ssMousetrack: Analysing computerized tracking data via Bayesian state-space models in {R}

Recent technological advances have provided new settings to enhance individual-based data collection and computerized-tracking data have became common in many behavioral and social research. By adopting instantaneous tracking devices such as computer-mouse, wii, and joysticks, such data provide new insights for analysing the dynamic unfolding of response process. ssMousetrack is a R package for modeling and analysing computerized-tracking data by means of a Bayesian state-space approach. The package provides a set of functions to prepare data, fit the model, and assess results via simple diagnostic checks. This paper describes the package and illustrates how it can be used to model and analyse computerized-tracking data. A case study is also included to show the use of the package in empirical case studies

Absence of `fragility' and mechanical response of jammed granular materials

We perform molecular dynamic (MD) simulations of frictional non-thermal particles driven by an externally applied shear stress. After the system jams following a transient flow, we probe its mechanical response in order to clarify whether the resulting solid is 'fragile'. We find the system to respond elastically and isotropically to small perturbations of the shear stress, suggesting absence of fragility. These results are interpreted in terms of the energy landscape of dissipative systems. For the same values of the control parameters, we check the behaviour of the system during a stress cycle. Increasing the maximum stress value, a crossover from a visco-elastic to a plastic regime is observed.Comment: 6 pages, 9 figures, accepted in Granular Matter on 01-02-201

Pacman Percolation and the Glass Transition

We investigate via Monte Carlo simulations the kinetically constrained Kob-Andersen lattice glass model showing that, contrary to current expectations, the relaxation process and the dynamical heterogeneities seems to be characterized by different time scales. Indeed, we found that the relaxation time is related to a reverse percolation transition, whereas the time of maximum heterogeneity is related to the spatial correlation between particles. This investigation leads to a geometrical interpretation of the relaxation processes and of the different observed time scales.Comment: 12 pages, 8 figures. arXiv admin note: text overlap with arXiv:1109.428

Spatial correlations of elementary relaxation events in glass-forming liquids

The dynamical facilitation scenario, by which localized relaxation events promote nearby relaxation events in an avalanching process, has been suggested as the key mechanism connecting the microscopic and the macroscopic dynamics of structural glasses. Here we investigate the statistical features of this process via the numerical simulation of a model structural glass. First we show that the relaxation dynamics of the system occurs through particle jumps that are irreversible, and that cannot be decomposed in smaller irreversible events. Then we show that each jump does actually trigger an avalanche. The characteristic of this avalanche change on cooling, suggesting that the relaxation dynamics crossovers from a noise dominated regime where jumps do not trigger other relaxation events, to a regime dominated by the facilitation process, where a jump trigger more relaxation events.Comment: 8 pages, 6 figure

Particle jumps in structural glasses

Particles in structural glasses rattle around temporary equilibriumpositions, that seldom change through a process which is much faster than the relaxation time, known as particle jump. Since the relaxation of the system is due to the accumulation of many such jumps, it could be possible to connect the single particle short time motion to the macroscopic relaxation by understanding the features of the jump dynamics. Here we review recent results in this research direction, clarifying the features of particles jumps that have been understood and those that are still under investigation, and examining the role of particle jumps in different theories of the glass transition.Comment: 10 pages, 4 figures, Review articl

Cage-jump motion reveals universal dynamics and non-universal structural features in glass forming liquids

The sluggish and heterogeneous dynamics of glass forming liquids is frequently associated to the transient coexistence of two phases of particles, respectively with an high and low mobility. In the absence of a dynamical order parameter that acquires a transient bimodal shape, these phases are commonly identified empirically, which makes difficult investigating their relation with the structural properties of the system. Here we show that the distribution of single particle diffusivities can be accessed within a Continuous Time Random Walk description of the intermittent motion, and that this distribution acquires a transient bimodal shape in the deeply supercooled regime, thus allowing for a clear identification of the two coexisting phase. In a simple two-dimensional glass forming model, the dynamic phase coexistence is accompanied by a striking structural counterpart: the distribution of the crystalline-like order parameter becomes also bimodal on cooling, with increasing overlap between ordered and immobile particles. This simple structural signature is absent in other models, such as the three-dimesional Kob-Andersen Lennard-Jones mixture, where more sophisticated order parameters might be relevant. In this perspective, the identification of the two dynamical coexisting phases opens the way to deeper investigations of structure-dynamics correlations.Comment: Published in the J. Stat. Mech. Special Issue "The Role of Structure in Glassy and Jammed Systems

Dynamical Correlation Length and Relaxation Processes in a Glass Former

We investigate the relaxation process and the dynamical heterogeneities of the kinetically constrained Kob--Anderson lattice glass model, and show that these are characterized by different timescales. The dynamics is well described within the diffusing defect paradigm, which suggest to relate the relaxation process to a reverse--percolation transition. This allows for a geometrical interpretation of the relaxation process, and of the different timescales

Cage Size and Jump Precursors in Glass-Forming Liquids: Experiment and Simulations

Glassy dynamics is intermittent, as particles suddenly jump out of the cage formed by their neighbours, and heterogeneous, as these jumps are not uniformly distributed across the system. Relating these features of the dynamics to the diverse local environments explored by the particles is essential to rationalize the relaxation process. Here we investigate this issue characterizing the local environment of a particle with the amplitude of its short time vibrational motion, as determined by segmenting in cages and jumps the particle trajectories. Both simulations of supercooled liquids and experiments on colloidal suspensions show that particles in large cages are likely to jump after a small time-lag, and that, on average, the cage enlarges shortly before the particle jumps. At large time-lags, the cage has essentially a constant value, which is smaller for longer-lasting cages. Finally, we clarify how this coupling between cage size and duration controls the average behaviour and opens the way to a better understanding of the relaxation process in glass--forming liquids.Comment: Letter, 4 figure

A Maximum Entropy Procedure to Solve Likelihood Equations

In this article, we provide initial findings regarding the problem of solving likelihood equations by means of a maximum entropy (ME) approach. Unlike standard procedures that require equating the score function of the maximum likelihood problem at zero, we propose an alternative strategy where the score is instead used as an external informative constraint to the maximization of the convex Shannon\u2019s entropy function. The problem involves the reparameterization of the score parameters as expected values of discrete probability distributions where probabilities need to be estimated. This leads to a simpler situation where parameters are searched in smaller (hyper) simplex space. We assessed our proposal by means of empirical case studies and a simulation study, the latter involving the most critical case of logistic regression under data separation. The results suggested that the maximum entropy reformulation of the score problem solves the likelihood equation problem. Similarly, when maximum likelihood estimation is difficult, as is the case of logistic regression under separation, the maximum entropy proposal achieved results (numerically) comparable to those obtained by the Firth\u2019s bias-corrected approach. Overall, these first findings reveal that a maximum entropy solution can be considered as an alternative technique to solve the likelihood equation