy-tailed distributions of rotation times stemming from the intrinsic noise in the chemotactic mechanism. Currently, there is no direct experimental evidence that the stochasticity in the chemotactic machinery affect the macroscopic motility of bacteria. In stark contrast with the accepted vision of run-and-tumble, here we report a large behavioral variability of wild-type \emph{E. coli}, revealed in their three-dimensional trajectories. At short observation times, a large distribution of run times is measured on a population and attributed to the slow fluctuations of a signaling protein triggering the flagellar motor reversal. Over long times, individual bacteria undergo significant changes in motility. We demonstrate that such a large distribution of run times introduces measurement biases in most practical situations. Our results reconcile the notorious conundrum between run time observations and motor switching statistics. We finally propose that statistical modeling of transport properties currently undertaken in the emerging framework of active matter studies, should be reconsidered under the scope of this large variability of motility features.

physics.bio-ph↗

arXiv2019

Magnetotactic bacteria in a droplet self-assemble into a rotary motor

From intracellular protein trafficking to large scale motion of animal groups, the physical concepts driving the self-organization of living systems are still largely unraveled. Selforganization of active entities, leading to novel phases and emergent macroscopic properties, recently shed new lights on these complex dynamical processes. Here we show that, under the application of a constant magnetic field, motile magnetotactic bacteria confined in water-in-oil droplets self-assemble into a rotary motor exerting a torque on the external oil phase. A collective motion in the form of a large-scale vortex, reversable by inverting the field direction, builds-up in the droplet with a vorticity perpendicular to the magnetic field. We study this collective organization at different concentrations, magnetic fields and droplets radii and reveal the formation of two torque-generating areas close to the droplet interface. We characterize quantitatively the mechanical energy extractable from this new biological and self-assembled motor.

cond-mat.soft↗

arXiv2019

Hyperuniform states generated by a critical friction field

Hyperuniform states are an efficient way to fill up space for disordered systems. In these states the particle distribution is disordered at the short scale but becomes increasingly uniform when looked at large scales. Hyperuniformity appears in several systems, in static or quasistatic regimes as well as close to transitions to absorbing states. Here, we show that a vibrated granular layer, at the critical point of the liquid-to-solid transition, displays dynamic hyperuniformity. Prior to the transition, patches of the solid phase form, with length scales and mean lifetimes that diverge critically at the transition point. When reducing the wavenumber, density fluctuations encounter increasingly more patches that block their propagation, resulting in a static structure factor that tends to zero for small wavenumbers at the critical point, which is a signature of hyperuniformity. A simple model demonstrates that this coupling of a density field to a highly fluctuating scalar friction field gives rise to dynamic hyperuniform states. Finally, we show that the structure factor detects better the emergence of hyperuniformity, compared to the particle number variance.

cond-mat.stat-mech↗

arXiv2019

Swimming bacteria in Poiseuille flow: the quest for active Bretherton-Jeffery trajectories

Using a 3D Lagrangian tracking technique, we determine experimentally the trajectories of non-tumbling E. coli mutants swimming in a Poiseuille flow. We identify a typology of trajectories in agreement with a kinematic "active Bretherton-Jeffery" model, featuring an axi-symmetric self-propelled ellipsoid. In particular, we recover the "swinging" and "shear tumbling" kinematics predicted theoretically by Zöttl et al. Moreover using this model, we derive analytically new features such as quasi-planar piece-wise trajectories, associated with the high aspect ratio of the bacteria, as well as the existence of a drift angle around which bacteria perform closed cyclic trajectories. However, the agreement between the model predictions and the experimental results remains local in time, due to the presence of Brownian rotational noise.

physics.flu-dyn↗

arXiv2019

E. coli "super-contaminates" narrow ducts fostered by broad run-time distribution

One striking feature of bacterial motion is their ability to swim upstream along corners and crevices, by leveraging hydrodynamic interactions. This motion through anatomic ducts or medical devices might be at the origin of serious infections. However, it remains unclear how bacteria can maintain persistent upstream motion while exhibiting run-and-tumble dynamics. Here we demonstrate that E. coli can travel upstream in microfluidic devices over distances of 15 millimeters in times as short as 15 minutes. Using a stochastic model relating the run times to the time bacteria spend on surfaces, we quantitatively reproduce the evolution of the contamination profiles when considering a broad distribution of run times. Interestingly, the experimental data cannot be reproduced using the usually accepted exponential distribution of run times. Our study demonstrates that the run-and-tumble statistics determine macroscopic bacterial transport properties. This effect, that we name "super-contamination", could explain the fast onset of some life-threatening medical emergencies.

cond-mat.soft↗

arXiv2019

Non-ideal rheology of semidilute bacterial suspensions

The rheology of semidilute bacterial suspensions is studied with the tools of kinetic theory, considering binary interactions, going beyond the ideal gas approximation. Two models for the interactions are considered, which encompass both the steric and short range interactions. In these, swimmers can either align polarly regardless of the state previous to the collision or they can align axially, being possible the end up antiparallel if the relative angle between directors is large. In both cases, it is found that an ordered phase develops when increasing the density, where the shear stress oscillates with large amplitudes, when a constant shear rate is imposed. This oscillation disappears for large shear rates in a continuous or discontinuous transition, depending if the aligning is polar or axial, respectively. For pusher swimmers these non-linear effects can produce an increase on the shear stress, contrary to the prediction of viscosity reduction made for the dilute regime with the ideal gas approximation.

cond-mat.soft↗