Nonmonotonous Translocation Time of Polymers across Pores.

Polymers confined in corrugated channels, i.e., channels of varying amplitude, display multiple local maxima and minima of the diffusion coefficient upon increasing their degree of polymerization N. We propose a theoretical effective free energy for linear polymers based on a Fick-Jacobs approach. We validate the predictions against numerical data, obtaining quantitative agreement for the effective free energy, the diffusion coefficient, and the mean first passage time. Finally, we employ the effective free energy to compute the polymer lengths N_{min} at which the diffusion coefficient presents a minimum: we find a scaling expression that we rationalize with a blob model. Our results could be useful to design porous adsorbers, that separate polymers of different sizes without the action of an external flow.

Rheology of Pseudomonas fluorescens biofilms: From experiments to predictive DPD mesoscopic modeling.

Bacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria cross-linked to a self-produced network of extracellular polymeric substances (EPSs) embedded in water. Structural principles for numerical modeling aim at describing mesoscopic viscoelasticity without losing details on the underlying interactions existing in wide regimes of deformation under hydrodynamic stress. Here, we approach the computational challenge to model bacterial biofilms for predictive mechanics in silico under variable stress conditions. Up-to-date models are not entirely satisfactory due to the plethora of parameters required to make them functioning under the effects of stress. As guided by the structural depiction gained in a previous work with Pseudomonas fluorescens [Jara et al., Front. Microbiol. 11, 588884 (2021)], we propose a mechanical modeling by means of Dissipative Particle Dynamics (DPD), which captures the essentials of topological and compositional interactions between bacterial particles and cross-linked EPS-embedding under imposed shear. The P. fluorescens biofilms have been modeled under mechanical stress mimicking shear stresses as undergone in vitro. The predictive capacity for mechanical features in DPD-simulated biofilms has been investigated by varying the externally imposed field of shear strain at variable amplitude and frequency. The parametric map of essential biofilm ingredients has been explored by making the rheological responses to emerge among conservative mesoscopic interactions and frictional dissipation in the underlying microscale. The proposed coarse grained DPD simulation qualitatively catches the rheology of the P. fluorescens biofilm over several decades of dynamic scaling.

Intrinsic structure perspective for MIPS interfaces in two-dimensional systems of active Brownian particles.

Suspensions of active Brownian particles (ABPs) undergo motility-induced phase separation (MIPS) over a wide range of mean density and activity strength, which implies the spontaneous aggregation of particles due to the persistence of their direction of motion, even in the absence of an explicit attraction. Both similarities and qualitative differences have been obtained when the MIPS is analysed in the same terms as a liquid-gas phase coexistence in an equilibrium attractive system. Negative values of the mechanical surface tension have been reported, from the total forces across the interface, while stable fluctuations of the interfacial line could be interpreted as a positive capillary surface tension; in equilibrium liquid surfaces, these two magnitudes are equal. We present here the analysis of 2D-ABP interfaces in terms of the intrinsic density and force profiles, calculated with the particle distance to the instantaneous interfacial line. Our results provide new insight into the origin of MIPS from the local rectification of the random active force on the particles near the interface. As has been reported, this effect acts as an external potential that produces a pressure gradient across the interface, such that the mechanical surface tension of the MIPS cannot be described as that of equilibrium coexisting phases; however, our analysis shows that most of that effect comes from the tightly caged particles at the dense (inner) side of the MIPS interface, rather than from the free moving particles at the outer side that collide with the dense cluster. Moreover, a clear correlation appears between the decay of the hexatic order parameter at the dense slab and the end of the MIPS as the strength of the active force is lowered. We show that, using the strong active forces required for MIPS, the interfacial structure and properties are very similar for ABPs with purely repulsive interactions (the Weeks-Chandler-Andersen-Lennard-Jones (WCA-LJ) model truncated at its minimum) and when the interaction includes a range of the LJ attractive force.

Dynamical anomalies and structural features of active Brownian particles characterized by two repulsive length scales.

In this work, we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two length scales-a soft shell and a hard core. Depending on the ratio between the strength of the soft shell barrier and the activity, we find two regimes: If this ratio is much larger or smaller than 1, the observed behavior is comparable with ABPs interacting via a single length scale potential. If this ratio is similar to 1, the two length scales are relevant for both structure and dynamical properties. On the structural side, when the system exhibits a motility induced phase separation, the dense phase is characterized by new and more complex structures compared with the hexatic phase observed in single length scale systems. From the dynamic analysis, we find, to our knowledge, the first manifestation of a dynamic heterogeneity in active particles, reminiscent of the glassy dynamics widely studied in passive colloids.

Collective motion of run-and-tumble repulsive and attractive particles in one-dimensional systems.

Active matter deals with systems whose particles consume energy at the individual level in order to move. To unravel features such as the emergence of collective structures, several models have been suggested, such as the on-lattice model of run-and-tumble particles implemented via the persistent exclusion process (PEP). In our work, we study a one-dimensional system of run-and-tumble repulsive or attractive particles, both on-lattice and off-lattice. Additionally, we implement cluster motility dynamics in the on-lattice case (since in the off-lattice case, cluster motility arises from the individual particle dynamics). While we observe important differences between discrete and continuous dynamics, few common features are of particular importance. Increasing particle density drives aggregation across all different systems explored. For non-attractive particles, the effects of particle activity on aggregation are largely independent of the details of the dynamics. In contrast, once attractive interactions are introduced, the steady-state, which is completely determined by the interplay between these and the particles' activity, becomes highly dependent on the details of the dynamics.

Influence of water models on water movement through AQP1.

Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.

Characterization of MIPS in a suspension of repulsive active Brownian particles through dynamical features.

We study a two-dimensional system composed by Active Brownian Particles (ABPs), focusing on the onset of Motility Induced Phase Separation (MIPS), by means of molecular dynamics simulations. For a pure hard-disk system with no translational diffusion, the phase diagram would be completely determined by their density and Péclet number. In our model, two additional effects are present: translational noise and the overlap of particles; we study the effects of both in the phase space. As we show, the second effect can be mitigated if we use, instead of the standard Weeks-Chandler-Andersen potential, a stiffer potential: the pseudo-hard sphere potential. Moreover, in determining the boundary of our phase space, we explore different approaches to detect MIPS and conclude that observing dynamical features, via the non-Gaussian parameter, is more efficient than observing structural ones, such as through the local density distribution function. We also demonstrate that the Vogel-Fulcher equation successfully reproduces the decay of the diffusion as a function of density, with the exception of very high densities. Thus, in this regard, the ABP system behaves similar to a fragile glass.

Phase behaviour and dynamical features of a two-dimensional binary mixture of active/passive spherical particles.

In this work we have characterized the phase behaviour and the dynamics of bidimensional mixtures of active and passive Brownian particles. We have evaluated state diagrams at several concentrations of the passive components finding that, while passive agents tend to hinder phase separation, active agents force crystal-like structures on passive colloids. In order to study how passive particles affect the dynamics of the mixture, we have computed the long-time diffusion coefficient of each species, concluding that active particles induce activity and super-diffusive behaviour on passive ones. Interestingly, at the density at which the system enters a MIPS state the active particles' diffusivity shows an inflection point and the passive particles' one goes through a maximum, due to the change in the dynamics of the active components, as shown in the displacement's probability distribution function.

Trapping flocking particles with asymmetric obstacles.

Asymmetric obstacles can be exploited to direct the motion and induce sorting of run-and-tumble particles. In this work, we show that flocking particles which follow the Vicsek model aligning rules experience collective trapping in the presence of a wall of funnels made of chevrons, concentrating at the opposite side of the wall of funnels to run-and-tumble particles. Flocking particles can be completely trapped or exhibit a dynamical trapping behaviour; these two regimes open the door to the design of a system with two perpendicular flows of active particles. This systematic study broadens our understanding of the emergence of collective motion of microorganisms in confined environments and directs the design of new microfluidic devices able to control these collective behaviours.

Effect of dissolved salt on the anomalies of water at negative pressure.

Adding salt to water at ambient pressure affects its thermodynamic properties. At low salt concentration, anomalies such as the density maximum are shifted to lower temperature, while at large enough salt concentration, they cannot be observed any more. Here, we investigate the effect of salt on an anomaly recently observed in pure water at negative pressure: the existence of a sound velocity minimum along isochores. We compare experiments and simulations for an aqueous solution of sodium chloride with molality around 1.2 mol kg-1, reaching pressures beyond -100 MPa. We also discuss the origin of the minima in the sound velocity and emphasize the importance of the relative position of the temperatures of sound velocity and density anomalies.

An Active Approach to Colloidal Self-Assembly.

In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and we suggest possible strategies for how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise to the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.

Heterogeneous versus homogeneous crystal nucleation of hard spheres.

Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the fluid is unavoidably in contact with the walls of the sample cell, where heterogeneous crystallization may take place. In this work we use simulations to investigate the competition between homogeneous and heterogeneous crystallization. We report simulations of wall-induced nucleation for different confining walls. Combining the results of these simulations with earlier studies of homogeneous crystallization allows us to assess the competition between homogeneous and heterogeneous nucleation as a function of the wall type, fluid density and the system size. On flat walls, heterogeneous nucleation will typically overwhelm homogeneous nucleation. Even for surfaces randomly coated with spheres with a diameter that was some three times larger than that of the fluid spheres - as has been used in some experiments - heterogeneous nucleation is likely to be dominant for volume fractions smaller than ∼0.535. Only for a disordered coating that has the same structure as the liquid did we find that nucleation was likely to occur in the bulk. Hence, such coatings might be used to suppress heterogeneous nucleation in experiments. Finally, we report the apparent homogeneous nucleation rate taking into account the formation of crystallites both in the bulk and at the walls. We find that the apparent overall nucleation rates coincide with those reported in "homogeneous nucleation" experiments. This suggests that heterogeneous nucleation at the walls could partly explain the large discrepancies found between experimental measurements and simulation estimates of the homogeneous nucleation rate.

Ice Ih vs. ice III along the homogeneous nucleation line.

Pure water can be substantially supercooled below the melting temperature. The pressures and temperatures where water is observed to freeze in supercooling experiments define the so-called homogeneous nucleation line. The slope of such a line changes from negative to positive as pressure increases. In our work, we use computer simulations with the TIP4P/Ice water model to investigate such a change of slope. The simulation prediction for the melting and the homogeneous nucleation lines is in reasonable agreement with the experiment. We find, in accordance with a previous hypothesis, that the aforementioned slope sign inversion can be explained by a change in the nucleating ice polymorph from ice Ih to ice III. Moreover, we underline the kinetic character of the homogeneous nucleation line by defining different lines for different values of the nucleation rate. We analyse in detail the factors that affect the competition between ices Ih and III in the framework of classical nucleation theory.

Molecular mechanism for cavitation in water under tension.

Despite its relevance in biology and engineering, the molecular mechanism driving cavitation in water remains unknown. Using computer simulations, we investigate the structure and dynamics of vapor bubbles emerging from metastable water at negative pressures. We find that in the early stages of cavitation, bubbles are irregularly shaped and become more spherical as they grow. Nevertheless, the free energy of bubble formation can be perfectly reproduced in the framework of classical nucleation theory (CNT) if the curvature dependence of the surface tension is taken into account. Comparison of the observed bubble dynamics to the predictions of the macroscopic Rayleigh-Plesset (RP) equation, augmented with thermal fluctuations, demonstrates that the growth of nanoscale bubbles is governed by viscous forces. Combining the dynamical prefactor determined from the RP equation with CNT based on the Kramers formalism yields an analytical expression for the cavitation rate that reproduces the simulation results very well over a wide range of pressures. Furthermore, our theoretical predictions are in excellent agreement with cavitation rates obtained from inclusion experiments. This suggests that homogeneous nucleation is observed in inclusions, whereas only heterogeneous nucleation on impurities or defects occurs in other experiments.

Collective behavior of Vicsek particles without and with obstacles⋆.

In our work we have studied a two-dimensional suspension of finite-size Vicsek hard disks, whose time evolution follows an event-driven dynamics between subsequent time steps. Having compared its collective behaviour with the one expected for a system of scalar Vicsek point-like particles, we have analysed the effect of considering two possible bouncing rules between the disks: a Vicsek-like rule and a pseudo-elastic one, focusing on the order-disorder transition. Next, we have added to the two-dimensional suspension of hard-disk Vicsek particles disk-like passive obstacles of two types: either fixed in space or moving according to the same event-driven dynamics. We have performed a detailed analysis of the particles' collective behaviour observed for both fixed and moving obstacles. In the fixed obstacles case, we have observed formation of clusters at low noise, in agreement with previous studies. When using moving passive obstacles, we found that that order of active particles is better destroyed as the drag of obstacles increases. In the no drag limit an interesting result was found: introduction of low drag passive particles can lead in some cases to a more ordered state of active flocking particles than what they show in bulk.

Viscosity and self-diffusion of supercooled and stretched water from molecular dynamics simulations.

Among the numerous anomalies of water, the acceleration of dynamics under pressure is particularly puzzling. Whereas the diffusivity anomaly observed in experiments has been reproduced in several computer studies, the parallel viscosity anomaly has received less attention. Here we simulate viscosity and the self-diffusion coefficient of the TIP4P/2005 water model over a broad temperature and pressure range. We reproduce the experimental behavior and find additional anomalies at negative pressure. The anomalous effect of pressure on dynamic properties becomes more pronounced upon cooling, reaching two orders of magnitude for viscosity at 220 K. We analyze our results with a dynamic extension of a thermodynamic two-state model, an approach which has proved successful in describing experimental data. Water is regarded as a mixture of interconverting species with contrasting dynamic behaviors, one being strong (Arrhenius) and the other fragile (non-Arrhenius). The dynamic parameters of the two-state models are remarkably close between experiment and simulations. The larger pressure range accessible to simulations suggests a modification of the dynamic two-state model, which in turn also improves the agreement with experimental data. Furthermore, our simulations demonstrate the decoupling between viscosity η and self-diffusion coefficient D as a function of temperature T. The Stokes-Einstein relation, which predicts a constant Dη/T, is violated when T is lowered, in connection with the Widom line defined by an equal fraction of the two interconverting species. These results provide a unifying picture of thermodynamics and dynamics in water and call for experiments at negative pressure.

A simulation study of homogeneous ice nucleation in supercooled salty water.

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

Morphology of clusters of attractive dry and wet self-propelled spherical particle suspensions.

In order to assess the effect of hydrodynamics in the assembly of active attractive spheres, we simulate a semi-dilute suspension of attractive self-propelled spherical particles in a quasi-two dimensional geometry comparing the case with and without hydrodynamics interactions. To start with, independent of the presence of hydrodynamics, we observe that depending on the ratio between attraction and propulsion, particles either coarsen or aggregate forming finite-size clusters. Focusing on the clustering regime, we characterize two different cluster parameters, i.e. their morphology and orientational order, and compare the case when active particles behave either as pushers or pullers (always in the regime where inter-particle attractions compete with self-propulsion). Studying cluster phases for squirmers with respect to those obtained for active Brownian disks (indicated as ABPs), we have shown that hydrodynamics alone can sustain a cluster phase of active swimmers (pullers), while ABPs form cluster phases due to the competition between attraction and self-propulsion. The structural properties of the cluster phases of squirmers and ABPs are similar, although squirmers show sensitivity to active stresses. Active Brownian disks resemble weakly pusher squirmer suspensions in terms of cluster size distribution, structure of the radius of gyration on the cluster size and degree of cluster polarity.

Two-structure thermodynamics for the TIP4P/2005 model of water covering supercooled and deeply stretched regions.

One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes the ideal entropy of mixing of these two structures, a liquid-liquid phase transition, terminated at a liquid-liquid critical point, is predicted. Various versions of the "two-structure equation of state" (TSEOS) based on this concept have shown remarkable agreement with both experimental data for metastable, deeply supercooled water and simulations of molecular water models. However, existing TSEOSs were not designed to describe the negative pressure region and do not account for the stability limit of the liquid state with respect to the vapor. While experimental data on supercooled water at negative pressures may shed additional light on the source of the anomalies of water, such data are very limited. To fill this gap, we have analyzed simulation results for TIP4P/2005, one of the most accurate classical water models available. We have used recently published simulation data, and performed additional simulations, over a broad range of positive and negative pressures, from ambient temperature to deeply supercooled conditions. We show that, by explicitly incorporating the liquid-vapor spinodal into a TSEOS, we are able to match the simulation data for TIP4P/2005 with remarkable accuracy. In particular, this equation of state quantitatively reproduces the lines of extrema in density, isothermal compressibility, and isobaric heat capacity. Contrary to an explanation of the thermodynamic anomalies of water based on a "retracing spinodal," the liquid-vapor spinodal in the present TSEOS continues monotonically to lower pressures upon cooling, influencing but not giving rise to density extrema and other thermodynamic anomalies.