# Rodrigo Soto

## Contact Details

NameRodrigo Soto |
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## Pubs By Year |
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## Pub CategoriesPhysics - Soft Condensed Matter (15) Physics - Statistical Mechanics (15) Physics - Biological Physics (5) Physics - Materials Science (3) Physics - Other (2) Physics - Mesoscopic Systems and Quantum Hall Effect (2) Quantum Physics (2) Physics - Fluid Dynamics (2) Computer Science - Distributed; Parallel; and Cluster Computing (1) |

## Publications Authored By Rodrigo Soto

A novel parallel simulation algorithm on the GPU, implemented in CUDA and C++, is presented for the simulation of Brownian particles that display excluded volume repulsion and interact with long and short range forces. When an explicit Euler-Maruyama integration step is performed to take into account the pairwise forces and Brownian motion, particle overlaps can appear. The excluded volume property brings up the need for correcting these overlaps as they happen, since predicting them is not feasible due to the random displacement of Brownian particles. Read More

The emergence of clustering and coarsening in crowded ensembles of self-propelled agents is studied using a lattice model in one-dimension. The persistent exclusion process, where particles move at directions that change randomly at a low tumble rate $\alpha$, is extended allowing sites to be occupied by more than one particle, with a maximum $n_\text{max}$ per site. Three phases are distinguished. Read More

We describe the collective behavior of a system of many inelastic spherical particles inside a box which is being periodically vibrated. The box is shallow, with large horizontal dimensions, while the height is less than two particle diameters. The vibrations are not symmetric: the time the box is moving up is, in general, different to the time it is moving down. Read More

Despite the ubiquitousness and technological and scientific importance of granular matter, our understanding is still very poor compared to molecular fluids and solids. Until today, there is no unified description, which indeed seems unreachable. However, it has been proposed that important advances could be attained for noncohesive, hard-sphere like systems, by combining fluid dynamics with phase-field modeling through an appropriate order parameter (Aranson and Tsimring, 2006). Read More

Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not exhibit any form of dynamical activity, the concentration fields resulting from their chemical activity decay as $1/r$ and produce gradients that attract or repel other colloids depending on their surface chemistry and ambient variables. This results in a non-equilibrium analogue of ionic systems, but with the remarkable novel feature of action-reaction symmetry breaking. Read More

We experimentally study the critical properties of the non-equilibrium solid-liquid-like transition that takes place in vibrated granular matter. The critical dynamics is characterized by the coupling of the density field with the bond-orientational order parameter $Q_4$, which measures the degree of local crystallization. Two setups are compared, which present the transition at different critical accelerations as a a result of modifying the energy dissipation parameters. Read More

The shear viscosity in the dilute regime of a model for confined granular matter is studied by simulations and kinetic theory. The model consists on projecting into two dimensions the motion of vibrofluidized granular matter in shallow boxes by modifying the collision rule: besides the restitution coefficient that accounts for the energy dissipation, there is a separation velocity that is added in each collision in the normal direction. The two mechanisms balance on average, producing stationary homogeneous states. Read More

A granular system confined in a quasi two-dimensional box that is vertically vibrated can transit to an absorbing state in which all particles bounce vertically in phase with the box, with no horizontal motion. In principle, this state can be reached for any density lower than the one corresponding to one complete monolayer, which is then the critical density. Below this critical value, the transition to the absorbing state is of first order, with long metastable periods, followed by rapid transitions driven by homogeneous nucleation. Read More

A heterogeneous and dilute suspension of catalytically active colloids is studied as a non-equilibrium analogue of ionic systems, which has the remarkable feature of action-reaction symmetry breaking. Symmetrically coated colloids are found to join up to form self-assembled molecules that could be inert or have spontaneous activity in the form of net translational velocity and spin depending on their symmetry properties and their constituents. The type of activity can be adjusted by changing the surface chemistry and ambient variables that control the surface reactions and the phoretic drift. Read More

The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate $\alpha$. In stationary state, the system is found to break into dense clusters in which particles are trapped or stopped from moving. The characteristic size of these clusters predominantly scales as $\alpha^{-0. Read More

In this supplementary paper we present some details on the solid-liquid interface detection, the deduction of the non-equilibrium free energy, the analysis of the granular temperature and energy per mode, a validation of the small slope approximation, a description of the Langevin dynamics, and the error analysis. Read More

Confined granular fluids, placed in a shallow box that is vibrated vertically, can achieve homogeneous stationary states thanks to energy injection mechanisms that take place throughout the system. These states can be stable even at high densities and inelasticities allowing for a detailed analysis of the hydrodynamic modes that govern the dynamics of granular fluids. Analyzing the decay of the time correlation functions it is shown that there is a crossover between a quasielastic regime in which energy evolves as a slow mode, to a inelastic regime, with energy slaved to the other conserved fields. Read More

One of the most noticeable collective motion of non-cohesive granular matter is clustering under certain conditions. In particular, when a quasi-two-dimensional monolayer of mono-disperse non-cohesive particles is vertically vibrated, a solid-liquid-like transition occurs when the driving amplitude exceeds a critical value. Here, the physical mechanism underlying particle clustering relies on the strong interactions mediated by grain collisions, rather than on grain-grain cohesive forces. Read More

Self-propelled microorganisms, such as unicellular algae or bacteria, swim along their director relative to the fluid velocity. Under a steady shear flow the director rotates in close orbit, a periodic structure that is preserved under an oscillatory shear flow. If the shear flow is subjected to small fluctuations produced by small irregularities in the microchannel or by other swimmers nearby, the director dynamics becomes stochastic. Read More

Recently, a method based on stochastic quantization has been proposed to compute the Casimir force and its fluctuations in arbitrary geometries. It relies on the spectral decomposition of the Laplacian operator in the given geometry. Both quantum and thermal fluctuations are considered. Read More

We present an experimental study of density and order fluctuations in the vicinity of the solid-liquid-like transition that occurs in a vibrated quasi-two-dimensional granular system. The two-dimensional projected static and dynamic correlation functions are studied. We show that density fluctuations, characterized through the structure factor, increase in size and intensity as the transition is approached, but they do not change significantly at the transition itself. Read More

We present a simple model for bacteria like \emph{Escherichia coli} swimming near solid surfaces. It consists of two spheres of different radii connected by a dragless rod. The effect of the flagella is taken into account by imposing a force on the tail sphere and opposite torques exerted by the rod over the spheres. Read More

In this paper we show how the stochastic quantization method developed by Parisi and Wu can be used to obtain Casimir forces. Both quantum and thermal fluctuations are taken into account by a Langevin equation for the field. The method allows the Casimir force to be obtained directly, derived from the stress tensor instead of the free energy. Read More

In a mixture of two species of grains of equal size but different mass, placed in a vertically vibrated shallow box, there is spontaneous segregation. Once the system is at least partly segregated and clusters of the heavy particles have formed, there are sudden peaks of the horizontal kinetic energy of the heavy particles, that is otherwise small. Together with the energy peaks the clusters rapidly expand and the segregation is partially lost. Read More

A molecular dynamics study of a two dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid transition occurs. When the melting temperature $T_c$ is approached from below, there is a proliferation of dislocation pairs and the elastic constant approaches the value predicted by the KTHNY theory. Read More

We consider two systems of active swimmers moving close to a solid surface, one being a living population of wild-type \textit{E. coli} and the other being an assembly of self-propelled Au-Pt rods. In both situations, we have identified two different types of motion at the surface and evaluated the fraction of the population that displayed ballistic trajectories (active swimmers) with respect to those showing random-like behavior. Read More

It has been recently reported that a granular mixture in which grains differ in their restitution coefficients presents segregation: the more inelastic particles sink to the bottom. When other segregation mechanisms as buoyancy and the Brazil nut effect are present, the inelasticity induced segregation can compete with them. First, a detailed analysis, based on numerical simulations of two dimensional systems, of the competition between buoyancy and the inelasticity induced segregation is presented, finding that there is a transition line in the parameter space that determines which mechanism is dominant. Read More

A new numerical method is presented to efficiently simulate the inelastic hard sphere (IHS) model for granular media, when fluid and frozen regions coexist in the presence of gravity. The IHS model is extended by allowing particles to change their dynamics into either a frozen state or back to the normal collisional state, while computing the dynamics only for the particles in the normal state. Careful criteria, local in time and space, are designed such that particles become frozen only at mechanically stable positions. Read More

Casimir forces can appear between intrusions placed in different media driven by several fluctuation mechanisms, either in equilibrium or out of it. Herein, we develop a general formalism to obtain such forces from the dynamical equations of the fluctuating medium, the statistical properties of the driving noise, and the boundary conditions of the intrusions (which simulate the interaction between the intrusions and the medium). As a result, an explicit formula for the Casimir force over the intrusions is derived. Read More

We consider a non-interacting one-dimensional gas accelerated by a constant and uniform external field. The energy absorbed from the field is transferred via elastic collisions to a bath of scattering obstacles. At gas-obstacle encounters the particles of the gas acquire a fixed kinetic energy. Read More

A jet of non-Brownian particles confined in a thin cell and driven by gravitational force is studied both numerically and theoretically. We present a theoretical scheme aimed to describe such a system in the Stokes regime. We focus on the dynamics of the interface between the suspension and the pure fluid. Read More

We study, via hydrodynamic equations, the granular temperature profile of a granular fluid under gravity and subjected to energy injection from a base. It is found that there exists a turn-up in the granular temperature and that, far from the base, it increases linearly with height. We show that this phenomenon, observed previously in experiments and computer simulations, is a direct consequence of the heat flux law, different form Fourier's, in granular fluids. Read More

A granular gas subjected to a permanent injection of energy is described by means of hydrodynamic equations derived from a moment expansion method. The method uses as reference function not a Maxwellian distribution $f_{\sf M}$ but a distribution $f_0 = \Phi f_{\sf M}$, such that $\Phi$ adds a fourth cumulant $\kappa$ to the velocity distribution. The formalism is applied to a stationary conductive case showing that the theory fits extraordinarily well the results coming from our molecular dynamic simulations once we determine $\kappa$ as a function of the inelasticity of the particle-particle collisions. Read More

We report and explain a convective phenomenon observed in molecular dynamics simulations that cannot be classified either as a hydrodynamics instability nor as a macroscopically forced convection. Two complementary arguments show that the velocity field by a thermalizing wall is proportional to the ratio between the heat flux and the pressure. This prediction is quantitatively corroborated by our simulations. Read More