Turning catalytically active pores into active pumps.

We develop a semi-analytical model of self-diffusioosmotic transport in active pores, which includes advective transport and the inverse chemical reaction that consumes solute. In previous work [Antunes et al., Phys. Rev. Lett. 129, 188003 (2022)], we have demonstrated the existence of a spontaneous symmetry breaking in fore-aft symmetric pores that enables them to function as a micropump. We now show that this pumping transition is controlled by three timescales. Two timescales characterize advective and diffusive transport. The third timescale corresponds to how long a solute molecule resides in the pore before being consumed. Introducing asymmetry to the pore (either via the shape or the catalytic coating) reveals a second type of advection-enabled transition. In asymmetric pores, the flow rate exhibits discontinuous jumps and hysteresis loops upon tuning the parameters that control the asymmetry. This work demonstrates the interconnected roles of shape and catalytic patterning in the dynamics of active pores and shows how to design a pump for optimum performance.

Pumping and Mixing in Active Pores.

We show both numerically and analytically that a chemically patterned active pore can act as a micro- or nanopump for fluids, even if it is fore-aft symmetric. This is possible due to a spontaneous symmetry breaking which occurs when advection rather than diffusion is the dominant mechanism of solute transport. We further demonstrate that, for pumping and tuning the flow rate, a combination of geometrical and chemical inhomogeneities is required. For certain parameter values, the flow is unsteady, and persistent oscillations with a tunable frequency appear. Finally, we find that the flow exhibits convection rolls and hence promotes mixing in the low Reynolds number regime.

Computational methods and theory for ion channel research.

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Numerical simulations of self-diffusiophoretic colloids at fluid interfaces.

The dynamics of active colloids is very sensitive to the presence of boundaries and interfaces which therefore can be used to control their motion. Here we analyze the dynamics of active colloids adsorbed at a fluid-fluid interface. By using a mesoscopic numerical approach which relies on an approximated numerical solution of the Navier-Stokes equation, we show that when adsorbed at a fluid interface, an active colloid experiences a net torque even in the absence of a viscosity contrast between the two adjacent fluids. In particular, we study the dependence of this torque on the contact angle of the colloid with the fluid-fluid interface and on its surface properties. We rationalize our results via an approximate approach which accounts for the appearance of a local friction coefficient. By providing insight into the dynamics of active colloids adsorbed at fluid interfaces, our results are relevant for two-dimensional self assembly and emulsion stabilization by means of active colloids.

Self-diffusiophoresis induced by fluid interfaces.

The influence of a fluid-fluid interface on self-phoresis of chemically active, axially symmetric, spherical colloids is analyzed. Distinct from the studies of self-phoresis for colloids trapped at fluid interfaces or in the vicinity of hard walls, here we focus on the issue of self-phoresis close to a fluid-fluid interface. In order to provide physically intuitive results highlighting the role played by the interface, the analysis is carried out for the case that the symmetry axis of the colloid is normal to the interface; moreover, thermal fluctuations are not taken into account. Similarly to what has been observed near hard walls, we find that such colloids can be set into motion even if their whole surface is homogeneously active. This is due to the anisotropy along the direction normal to the interface owing to the partitioning by diffusion, among the coexisting fluid phases, of the product of the chemical reaction taking place at the colloid surface. Different from results corresponding to hard walls, in the case of a fluid interface the direction of motion, i.e., towards the interface or away from it, can be controlled by tuning the physical properties of one of the two fluid phases. This effect is analyzed qualitatively and quantitatively, both by resorting to a far-field approximation and via an exact, analytical calculation which provides the means for a critical assessment of the approximate analysis.

Bistability, Oscillations, and Bidirectional Motion of Ensemble of Hydrodynamically Coupled Molecular Motors.

We analyze the collective behavior of hydrodynamically coupled molecular motors. We show that the local fluxes induced by motor displacement can induce the experimentally observed bidirectional motion of cargoes and vesicles. By means of a mean-field approach we show that sustained oscillations as well as bistable collective motor motion arise even for very large collection of motors, when thermal noise is irrelevant. The analysis clarifies the physical mechanisms responsible for such dynamics by identifying the relevant coupling parameter and its dependence on the geometry of the hydrodynamic coupling as well as on system size. We quantify the phase diagram for the different phases that characterize the collective motion of hydrodynamically coupled motors and show that sustained oscillations can be reached for biologically relevant parameters, hence, demonstrating the relevance of hydrodynamic interactions in intracellular transport.

Collective dynamics of chemically active particles trapped at a fluid interface.

Chemically active colloids generate changes in the chemical composition of their surrounding solution and thereby induce flows in the ambient fluid which affect their dynamical evolution. Here we study the many-body dynamics of a monolayer of spherically symmetric active particles trapped at a fluid-fluid interface. To this end we consider a model for the large-scale spatial distribution of particles which incorporates the direct pair interaction (including also the capillary interaction which is caused specifically by the interfacial trapping) as well as the effect of hydrodynamic interactions (including the Marangoni flow induced by the response of the interface to the chemical activity). The values of the relevant physical parameters for typical experimental realizations of such systems are estimated and various scenarios, which are predicted by our approach for the dynamics of the monolayer, are discussed. In particular, we show that the chemically-induced Marangoni flow can prevent the clustering instability driven by the capillary attraction.

Erratum: Effective Interaction between Active Colloids and Fluid Interfaces Induced by Marangoni Flows [Phys. Rev. Lett. 116, 078301 (2016)].

This corrects the article DOI: 10.1103/PhysRevLett.116.078301.

Active colloids at fluid interfaces.

If an active Janus particle is trapped at the interface between a liquid and a fluid, its self-propelled motion along the interface is affected by a net torque on the particle due to the viscosity contrast between the two adjacent fluid phases. For a simple model of an active, spherical Janus colloid we analyze the conditions under which translation occurs along the interface and we provide estimates of the corresponding persistence length. We show that under certain conditions the persistence length of such a particle is significantly larger than the corresponding one in the bulk liquid, which is in line with the trends observed in recent experimental studies.

Effective Interaction between Active Colloids and Fluid Interfaces Induced by Marangoni Flows.

We show theoretically that near a fluid-fluid interface a single active colloidal particle generating, e.g., chemicals or a temperature gradient experiences an effective force of hydrodynamic origin. This force is due to the fluid flow driven by Marangoni stresses induced by the activity of the particle; it decays very slowly with the distance from the interface, and can be attractive or repulsive depending on how the activity modifies the surface tension. We show that, for typical systems, this interaction can dominate the dynamics of the particle as compared to Brownian motion, dispersion forces, or self-phoretic effects. In the attractive case, the interaction promotes the self-assembly of particles into a crystal-like monolayer at the interface.