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In the statistical mechanics approach to liquid-state theory, understanding the role of the intermolecular potential in determining thermodynamic and structural properties is crucial. The Fisher--Widom (FW) line, which separates regions in the temperature vs density plane where the decay of the total correlation function is monotonic or oscillatory, provides insights into the dominance of the attractive or repulsive part of the interactions. Stopper et al. have recently conjectured [J. Chem. Phys. \textbf{151}, 014501 (2019)] that the line of vanishing excess isothermal compressibility approximates the FW line in simple fluids. Here, we investigate this conjecture using the Jagla potential and also explore the line of vanishing excess pressure. We employ theoretical approximations and Monte Carlo simulations to study one-dimensional and three-dimensional systems. While exact results for the one-dimensional case do not support the conjecture, our Monte Carlo simulations for the three-dimensional fluid validate it. Our findings not only contribute to the understanding of the relationship between the three transition lines but also provide valuable insights into the thermodynamic and structural behaviour of simple fluids., Comment: 17 pages, 5 figures; v2: addition of the Widom line plus other minor changes. Rull-Abascal Special Issue for Statistical Physics in Spain

We study an air-fluidized granular monolayer, composed of plastic spheres which roll on a metallic grid. The air current is adjusted so that the spheres never loose contact with the grid, so that the dynamics may be regarded as pseudo two-dimensional (or two-dimensional, if the effects of sphere rolling are not taken into account). We find two surprising continuous transitions, both of them displaying two coexisting phases. Moreover, in all cases, we found the coexisting phases display strong energy non-equipartition. In the first transition, at weak fludization, a glassy phase coexists with a disordered fluid-like phase. In the second transition, a hexagonal crystal coexists with the fluid phase. We analyze, for these two-phase systems, the specific diffusive properties of each phase, as well as the velocity correlations. Surprisingly, we find a glass phase at very low packing fraction and for a wide range of granular temperatures. Both phases are characterized also by a strong anti-correlated velocities upon collision. Thus, the dynamics observed for this quasi two-dimensional system unveils phase transitions with peculiar properties, very different from the predicted behavior in well know theories for their equilibrium counterparts., Comment: 15 pages, 10 figures. To appear in Entropy (MDPI), 2022

Biaxial nematic ($N_B$) liquid crystals have been indicated as promising candidates for the design of next-generation displays with novel electro-optical properties and faster switching times. While at the molecular scale their existence is still under debate, experimental evidence, supported by theory and simulation, has unambiguously proved that suitable colloidal particles can indeed form $N_B$ fluids under specific conditions. While this discovery has sparked a widespread interest in the characterisation of the phase behaviour of $N_B$ liquid crystals, significantly less attention has been devoted to the study of their transport properties. To bridge this gap, by Dynamic Monte Carlo simulations we have investigated the equilibrium dynamics of field-induced $N_B$ phases comprising monodisperse hard cuboids. In particular, we calculated the long-time self-diffusion coefficients of cuboids over a wide range of anisotropies, spanning prolate to oblate geometries. Additionally, we have compared these diffusivities with those that, upon switching the external field off, are measured in the thermodynamically-stable isotropic or uniaxial nematic phases at the same density. Our results indicate that while prolate cuboids diffuse significantly faster in biaxial nematics than in less ordered fluids, we do not observe such an increase with oblate cuboids at high packing fractions. We show that these changes are most likely due to the field-induced freezing of the axes perpendicular to the nematic director, along with a substantial increase in the ordering of the resulting $N_B$ phase., Comment: 11 pages, 6 figures

We study, experimentally, the dynamics of a binary mixture of air-fluidized disks. The disks are chiral since they incorporate a set of blades with constant tilt. Both species are identical except for their blades tilt angle, which is rotated by 180o in the second species. We analyze the phase behavior of the system. Our analysis reveals a wide range of different fluid dynamics, including chiral flow. This chiral flow features in its base state a large vortex. We report, for certain ranges of relative particle density of each species, inversion of the vorticity of this vortex. We discuss on the possible mechanisms behind these chiral flow transitions., Comment: Additional data can be found in: https://doi.org/10.5281/zenodo.6647704

Diffusion is a fundamental aspect of transport processes in biological systems, and thus, in the development of life itself. And yet, the diffusive dynamics of active fluids with directed rotation, known as chiral fluids, has not been analyzed in detail so far. Here, we describe the diffusive regimes of a two-dimensional chiral fluid, composed in this case of a set of identical disk-shaped rotors. We found strong experimental evidence of odd diffusion. This odd diffusion emerges in the form of a two-dimensional tensor with an antisymmetric part. In particular, we show that chiral diffusion is complex, featuring transitions between super, quasi-normal, and sub diffusion, and very slowly aging. Moreover, we show that the diffusion tensor elements, including off-diagonal elements; i.e., odd diffusion coefficient, change sign according to flow vorticity. Therefore, the chiral fluid has a self regulated diffusion, controlled by its vorticity., Comment: Accepted in Communications Physics. 8 pages, 4 figures

The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to forecast the appearance of unseen variants. Using sequence data from other coronaviruses, pre-existing to SARS-CoV-2, we build statistical models that do not only capture amino-acid conservation but more complex patterns resulting from epistasis. We show that these models are notably superior to conservation profiles in estimating the already observable SARS-CoV-2 variability. In the receptor binding domain of the spike protein, we observe that the predicted mutability correlates well with experimental measures of protein stability and that both are reliable mutability predictors (ROC AUC ~0.8). Most interestingly, we observe an increasing agreement between our model and the observed variability as more data become available over time, proving the anticipatory capacity of our model. When combined with data concerning the immune response, our approach identifies positions where current variants of concern are highly overrepresented. These results could assist studies on viral evolution, future viral outbreaks and, in particular, guide the exploration and anticipation of potentially harmful future SARS-CoV-2 variants., Comment: 21 pages + supplementary information

We study the velocity autocorrelations in an experimental configuration of confined two-dimensional active rotors (disks). We report persistent small scale oscillations in both rotational and translational velocity autocorrelations, with their characteristic frequency increasing as rotational activity increases. While these small oscillations are qualitatively similar in all experiments, we found that, at strong particle rotational activity, the large scale particle spin fluctuations tend to vanish, with the small oscillations around zero persisting in this case, and spins remain predominantly and strongly anti-correlated at longer times. For weaker rotational activity, however, spin fluctuations become increasingly larger and angular velocities remain de-correlated at longer times. We discuss in detail how the autocorrelation oscillations are related to the rotational activity and why this feature is generically a signal of the emergence of chirality in the dynamics of a particulate system., Comment: * Phys. Fluids, to appear (2023) * 11 pages, 8 figures. * For experiments data and movies see https://doi.org/10.5281/zenodo.5141570 * For the original angle tracking code see https://doi.org/10.5281/zenodo.7226254

During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous proteins, to propose stochastic models of experimental protein evolution. These models predict quantitatively important features of experimentally evolved sequence libraries, like fitness distributions and position-specific mutational spectra. They also allow us to efficiently simulate sequence libraries for a vast array of combinations of experimental parameters like sequence divergence, selection strength and library size. We showcase the potential of the approach in re-analyzing two recent experiments to determine protein structure from signals of epistasis emerging in experimental sequence libraries. To be detectable, these signals require sufficiently large and sufficiently diverged libraries. Our modeling framework offers a quantitative explanation for the variable success of recently published experiments. Furthermore, we can forecast the outcome of time- and resource-intensive evolution experiments, opening thereby a way to computationally optimize experimental protocols., Comment: 16 pages, 14 figures

We study in this work the 2D dynamics of an experimental system of disk-shaped rotors, fluidized by turbulent upflow. Contrary to previous knowledge, our experiments show the same particle chiral geometry can produce flows with different chiralities. In particular, we unveil a conspicuous complex chiral flow, which displays multiple persistent vortexes with either sign, located randomly in the system. This peculiar phase mediates a continuous transition, which takes place as the kinetic energy input increases, from a flow with positive chirality (one vortex rotating in the same direction as particles spin) to a flow with negative chirality (one vortex in opposite sense to particle spin). We find that these surprising transitions are determined by the specific state of the statistical correlations between particle spin and translational velocity. We discuss how these correlations are determined in turn by the combined action of a series of mechanisms (for instance, heat dissipation at the boundaries, particle activity, average kinetic energy...), several of which are unveiled here., Comment: 15 pages, 6 figures (including supplementary material). To appear in Phys. Rev. Research (2022)

We study in this work the dynamics of a collection of identical hollow spheres (ping-pong balls) that rest on a horizontal metallic grid. Fluidization is achieved by means of a turbulent air current coming from below. The upflow is adjusted so that the particles do not levitate over the grid, resulting in quasi-two-dimensional dynamics. We show that the behavior of diffusion and correlations in this system is particularly rich. Noticeably as well (and related to the complex dynamical behavior), a variety of phases appear, with important peculiarities with respect to analogous setups. We observe gas, liquid, glass, and hexagonal crystal phases. Most notably, we show that the melting of the hexagonal crystal occurs in coexistence with a liquid phase. This strikingly differs from the corresponding transition in a purely two-dimensional systems of air-fluidized disks, for which no phase coexistence has been reported in the literature., Comment: 14 pages, 9 figures; supplementary material with additional figures, experiment movies and experimental data available in external link

We study in this work a system of granular disks enclosed in a rectangular region. Granular disks are arranged, at high particle density, in a hexagonal lattice. Specifically, we are interested in the conditions for mechanical signal transmission. Two different potentials are considered. Our results are obtained by means of soft disks computer simulations. We analytically determine the eigenfrequencies spectra of the system from the corresponding Hessian matrix. Alternatively, the eigenfrequencies can also be obtained from the time evolution of molecular dynamics simulations. Previous works have shown that mechanical signal transmission in granular matter can be used to develop acoustic switches. Our results reveal that the working range of the granular switch changes dramatically for different interaction models. In particular, strong anisotropies in signal transmission may appear for certain interparticle forces., Comment: Conference proceeding,7 pages

We perform experiments with a granular system that consists of a collection of identical hollow spheres (ping-pong balls). Particles rest on a horizontal metallic grid and are confined within a circular region. Fluidization is achieved by means of a turbulent air current coming from below. Air flow is adjusted so that the balls do not elevate over the grid, as an approach to 2D dynamics. With a high-speed camera, we take images of the system. From these images we can infer horizontal particle positions and velocities by means of particle-tracking algorithms. With the obtained data we analyze: a) the systematic measurement error in the determination of positions and velocities from our digital images; b) the degree of homogeneity achieved in our experiments (which depends on possible deviations of the grid from the horizontal and on the homogeneity of turbulent air wakes). Interestingly, we have observed evidences of crystallization at high enough densities., Comment: Conference proceeding, Traffic and Granular Flow 2019

Previous experimental and theoretical evidence has shown that convective flow may appear in granular fluids if subjected to a thermal gradient and gravity (Rayleigh-B\'enard-type convection). In contrast to this, we present here evidence of gravity-free thermal convection in a granular gas, with no presence of external thermal gradients either. Convection is here maintained steady by internal gradients due to dissipation and thermal sources at the same temperature. The granular gas is composed by identical disks and is enclosed in a rectangular region. Our results are obtained by means of an event-driven algorithm for inelastic hard disks., Comment: 5 pages, 5 figures. Supplementary material only in published in journal version

The structural properties of the Jagla fluid are studied by Monte Carlo (MC) simulations, numerical solutions of integral equation theories, and the (semi-analytical) rational-function approximation (RFA) method. In the latter case, the results are obtained from the assumption (supported by our MC simulations) that the Jagla potential and a potential with a hard core plus an appropriate piecewise constant function lead to practically the same cavity function. The predictions obtained for the radial distribution function, $g(r)$, from this approach are compared against MC simulations and integral equations for the Jagla model, and also for the limiting cases of the triangle-well potential and the ramp potential, with a general good agreement. The analytical form of the RFA in Laplace space allows us to describe the asymptotic behavior of $g(r)$ in a clean way and compare it with MC simulations for representative states with oscillatory or monotonic decay. The RFA predictions for the Fisher--Widom and Widom lines of the Jagla fluid are obtained., Comment: 12 pages, 10 figures; v2: structure factor included