Publications

Publications of the main researchers of the Millennium Nucleus Physics of Active Matter

PUBLICATIONS 2021-2023

Active mixtures in a narrow channel: motility diversity changes cluster sizes
The continuous motion of bacteria produces clusters with a stationary cluster size distribution.
Here, we develop a minimal model for bacteria in a narrow channel to assess the relative
importance of motility diversity and confinement. We show that the greater variety in the motilities -which occurs naturally in a biological situation- the greater are the conglomerates.
Using parameters fitted from experiments with Escherichia coli bacteria, we predict that the error in estimating the average size, without considering polydispersity, is around 60%.
Active mixtures in a narrow channel: motility diversity changes cluster sizes
De Castro P.,Diles S., Soto R.,Sollichcd P.
Soft Matter http://rsc.li/soft-matter-journal.January 2021
DOI: 10.1039/d0sm02052d
Magnetotactic bacteria in a droplet self-assemble into a rotary motor
A class of bacteria, called magnetotactic (MTB), are organisms that naturally can grow an internal microscopic magnet that allows them to align with an external magnetic
field.When we confine them inside a microdroplet and apply a constant magnetic field, bacteria start swimming in circles making the drop rotate.
Magnetotactic bacteria in a droplet self-assemble into a rotary motor. Vincenti, G. Ramos, M. L. Cordero, C. Douarche, R. Soto, E.Clément. Nature Communications, 10, 5082 (2019)
https://doi.org/10.1038/s41467-019-13031-6

PUBLICATIONS 2018-2020

E. coli “super-contaminates” narrow ducts fostered by broad run-time distribution
One characteristic of bacterial motion is its capacity to swim upstream. This movement takes place in anatomic conducts or medical devices. In this study, we demonstrate that in microfluidic devices, E. coli can travel distances up to 15mm in just 15 minutes against the current. This effect, we denominate “super-contamination” due to the broad run-time distribution of the swim in the E. coli, could explain the rapid appearance of some potentially fatal medical emergencies.
E. coli “super-contaminates” narrow ducts fostered by broad run-time distribution
Figueroa-Morales N.; Rivera A., Soto R., Lindner A., Altshuler E., Clément E.
Science Advances 6 (11), eaay0155. (2020)
https://advances.sciencemag.org/content/6/11/eaay0155
Run-and-tumble bacteria slowly approaching the diffusive regime
The bacteria run-and-tumble dynamic gives birth to both; a ballistic movement due to its
persistence and a diffusion process due to its consecutive tumbles. Here, we investigate how long
it takes for a diluted bacterial suspension to reach a diffusion regimen, likewise, the importance of
the deviations concerning this regime for intermediate times.
Run-and-tumble bacteria slowly approaching the diffusive regime
Villa-Torrealba A., Chávez-Raby C., De Castro P., Soto R.
Physical Review E101, 062607 (2020)
https://doi.org/10.1103/PhysRevE.101.062607
Understanding contagion dynamics through microscopic processes in active Brownian particles
Along with the universally recognized SIR model, several approaches have been used to
comprehend the contagion dynamics of the interacting particles. Here, active Brownian
particles (ABP) are introduced to model the contagion dynamics of living agents that
perform a horizontal transmission in time and space of an infectious disease..
Understanding contagion dynamics through microscopic processes in active Brownian particles.
Norambuena, A., Valencia, F. J., Guzmán-Lastra, F.
Scientific Reports, 10(1), 1-7. (2020).
https://www.nature.com/articles/s41598-020-77860-y 
Towards an analytical description of active microswimmers in clean and in surfactant-covered drops
Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmers moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. We find that the
presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation..
Towards an analytical description of active microswimmers in clean and in surfactant-covered drops.
Sprenger, A. R., Shaik, V. A., Ardekani, A. M., Lisicki, M., Mathijssen, A. J., Guzmán-Lastra, F Löwen H., Menzel A., Daddi-Moussa-Ider A.
The European Physical Journal E, 43(9), 1-18. (2020).
https://link.springer.com/article/10.1140/epje/i2020-11980-9 
Diffusion in a porous media
Diffusion is a universal process of high importance, for example, in the transport of molecules inside the cells, chemical signals inside the brain, or nutrients in the soil. The geometry of the media has a strong influence in the process, and that is what we demonstrate in the present study, where we used several random microchannels networks to experimentally determine the effect of the effective area of the networks and the size of the measurement area in the effective properties of the same.
Local details versus effective medium approximation: A study of diffusion in microfluidic random networks made from Voronoi tessellations.
W. Ponce, M. L. Cordero.
Phys. Rev. E 101, 023110 (2020).
https://doi.org/10.1103/PhysRevE.101.023110  
Hybrid micromotors for detection of gastric cancer
In the present article, we study tiny micromotors formed by microtubes of different materials, so they can show different properties. This study was especially about catalytic micromotors (impulsed using a chemical reaction), magnetic micromotors (impulsed using an external magnetic field), or hybrid micromotors (impulsed by a mixture of both processes.)
Effects of preparation on catalytic, magnetic and hybrid micromotors on their functional features and application in gastric cancer biomarker detection.
D. F. Báez, Ramos, A. Corvalán, M. L. Cordero, S. Bollo, M. J. Kogan.
Sens. Act. B 310, 127843 (2020).
https://doi.org/10.1016/j.snb.2020.127843  
Nonideal rheology of semi-dilute bacterial suspensions
IIn this article, we study the viscous response of bacterial suspensions in a semi-dilute regimen.
Considering the interactions that create alignment between bacteria, we showed that the viscous
effort produced by the bacterial activity is oscillatory, even with a stationary flux.
Nonideal rheology of semidilute bacterial suspensions
Guzmán M., Soto R.
Physical Review e99, 012613 (2019)
https://doi.org/10.1103/PhysRevE.99.012613
Cell migration driven by substrate deformation gradients
This study proposes the existence of a mechanism that is similar to another mechanism already
known -named durotaxis-, where cells, instead of migrating to the hard zones, migrate to the
stretched zones. We postulate that some cases of cellular migration, where cells move guided by
chemical signs, can be cases of “straintaxis” and not only durotaxis, as previously believed.
Cell migration driven by substrate deformation gradients
Márquez S., Reig G., Concha M. Soto R.
Phys. Biol. 16 (2019) 066001
https://doi.org/10.1088/1478-3975/ab39c7
Active colloidal chains with cilia- and flagella-like motion
In this study we demonstrate that simplified systems, consisting only of a few particles with non-reciprocal interaction and head–tail asymmetry, show beating motion and self-propulsion. Both properties are present in many non-equilibrium models thus making our results a general feature of active matter.
Active colloidal chains with cilia- and flagella-like motion
González y R. Soto
New Journal of Physics 20,053014 (2018)
http://iopscience.iop.org/article/10.1088/1367-2630/aabe3c 
Vertex model instabilities for tissues subject to cellular activity or applied stresses
The vertex model is widely used to describe the epithelial tissues dynamic due to its simplicity and
versatility and the easy inclusion of biophysics parameters. This study shows that when cells
modify their equilibrium perimeter because of its activity, or the tissues are subject to external
tensions, the tissue becomes unstable, and cells become considerably deformed. These deformations could be able to trigger morphogenetic processes.
Vertex model instabilities for tissues subject to cellular activity or applied stresses
Pérez F., Joanny J., Soto R.
Physical Review E102, 052604 (2020).                                                                         https://doi.org/10.1103/PhysRevE.102.052604
Does the 3D Spatial exploration reflect the temporal variability of the E. coli motor?
Most of the theoretical approaches used to model bacteria transport have their base on its run-and-tumble movement. It is typically supposed that the rate of tumbles is constant. By studying the tridimensional trajectories of E. coli, we show there is extensive variability in the behavior of E. coli, characterized by a fluctuant rate of tumbles related to the chemotaxis mechanism of this bacteria.
3D Spatial Exploration by E. coli Echoes Motor Temporal Variability
Figueroa-Morales N., Soto R, Junot G.,Darnige T.,Douarche C. ,Martínez V. , Lindner A., Clement E.
https://doi.org/10.1103/PhysRevX.10.021004
Bacteria driving droplets
In this study, we confined bacteria inside microdroplets. Bacteria swim inside de drop, merge and form ephemeral structures, causing the drop motion. Like the bacteria motion, the drop motion is also fluctuant and aleatory, and this fact is related to the movement of bacteria near the drop surface.
Bacteria driving droplets
G. Ramos, M. L. Cordero, R. Soto.
Soft Matter 16, 1359 (2020).
https://doi.org/10.1039/C9SM01839E  
Active carpets drive non-equilibrium diffusion and enhanced molecular fluxes
These ‘active carpets’ locally inject energy into their surrounding fluid. Whereas Fick’s laws of diffusion are established near equilibrium, it is unclear how to solve non-
equilibrium transport driven by such boundary-actuated fluctuations. Here, we derive the enhanced diffusivity of molecules or passive particles as a function of distance from an active carpet.
Active carpets drive non-equilibrium diffusion and enhanced molecular fluxes.
Guzmán-Lastra, F., Löwen, H., & Mathijssen, A. J.
Nature Communications, 12(1), 1-15. (2021).
https://www.nature.com/articles/s41467-021-22029-y 
Perfect Brewster transmission through ultrathin perforated films
When an acoustic wave has incidence in a perforated film, the wave transmission is
typically low, except for certain particular angles named Brewster angles.
We study, theoretically and numerally, the effect of the acoustic properties and the
geometry of the surface in the wave transmission.
Perfect Brewster transmission through ultrathin perforated films.
K.Pham, A.Maurel ,J.-F.Mercier, S.Félix, M.L.Cordero, C.Horvath
Wave motion 93, 102485 (2020).
https://doi.org/10.1016/j.wavemoti.2019.102485 
Membrane penetration and trapping of an active particle
In this article, we explore the interaction between an active particle and a cell membrane. We show that the active particle may either get trapped near the membrane or penetrate through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. We also present state diagrams that carefully outline which state occurs in terms of only a few generic aspects; membrane elasticity, bending rigidity, resistance, and size of the active particle.
Membrane penetration and trapping of an active particle.
Daddi-Moussa-Ider, A., Goh, S., Liebchen, B., Hoell, C., Mathijssen, A. J., Guzmán-Lastra, F.,Scholz C., Menzel A., Löwen H.
The Journal of chemical physics, 150(6), 064906 (2019).
https://aip.scitation.org/doi/abs/10.1063/1.5080807
GPU parallel simulation algorithm of Brownian particles
In this article, we developed an algorithm that allows us to simulate computationally millions of microscopic particles. Using advanced geometric tools, we perform an efficient
simulation in graphic units (GPU). In the image, we show the case of a mixture of gold and platinum particles in an
oxygenated water solution.
GPU parallel simulation algorithm of Brownian particles with excluded volume using Delaunay triangulations
F Carter, N Hitschfeld, C Navarro, R Soto
Computer Physics Communications 229, 148 (2018)
https://www.sciencedirect.com/science/article/pii/S0010465518301061
Magnetotactic bacteria in a droplet self-assemble into a rotary motor
A class of bacteria, called magnetotactic (MTB), are organisms that naturally can grow an internal microscopic magnet that allows them to align with an external magnetic
field.When we confine them inside a microdroplet and apply a constant magnetic field, bacteria start swimming in circles making the drop rotate.
Magnetotactic bacteria in a droplet self-assemble into a rotary motor. Vincenti, G. Ramos, M. L. Cordero, C. Douarche, R. Soto, E.Clément. Nature Communications, 10, 5082 (2019)
https://doi.org/10.1038/s41467-019-13031-6
Propiedades críticas de materiales granulares
Los fenómenos críticos asociados a la transición de líquido a sólido de sistemas granulares vibrados cuasi bidimensionales se estudian utilizando simulaciones de dinámica molecular del modelo de esfera dura inelástica. En este estudio vemos que en sistemas cuasi unidimensionales, la transición es solo discontinua, limitada por un punto crítico, lo que indica que dos es la dimensión más baja por tener un punto tricrítico.
Critical phenomena in quasi-two-dimensional vibrated granular systems
M Guzmán, R Soto
Physical Review E 97, 012907 (2018)
https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.012907

PUBLICATIONS 2010 – 2017

Autores/AuthorsTítulo/TitleReferencia/Reference
G Castillo, N Mujica, N Sepulveda, J C Carlos Sobarzo, M Guzman, R SotoHyperuniform states generated by a critical friction field Phys. Rev. E (accepted 2019)
S Marquez, G Reig, M Concha, R SotoCell migration driven by substrate deformation gradients Phys. Biol. (accepted 2019)
A Daddi-Moussa-Ider, S Goh, B Liebchen, C Hoell, AJTM Mathijssen, F Guzmán-Lastra, C Scholz, AM Menzel, H LöwenMembrane penetration and trapping of an active particleJ. Chem. Phys. 150, 064906 (2019)
Gaspard Junot, Nuris Figueroa-Morales, Thierry Darnige, Anke Lindner, Rodrigo Soto, Harold Auradou, Eric ClémentSwimming bacteria in Poiseuille flow: The quest for active Bretherton-Jeffery trajectories
EPL 126, 44003 (2019)
S Gonzalez, R Soto
Directed assembly of active colloidal molecules New Journal of Physics 21, 033041 (2019)
M Guzmán, R SotoNonideal rheology of semidilute bacterial suspensions Phys. Rev. E 99, 012613 (2019)
N Sepúlveda, R SotoUniversality of active wetting transitions Phys. Rev. E 98, 052141 (2018)
V Garzó, R Brito, R SotoEnskog kinetic theory for a model of a confined quasi-two-dimensional granular fluid
Phys. Rev. E 98, 052904 (2018)
N. Hassan, M.L. Cordero, R. Sierpe, M. Almada, J. Juárez, M. Valdez, A. Riveros, E. Vargas, Ali Abou-Hassan, J.M. Ruso, M.J. KoganPeptide functionalized magneto-plasmonic nanoparticles obtained by microfluidics for inhibition of β-amyloid aggregationJ. Mater. Chem. B 6, 5091 (2018)
D Risso, R Soto, M GuzmánEffective two-dimensional model for granular matter with phase separation Phys. Rev. E 98, 022901 (2018)
F. Barra and C. LledóThe smallest absorption refrigerator: the thermodynamics of a system with quantum local detailed balance EPJ-ST 227, 231 (2018)
AJTM Mathijssen, F Guzmán-Lastra, A Kaiser, H LöwenSelf-organised active carpets drive replenishing nutrient currents Phys. Rev. Lett. 121, 248101 (2018)
S. González and R. Soto
Active colloidal chains with cilia- and flagella-like motion New Journal of Physics 20, 053014 (2018)
M Guzmán, R Soto
Critical phenomena in quasi-two-dimensional vibrated granular systems Physical Review E 97, 012907 (2018)
F Carter, N Hitschfeld, C Navarro, R SotoGPU parallel simulation algorithm of Brownian particles with excluded volume using Delaunay triangulations Computer Physics Communications 229, 148 (2018)
J. Thingna, F. Barra, M. EspositoKinetics and thermodynamics of a driven open quantum system Phys. Rev. E 96 052132 (2017)
German Reig, Mauricio Cerda, Néstor Sepúlveda, Daniela Flores, Victor Castañeda, Masazumi Tada, Steffen Härtel and Miguel Concha Extra-embryonic tissue spreading directs early embryo morphogenesis in killifish Nature Communications 8, 15431 (2017)
F. Barra and C. LledóStochastic thermodynamics of quantum maps with and without equilibrium Phys. Rev. E 96, 052144 (2017)
N Sepúlveda and R SotoWetting transitions displayed by persistent active particlesPhys. Rev. Lett. 119, 078001 (2017)
B Herrmann-Priesnitz, WR Calderón-Muñoz, A Valencia, R SotoThermal design exploration of a swirl flow microchannel heat sink for high heat flux applications based on numerical simulations Applied Thermal Engineering 109, 22-34 (2016)
Néstor Sepúlveda and Rodrigo Soto Coarsening and clustering in run-and-tumble dynamics with short-range exclusion Phys. Rev. E 94, 022603 (2016)
N Mujica and R SotoDynamics of noncohesive confined granular media

Recent Advances in Fluid Dynamics with Environmental Applications, 445(2016)
D.Churochkin, F. Barra, F. Lund, A. Maurel, V.
Pagneux
Multiple scattering of elastic waves by pinned dislocation segments in a continuum Wave Motion, 60 220 (2016)

F. Barra and M. EspositoDissipation in small systems: Landau-Zener approach. Phys. Rev. E. 93, 062118 (2016)
F. Barra, R. Espinoza-González, H. Fernández, F. Lund, A, Maurel and V. PagneuxThe Use of Ultrasound to Measure Dislocation Density Jom 67, 1856 (2015)
F. BarraThe thermodynamic cost of driving quantum systems by their boundaries Scientific Reports 5, 14873 (2015)
P. Cordero, D. Risso and R. Soto

Effect of the vibration profile on shallow granular systemsPhil. Trans. R. Soc. A 373, 20150116 (2015)
E. Rojas, M. Trulsson, B. Andreotti, E. Clement and R. Soto

Relaxation processes after instantaneous shear rate reversal in a dense granular flow
EPL 109, 64002 (2015)
Rodrigo Soto and Ramin Golestanian

Self-assembly of Active Colloidal Molecules with Dynamic Function

Phys. Rev. E 91, 052304 (2015)
G. Castillo, N, Mujica, and R. Soto
Universality and criticality of a second-order granular solid-liquid-like phase transition Phys. Rev. E 91, 012141 (2015)
J.-F. Mercier, M. L. Cordero, S. Félix, A. Ourir, and A. MaurelClassical homogenization to analyze the dispersion relations of spoof plasmons with geometrical and compositional effects
Proc. R. Soc. A 471, 20150472 (2015)
Cordero, ML; Maurel, A; Mercier, JF; Felix, S; Barra, FTuning the wavelength of spoof plasmons by adjusting the impedance contrast in an array of penetrable inclusions Appl. Phys. Lett. 107, 084104 (2015)
Horvath, C;Arratia, C;Cordero, MLMeasurement of the dispersion relation of a convectively unstable capillary jet under confinementPhysics of Fluids 27, 114103 (2015)
R. Soto, D. Risso, and R. BritoShear viscosity of a model for confined granular mediaPhysical Review E 2014
C. Parra-Rojas and R. Soto

Casimir effect in swimmer suspensionsPhysical Review E 2014
B. Néel, I. Rondini, A. Turzillo, N. Mujica, and R. SotoDynamics of a first-order transition to an absorbing statePhysical Review E 2014
Rodrigo Soto and Ramin Golestanian

Self-assembly of catalytically active colloidal molecules: Tailoring activity through surface chemistryPhys. Rev. Lett. 2014
Rodrigo Soto and Ramin Golestanian

Run-and-tumble in a crowded environment: persistent exclusion process for swimmersPhysical Review E 2014
S. Ajisaka, F. Barra and B. ZunkovicNonequilibrium quantum phase transitions in the XY model: comparison of unitary time evolution and reduced density matrix approaches New. J. Phys 16 (2014) 033028
Ulloa, C;Ahumada, A;Cordero, MLEffect of confinement on the deformation of microfluidic dropsPhysical Review E 2014
S. Ajisaka and F. BarraNonequilibrium mesoscopic Fermi-reservoir distribution and particle current through a coherent quantum system Phys. Rev. B 87 195114 (2013)
C. Parra-Rojas and R. SotoActive temperature and velocity correlations produced by a swimmer suspensionPhysical Review E 2013
Francisca Guzman-Lastra and Rodrigo Soto

Subdiffusive behavior of a dilute non-Brownian suspension under shearPhysical Review E 2013
R. Brito, D. Risso, and R. SotoHydrodynamic modes in a confined granular fluidPhysical Review E 2013
G. L. Miño *, J. Dunstan*, A. Rousselet, E. Clement , and R. SotoInduced Diffusion of Tracers in a Bacterial Suspension: Theory and ExperimentsJ. Fluid Mech 2013
L.-H. Luu, N. Mujica, and R. Soto

Capillarylike fluctuations of a solid-liquid interface in a noncohesive granular systemPhys. Rev. E 2013
Francisca Guzman-Lastra and Rodrigo Soto

Stochastic resonance on the transverse displacement of swimmers in an oscillatory shear flowPhys. Rev. E 2012
G. Castillo, N. Mujica, and R. SotoFluctuations and Criticality of a Granular Solid-Liquid-like Phase TransitionPhysical Review Letter 2012
N. Rivas, P. Cordero, D. Risso, and R. Soto

Characterization of the energy bursts in vibrated shallow granular systemsGranular Matter 2012
Jocelyn Dunstan, Gastón Miño*, Eric Clement , Rodrigo Soto

A two-sphere model for bacteria swimming near solid surfacesPhysical Fluids 2012
S. Ajisaka, F. Barra, C. Mejía-Monasterio, and T.
Prosen
Current in coherent quantum systems connected to mesoscopic Fermi reservoirsPhysica Scripta 2012
F. Barra, F. Lund, N. Mujica
and S. Rica
Shear modulus of an elastic solid under external pressure as a function of temperature: The case of heliumPhysical Review B 2012
S. Ajisaka, F. Barra, C. MejíaMonasterio,
and T. Prosen
Nonequlibrium particle and energy currents in quantum chains connected to mesoscopic Fermi reservoirsPhysical Review B. 2012
F. Barra, V. Pagneux and J. ZuñigaDiffusive transport of waves in a periodic waveguidePhysical Review E 2012
S. Ajisaka, F.
Barra, C. Mejía-Monasterio, and T. Prosen
Particle and energy transport in quantum disordered and quasi-periodic chains connected to mesoscopic Fermi reservoirsAIP Conference Proceedings 2012
P. Rodríguez-Lopez, R.Brito and R. SotoNumerical computation of Casimir forces via stochastic quantization

Int. J. Mod. Phys. Conf. Ser. 2012
N. Rivas, D. Risso, R. Soto, and P. CorderoEnergy bursts in vibrated shallow granular systemsAIP Conf. Proc. 2011
Nicolás Rivas, Patricio Cordero, Dino Risso, and Rodrigo Soto

Segregation in quasi two-dimensional granular system

New Journal of Physics 2011
Daniel Asenjo, Fernando Lund, Simón Poblete, Rodrigo Soto, Marcos Sotomayor

Characterization of the Melting Transition in Two Dimensions at Vanishing External Pressure Using Molecular Dynamics Simulations


Physical Review B 2011
N. Rivas, S. Ponce, B. Gallet, D. Risso, R. Soto, P. Cordero, and N. MujicaSudden chain energy transfer events in vibrated granular media

Physical Review Letter 2011

Pablo Rodriguez-Lopez*, Ricardo Brito , and Rodrigo Soto

Stochastic Quantization and Casimir Forces

EPL 2011
Cordero, ML;Gallaire, F;Baroud, CNQuantitative analysis of the dripping and jetting regimes in co-flowing capillary jetsPhysics of Fluids2011
Shuichi Tasaki, Shigeru Ajisaka and Felipe Barra

Quantum statistical mechanics in infinitely extended systems - C* algebraic approachBussei Kenkyu, 97, No. 3 483 (2011)
G. Miño, T.E. Mallouk, T. Darnige, M. Hoyos, J. Dauchet, J. Dunstan, R. Soto, Y. Wang, A. Rousselet, and E. Clement

Enhanced diffusion due to active swimmers at a solid surface

Phys. Rev. Letter 2011
A. Maurela, V. Pagneuxb, F. Barra, F. LundSurface acoustic waves in interaction with a dislocationUltrasonics 2010
Barra F, Maurel A, Pagneux V, Zuñiga J.Number of propagating modes of a diffusive periodic waveguide in the semiclassical limitPhysical Review E 2010