We investigate the average velocity of Brownian particles driven by a constant external force when constrained to move in two-dimensional, weakly-corrugated channels. We consider both the geometric confinement of the particles between solid walls as well as the soft confinement induced by a periodic potential. Using perturbation methods we show that the leading order correction to the marginal probability distribution of particles in the case of soft confinement is equal to that obtained in the case of geometric confinement, provided that the (configuration) integral over the cross-section of the confining potential is equal to the width of the solid channel. We then calculate the probability distribution and average velocity in the case of a sinusoidal variation in the width of the channels. The reduction on the average velocity is larger in the case of soft channels at small Péclet numbers and for relatively narrow channels and the opposite is true at large Péclet numbers and for wide channels. In the limit of large Péclet numbers the convergence to bulk velocity is faster in the case of soft channels. The leading order correction to the average velocity and marginal probability distribution agree well with Brownian Dynamics simulations for the two types of confinement and over a wide range of Péclet numbers.
The transport of suspended Brownian particles dc-driven along corrugated narrow channels is numerically investigated in the regime of finite damping. We show that inertial corrections cannot be neglected as long as the width of the channel bottlenecks is smaller than an appropriate particle diffusion length, which depends on the the channel corrugation and the drive intensity. Being such a diffusion length inversely proportional to the damping constant, transport through sufficiently narrow obstructions turns out to be always sensitive to the viscosity of the suspension fluid. The inertia corr…
We study the motion of an active Brownian particle (ABP) using overdamped Langevin dynamics on a two-dimensional substrate with periodic array of obstacles and in a quasi-one-dimensional corrugated channel comprised of periodically arrayed obstacles. The periodic arrangement of the obstacles enhances the persistent motion of the ABP in comparison to its motion in the free space. Persistent motion increases with the activity of the ABP. We note that the periodic arrangement induces directionality in ABP motion at late time, and it increases with the size of the obstacles. We also note that the …
The transport phenomenon(directional movement) of self-propelled Brownian particles moving in a smooth corrugated confined channel is investigated. It is found that large $x$ direction noise intensity should reduce particles directional movement when the angle Gaussian noise intensity is small. The average velocity has a maximum with increasing $x$ direction noise intensity when angle Gaussian noise intensity is large. $y$ directional noise has negligible effect on $x$ directional movement. Large angle Gaussian noise intensity should weaken the directional transport. Interestingly, the movemen…
The transport phenomenon of active particles confined in 3D(three dimensional) corrugated confined channel with Gaussian noises is investigated. Large noise intensity perpendicular to the symmetry axis is good for the diffusion and current along the axis. The generalized resonance transport phenomenon appears with increasing noise intensity parallel to the symmetry axis. Large noise intensity parallel to axis can suppress the diffusion. The diffusion coefficient has a maximum with increasing polar angle noise intensity. There exits an optimal value of parameter f that result in maximum movemen…
In many natural and artificial devices diffusive transport takes place in confined geometries with corrugated boundaries. Such boundaries cause both entropic and hydrodynamic effects, which have been studied only for the case of spherical particles. Here we experimentally investigate diffusion of particles of elongated shape confined into a corrugated quasi-two-dimensional channel. Elongated shape causes complex excluded-volume interactions between particle and channel walls which reduce the accessible configuration space and lead to novel entropic free energy effects. The extra rotational deg…
We investigate the transport of suspended Brownian particles dc driven along corrugated narrow channels in a regime of finite damping. We demonstrate that inertial corrections cannot be neglected as long as the width of the channel bottlenecks is smaller than an appropriate particle diffusion length, which depends on both, the temperature and the strength of the dc drive. Therefore, transport through sufficiently narrow constrictions turns out to be sensitive to the viscosity of the suspension fluid. Applications to colloidal systems are discussed.
We study the transport of Brownian particles through a corrugated channel caused by a force field containing curl-free (scalar potential) and divergence-free (vector potential) parts. We develop a generalized Fick-Jacobs approach leading to an effective one-dimensional description involving the potential of mean force. As an application, the interplay of a pressure-driven flow and an oppositely oriented constant bias is considered. We show that for certain parameters, the particle diffusion is significantly suppressed via the property of hyrodynamically enforced entropic particle trapping.
The dynamics of colloidal suspension confined within porous materials strongly differs from that in the bulk. In particular, within porous materials, the presence of boundaries with complex shapes entangles the longitudinal and transverse degrees of freedom inducing a coupling between the transport of the suspension and the density inhomogeneities induced by the walls. Colloidal suspension confined within model porous media are characterized by means of active microrheology where a net force is applied on a single colloid (tracer particle) whose transport properties are then studied. The traje…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like particle under the action of an effective potential. Such a model allows us to identify the relevant parameters controlling the polymers dynamics and, in particular, their translocation time. By comparing our analytical results with numerical simulations we show that, under suitable conditions, our model provides reliable predictions of the dynamics of both…
Broadband molecular dynamics simulation of fluid inertial effects in confined Brownian motion
Université de Mons（蒙斯大学）；Univ. Bordeaux, CNRS, LOMA, UMR 5798（波尔多大学，法国国家科学研究中心，LOMA联合实验室）；University of Vienna（维也纳大学）；Ecole Polytechnique, Institut Polytechnique de Paris（巴黎综合理工学院，巴黎理工学院）
Two-dimensionally nanoconfined water between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water under a periodic confining potential by means of computer simulations, both using empirical potentials and from first-principles. We propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude …
We derive an analytic expression for the mechanical pressure of a generic one-dimensional model of confined active Brownian particles (ABPs) that is valid for all values of Peclet number Pe and all confining scenarios. Our model reproduces the known scaling of bulk pressure with Pe^2 while in strong confinement pressure scales with Pe. Our analytic results are very well reproduced by simulations of ABPs in 2D. We use the pressure formula to calculate both the work performed by an active engine and its efficiency. In particular, efficiency is maximized for work cycles with finite period and not…
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and restricted to a finite domain. We investigate by analytic calculations and simulations how time-averaged observables (e.g., the time averaged mean squared displacement and displacement correlation) are affected by spatial confinement and dimensionality. In particular we study the degree of weak ergodicity breaking and scatter between different single trajecto…
We analyze the dynamics of a tracer particle embedded in a bath of hard spheres confined in a channel of varying section. By means of Brownian dynamics simulations we apply a constant force on the tracer particle and discuss the dependence of its mobility on the relative magnitude of the external force with respect to the entropic force induced by the confinement. A simple theoretical one-dimensional model is also derived, where the contribution from particle-particle and particle-wall interactions is taken from simulations with no external force. Our results show that the mobility of the trac…
We investigate the transport of Brownian particles in a two-dimensional potential under the action of a uniform external force. The potential is periodic in one direction and confines the particle to a narrow channel of varying cross-section in the other direction. We apply the standard long-wave asymptotic analysis in the narrow dimension and show that the leading order term is equivalent to that obtained previously from a direct extension of the Fick-Jacobs approximation. We also show that the confining potential has similar effects on the transport of Brownian particles to those induced by …
We show that when particles are suspended in an electrolyte confined between corrugated charged surfaces, electrokinetic flows lead to a new set of phenomena such as particle separation, mixing for low-Reynolds micro- and nano-metric devices and negative mobility. Our analysis shows that such phenomena arise, for incompressible fluids, due to the interplay between the electrostatic double layer and the corrugated geometrical confinement and that they are magnified when the width of the channel is comparable to the Debye length. Our characterization allows us to understand the physical origin o…
Quantitative measurement of fluid inertial effects in confined Brownian motion
Univ. Bordeaux, CNRS, LOMA, UMR 5798（波尔多大学）；Dpto. Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid（马德里自治大学凝聚态理论物理系）；Condensed Matter Physics Center, IFIMAC, Spain（IFIMAC凝聚态物理中心）；Mechanics Department, Ecole Polytechnique, Institut Polytechnique de Paris（巴黎理工学院高等学院力学系）
We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases of a flashing ratchet, a two-state model and a ratchet under the influence of a temperature gradient are analyzed in detail. We show the emergence of a strong cooperativity between the inherent rectification of the ratchet mechanism and the entropic bias of the fluctuations caused by spatial confinement. Net particle transport may take place in situations whe…
We study the rheology of confined suspensions of neutrally buoyant rigid monodisperse spheres in plane-Couette flow using Direct Numerical Simulations. We find that if the width of the channel is a (small) integer multiple of the sphere's diameter, the spheres self-organize into two-dimensional layers that slide on each other and the suspension's effective viscosity is significantly reduced. Each two-dimensional layer is found to be structurally liquid-like but their dynamics is frozen in time.
In the absence of advection, confined diffusion characterizes transport in many natural and artificial devices, such as ionic channels, zeolites, and nanopores. While extensive theoretical and numerical studies on this subject have produced many important predictions, experimental verifications of the predictions are rare. Here, we experimentally measure colloidal diffusion times in microchannels with periodically varying width and contrast results with predictions from the Fick-Jacobs theory and Brownian dynamics simulation. While the theory and simulation correctly predict the entropic effec…
We derive a general closed expression for the local pressure exerted onto the corrugated walls of a channel confining a fluid medium. When the fluid medium is at equilibrium the local pressure is a functional of the shape of the walls. It is shown that, due to the intrinsic non-local character of the interactions among the particles forming the fluid, the applicability of approximate schemes such as the concept of a surface of tension or morphometric thermodynamics is limited to wall curvatures small compared to the range of particle-particle interactions.
We review recent advances in rectification control of artificial microswimmers, also known as Janus particles, diffusing along narrow, periodically corrugated channels. The swimmer self-propulsion mechanism is modeled so as to incorporate a nonzero torque (propulsion chirality). We first summarize the effects of chirality on the autonomous current of microswimmers freely diffusing in channels of different geometries. In particular, left-right and upside-down asymmetric channels are shown to exhibit different transport properties. We then report new results on the dependence of the diffusivity …
We develop efficient numerical methods for performing many-body Brownian dynamics simulations of a recently-observed fingering instability in an active suspension of colloidal rollers sedimented above a wall [M. Driscoll, B. Delmotte, M. Youssef, S. Sacanna, A. Donev and P. Chaikin, Nature Physics, 2016, doi:10.1038/nphys3970]. We present a stochastic Adams-Bashforth integrator for the equations of Brownian dynamics, which has the same cost as but is more accurate than the widely-used Euler-Maruyama scheme, and uses a random finite difference to capture the stochastic drift proportional to the…
We investigate a two-dimensional system of active particles confined to a narrow annular domain. Despite the absence of explicit interactions among the velocities or the active forces of different particles, the system displays a transition from a disordered and stuck state to an ordered state of global collective motion where the particles rotate persistently clockwise or anticlockwise. We describe this behavior by introducing a suitable order parameter, the velocity polarization, measuring the global alignment of the particles' velocities along the tangential direction of the ring. We also m…
Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCC) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic b…
We introduce a Rigid-Body Fluctuating Immersed Boundary (RB-FIB) method to perform large-scale Brownian dynamics simulations of suspensions of rigid particles in fully confined domains, without any need to explicitly construct Green's functions or mobility operators. In the RB-FIB approach, discretized fluctuating Stokes equations are solved with prescribed boundary conditions in conjunction with a rigid-body immersed boundary method to discretize arbitrarily-shaped colloidal particles with no-slip or active-slip prescribed on their surface. We design a specialized Split--Euler--Maruyama tempo…
We study the Brownian motion of a charged colloid, confined between two charged walls, for small separation between the colloid and the walls. The system is embedded in an ionic solution. The combined effect of electrostatic repulsion and reduced diffusion due to hydrodynamic forces results in a specific motion in the direction perpendicular to the confining walls. The apparent diffusion coefficient at short times as well as the diffusion characteristic time are shown to follow a sigmoid curve as function of a dimensionless parameter. This parameter depends on the electrostatic properties and …
Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One monomer from the dumbbells interacts by a standard Lennard Jones potential and the other by a two-length scales shoulder potential, typically used for anomalous fluids. Here, we study the effects of remove the Brownian effects, typical from colloidal systems immersed in aqueous solution, and consider a molecular system, without the drag force and the random co…
We introduce methods for large scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and it "square" root are available for the given boundary conditions. W…
Molecular dynamics results on water confined in a silica pore in the low hydration regime are presented. Strong layering effects are found due to the hydrophilic character of the substrate. The local properties of water are studied as function of both temperature and hydration level. The interaction of the thin films of water with the silica atoms induces a strong distortion of the hydrogen bond network. The residence time of the water molecules is dependent on the distance from the surface. Its behavior shows a transition from a brownian to a non-brownian regime approaching the substrate in a…
Self-propelled particles move along circles rather than along a straight line when their driving force does not coincide with their propagation direction. Examples include confined bacteria and spermatozoa, catalytically driven nanorods, active, anisotropic colloidal particles and vibrated granulates. Using a non-Hamiltonian rate theory and computer simulations, we study the motion of a Brownian "circle swimmer" in a confining channel. A sliding mode close to the wall leads to a huge acceleration as compared to the bulk motion, which can further be enhanced by an optimal effective torque-to-fo…
In this article, results have been presented for the two-time correlation functions for a free and a harmonically confined Brownian particle in a simple shear flow. For a free Brownian particle, the motion along the direction of shear exhibit two distinct dynamics, with the mean-square-displacement being diffusive at short times while at late times scales as $t^3$. In contrast the cross-correlation $\la x(t) y(t) \ra $ scales quadratically for all times. In the case of a harmonically trapped Brownian particle, the mean-square-displacement exhibits a plateau determined by the strength of the co…
Using Brownian dynamics simulations, we investigate the effects of confinement, adsorption on surfaces and ion-ion interactions on the response of confined electrolyte solutions to oscillating electric fields in the direction perpendicular to the confining walls. Nonequilibrium simulations allow to characterize the transitions between linear and nonlinear regimes when varying the magnitude and frequency of the applied field but the linear response, characterized by the frequency-dependent conductivity, is more efficiently predicted from the equilibrium current fluctuations. To that end, we (re…
Directed transport of interacting active (self-propelled)Brownian particles is numerically investigated in confined geometries (entropic barriers). The self-propelled velocity can break thermodynamical equilibrium and induce the directed transport. It is found that the interaction between active particles can greatly affect the ratchet transport. For attractive particles, on increasing the interaction strength, the average velocity firstly decreases to its minima, then increases, and finally decreases to zero. For repulsive particles, when the interaction is very weak, there exists a critical …
The random motion of a Brownian particle confined in some finite domain is considered. Quite generally, the relevant statistical properties involve infinite series, whose coefficients are related to the eigenvalues of the diffusion operator. Unfortunately, the latter depend on space dimensionality and on the particular shape of the domain, and an analytical expression is in most circumstances not available. In this article, it is shown that the series may in some circumstances sum up exactly. Explicit calculations are performed for 2D diffusion restricted to a circular domain and 3D diffusion …
Active particles may happen to be confined in channels so narrow that they cannot overtake each other (Single File conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong inter-particle correlations developed in collective rearrangements. We consider a minimal model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) Single File picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian partic…
We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finite-volume Stokes solver to generate the action of the response functions "on the fly". Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically-correlated…
We investigate the segregation pattern formations of strongly and weakly fluctuated Brownian particle mixtures, which are confined in spherical containers with finite volumes. We consider systems where the container restricts the motions of particles combining two familiar methods: spherically symmetric linear potential and the container edge wall. In such systems, the following two segregation patterns are observed. When the container radius is large enough, more weakly fluctuated particles accumulate around the center of the container than strongly fluctuated particles. On the other hand, in…
We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of…
As a result of the competition between self-propulsion and excluded volume interactions, purely repulsive self-propelled spherical particles undergo a motility-induced phase separation (MIPS). We carry out a systematic computational study, considering several interaction potentials, systems confined by hard walls or with periodic boundary conditions, and different initial protocols. This approach allows us to identify that, despite its non-equilibrium nature, the equations of state of Active Brownian Particles (ABP) across MIPS verify the characteristic properties of first-order liquid-gas pha…
The structure and dynamics of confined suspensions of particles of arbitrary shape is of interest in multiple disciplines, from biology to engineering. Theoretical studies are often limited by the complexity of long-range particle-particle and particle-wall forces, including many-body fluctuating hydrodynamic interactions. Here, we report a computational study on the diffusion of spherical and cylindrical particles confined in a spherical cavity. We rely on an Immersed-Boundary General geometry Ewald-like method to capture lubrication and long-range hydrodynamics, and include appropriate non-s…
We show that one may view the self and the distinct part of the van Hove dynamic correlation function of a simple fluid as the one-body density distributions of a binary mixture that evolve in time according to dynamical density functional theory. For a test case of soft core Brownian particles the theory yields results for the van Hove function that agree quantitatively with those of our Brownian dynamics computer simulations. At sufficiently high densities the free energy landscape underlying the dynamics exhibits a barrier as a function of the mean particle displacement, shedding new light …
Overdamped Brownian motion of a self-propelled particle is studied by solving the Langevin equation analytically. On top of translational and rotational diffusion, in the context of the presented model, the "active" particle is driven along its internal orientation axis. We calculate the first four moments of the probability distribution function for displacements as a function of time for a spherical particle with isotropic translational diffusion as well as for an anisotropic ellipsoidal particle. In both cases the translational and rotational motion is either unconfined or confined to one o…
We present a simple and systematic procedure to determine the effective dynamics of a Brownian particle coupled to a rapidly fluctuating correlated medium, modeled as a scalar Gaussian field, under spatial confinement. The method allows us, in particular, to address the case in which the fluctuations of the medium are suppressed in the vicinity of the particle, as described by a quadratic coupling in the underlying Hamiltonian. As a consequence of the confinement of the correlated medium, the resulting effective Fokker-Planck equation features spatially dependent drift and diffusion coefficien…
We present an entirely microscopic formulation of viscoleasticity of a fluid starting from the microscopic Stokes-Oldroyd B Model assuming instantaneous hydrodynamic friction, and show that linearization leads to a form for the frequency dependent viscosity that can be directly applied to the Langevin equation. Interestingly, the calculated expression of viscosity can be directly mapped to the Jeffreys' model which is essentially macroscopic in nature with the bulk viscoelasticity of the fluid being characterized by a complex elastic modulus G(ω). Further, we demonstrate that the concerned Gre…
We present numerical results for the tagged-particle dynamics by solving the mode-coupling theory in confined geometry for colloidal liquids (cMCT). We show that neither the microscopic dynamics nor the type of intermediate scattering function qualitatively changes the asymptotic dynamics in vicinity of the glass transition. In particular, we find similar characteristics of confinement in the low-frequency susceptibility spectrum which we interpret as footprints of parallel relaxation. We derive predictions for the localization length and the scaling of the diffusion coefficient in the superco…
Diffusive properties of interacting magnetic dipoles confined in a parabolic narrow channel and in the presence of a periodic modulated (corrugated) potential along the unconfined direction are studied using Brownian dynamics simulations. We compare our simulation results with the analytical result for the effective diffusion coefficient of a single-particle by Festa and d'Agliano [Physica A \textbf{90}, 229 (1978)] and show the importance of inter-particle interaction on the diffusion process. We present results for the diffusion of magnetic dipoles as a function of linear density, strength o…
