Ionogels are porous monoliths providing nanometer-scale confinement of an ionic liquid within an oxide network. Various dynamic parameters and the detailed nature of phase transitions were investigated by using a neutron scattering technique, giving smaller time and space scales compared to earlier results from other techniques. By investigating the nature of the hydrogen mean square displacement (local mobility), qualitative information on diffusion and different phase transitions were obtained. The results presented herein show similar short-time molecular dynamics between pristine ionic liquids and confined ionic liquids through residence time and diffusion coefficient values, thus, explaining in depth the good ionic conductivity of ionogels. Full article

The stochastic model of the Feynman–Smoluchowski ratchet is proposed and solved using generalization of the Fick–Jacobs theory. The theory fully captures nonlinear response of the ratchet to the difference of heat bath temperatures. The ratchet performance is discussed using the mean velocity, the average heat flow between the two heat reservoirs and the figure of merit, which quantifies energetic cost for attaining a certain mean velocity. Limits of the theory are tested comparing its predictions to numerics. We also demonstrate connection between the ratchet effect emerging in the model and rotations of the probability current and explain direction of the mean velocity using simple discrete analogue of the model. Full article

Water structure and dynamics are affected by the presence of a nearby interface. Here, first we review recent results by molecular dynamics simulations about the effect of different carbon-based materials, including armchair carbon nanotubes and a variety of graphene sheets—flat and with corrugation—on water structure and dynamics. We discuss the calculations of binding energies, hydrogen bond distributions, water’s diffusion coefficients and their relation with surface’s geometries at different thermodynamical conditions. Next, we present new results of the crystallization and dynamics of water in a rigid graphene sieve. In particular, we show that the diffusion of water confined between parallel walls depends on the plate distance in a non-monotonic way and is related to the water structuring, crystallization, re-melting and evaporation for decreasing inter-plate distance. Our results could be relevant in those applications where water is in contact with nanostructured carbon materials at ambient or cryogenic temperatures, as in man-made superhydrophobic materials or filtration membranes, or in techniques that take advantage of hydrated graphene interfaces, as in aqueous electron cryomicroscopy for the analysis of proteins adsorbed on graphene. Full article

Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise). Full article

The high concentration of macromolecules (i.e., macromolecular crowding) in cellular environments leads to large quantitative effects on the dynamic and equilibrium biological properties. These effects have been experimentally studied using inert macromolecules to mimic a realistic cellular medium. In this paper, two different experimental in vitro systems of diffusing proteins which use dextran macromolecules as obstacles are computationally analyzed. A new model for dextran macromolecules based on effective radii accounting for macromolecular compression induced by crowding is proposed. The obtained results for the diffusion coefficient and the anomalous diffusion exponent exhibit good qualitative and generally good quantitative agreement with experiments. Volume fraction and hydrodynamic interactions are found to be crucial to describe the diffusion coefficient decrease in crowded media. However, no significant influence of the hydrodynamic interactions in the anomalous diffusion exponent is found. Full article

Contrary to microbial taxis, where a tactic response to external stimuli is controlled by complex chemical pathways acting like sensor-actuator loops, taxis of artificial microswimmers is a purely stochastic effect associated with a non-uniform activation of the particles’ self-propulsion. We study the tactic response of such swimmers in a spatio-temporally modulated activating medium by means of both numerical and analytical techniques. In the opposite limits of very fast and very slow rotational particle dynamics, we obtain analytic approximations that closely reproduce the numerical description. A swimmer drifts on average either parallel or anti-parallel to the propagation direction of the activating pulses, depending on their speed and width. The drift in line with the pulses is solely determined by the finite persistence length of the active Brownian motion performed by the swimmer, whereas the drift in the opposite direction results from the combination of the ballistic and diffusive properties of the swimmer’s dynamics. Full article

We report the observation of a temperature-controlled synchronization of two Brownian-particles in a binary mixture close to the critical point of the demixing transition. The two beads are trapped by two optical tweezers whose distance is periodically modulated. We notice that the motion synchronization of the two beads appears when the critical temperature is approached. In contrast, when the fluid is far from its critical temperature, the displacements of the two beads are uncorrelated. Small changes in temperature can radically change the global dynamics of the system. We show that the synchronisation is induced by the critical Casimir forces. Finally, we present the measure of the energy transfers inside the system produced by the critical interaction. Full article

The dynamics of a system of hard spheres enclosed between two parallel plates separated a distance smaller than two particle diameters is described at the level of kinetic theory. The interest focuses on the behavior of the quasi-two-dimensional fluid seen when looking at the system from above or below. In the first part, a collisional model for the effective two-dimensional dynamics is analyzed. Although it is able to describe quite well the homogeneous evolution observed in the experiments, it is shown that it fails to predict the existence of non-equilibrium phase transitions, and in particular, the bimodal regime exhibited by the real system. A critical revision analysis of the model is presented , and as a starting point to get a more accurate description, the Boltzmann equation for the quasi-two-dimensional gas has been derived. In the elastic case, the solutions of the equation verify an H-theorem implying a monotonic tendency to a non-uniform steady state. As an example of application of the kinetic equation, here the evolution equations for the vertical and horizontal temperatures of the system are derived in the homogeneous approximation, and the results compared with molecular dynamics simulation results. Full article

One of the central questions of humankind is: which chemical and physical conditions are necessary to make life possible? In this “origin-of-life” context, formamide plays an important role, because it has been demonstrated that prebiotic molecules can be synthesized from concentrated formamide solutions. Recently, it could be shown, using finite-element calculations combining thermophoresis and convection processes in hydrothermal pores, that sufficiently high formamide concentrations could be accumulated to form prebiotic molecules (Niether et al. (2016)). Depending on the initial formamide concentration, the aspect ratio of the pores, and the ambient temperature, formamide concentrations up to 85 wt % could be reached. The stationary calculations show an effective accumulation, only if the aspect ratio is above a certain threshold, and the corresponding transient studies display a sudden increase of the accumulation after a certain time. Neither of the observations were explained. In this work, we derive a simple heuristic model, which explains both phenomena. The physical idea of the approach is a comparison of the time to reach the top of the pore with the time to cross from the convective upstream towards the convective downstream. If the time to reach the top of the pore is shorter than the crossing time, the formamide molecules are flushed out of the pore. If the time is long enough, the formamide molecules can reach the downstream and accumulate at the bottom of the pore. Analysing the optimal aspect ratio as function of concentration, we find that, at a weight fraction of $w=0.5$ , a minimal pore height is required for effective accumulation. At the same concentration, the transient calculations show a maximum of the accumulation rate. Full article

Nonlinear relaxation phenomena in three different systems of condensed matter are investigated. (i) First, the phase dynamics in Josephson junctions is analyzed. Specifically, a superconductor-graphene-superconductor (SGS) system exhibits quantum metastable states, and the average escape time from these metastable states in the presence of Gaussian and correlated fluctuations is calculated, accounting for variations in the the noise source intensity and the bias frequency. Moreover, the transient dynamics of a long-overlap Josephson junction (JJ) subject to thermal fluctuations and non-Gaussian noise sources is investigated. Noise induced phenomena are observed, such as the noise enhanced stability and the stochastic resonant activation. (ii) Second, the electron spin relaxation process in a n-type GaAs bulk driven by a fluctuating electric field is investigated. In particular, by using a Monte Carlo approach, we study the influence of a random telegraph noise on the spin polarized transport. Our findings show the possibility to raise the spin relaxation length by increasing the amplitude of the external fluctuations. Moreover, we find that, crucially, depending on the value of the external field strength, the electron spin depolarization length versus the noise correlation time increases up to a plateau. (iii) Finally, the stabilization of quantum metastable states by dissipation is presented. Normally, quantum fluctuations enhance the escape from metastable states in the presence of dissipation. We show that dissipation can enhance the stability of a quantum metastable system, consisting of a particle moving in a strongly asymmetric double well potential, interacting with a thermal bath. We find that the escape time from the metastable region has a nonmonotonic behavior versus the system- bath coupling and the temperature, producing a stabilizing effect. Full article

We show that when Brownian motion takes place in a heterogeneous medium, the presence of local forces and transport coefficients leads to deviations from a Gaussian probability distribution that make that the ratio between forward and backward probabilities depend on the nature of the host medium, on local forces, and also on time. We have applied our results to two situations: diffusion in a disordered medium, and diffusion in a confined system. For such scenarios, we have shown that our theoretical predictions are in very good agreement with numerical results. Moreover, we have shown that the deviations from the Gaussian solution lead to the onset of rectification. Our predictions could be used to detect the presence of local forces and to characterize the intrinsic short-scale properties of the host medium—a problem of current interest in the study of micro- and nano-systems. Full article

We review our simulation results on properties of supercooled confined water. We consider two situations: water confined in a hydrophilic pore that mimics an MCM-41 environment and water at interface with a protein. The behavior upon cooling of the $\alpha$ relaxation of water in both environments is well interpreted in terms of the Mode Coupling Theory of glassy dynamics. Moreover, we find a crossover from a fragile to a strong regime. We relate this crossover to the crossing of the Widom line emanating from the liquid-liquid critical point, and in confinement we connect this crossover also to a crossover of the two body excess entropy of water upon cooling. Hydration water exhibits a second, distinctly slower relaxation caused by its dynamical coupling with the protein. The crossover upon cooling of this long relaxation is related to the protein dynamics. Full article