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Register a new userVicsek Model by Time-Interlaced Compression: a Dynamical Computable Information Density
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Collective behavior, both in real biological systems as well as in theoretical models, often displays a rich combination of different kinds of order. A clear-cut and unique definition of phase based on the standard concept of order parameter may therefore be complicated, and made even trickier by the lack of thermodynamic equilibrium. Compression-based entropies have been proved useful in recent years in describing the different phases of out-of-equilibrium systems. Here, we investigate the performance of a compression-based entropy, namely the Computable Information Density (CID), within the Vicsek model of collective motion. Our entropy is defined through a crude coarse-graining of the particle positions, in which the key role of velocities in the model only enters indirectly through the velocity-density coupling. We discover that such entropy is a valid tool in distinguishing the various noise regimes, including the crossover between an aligned and misaligned phase of the velocities, despite the fact that velocities are not used by this entropy. Furthermore, we unveil the subtle role of the time coordinate, unexplored in previous studies on the CID: a new encoding recipe, where space and time locality are both preserved on the same ground, is demonstrated to reduce the CID. Such an improvement is particularly significant when working with partial and/or corrupted data, as it is often the case in real biological experiments.
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The well-known Vicsek model describes the dynamics of a flock of self-propelled particles (SPPs). Surprisingly, there is no direct measure of the chaotic behavior of such systems. Here, we discuss the dynamical phase transition present in Vicsek systems in light of the largest Lyapunov exponent (LLE), which is numerically computed by following the dynamical evolution in tangent space for up to one million SPPs. As discontinuities in the neighbor weighting factor hinder the computations, we propose a smooth form of the Vicsek model. We find that there is chaotic behavior in the disordered phase, which supports the claim that the LLE can be useful as an indicator of phase transitions even for this out-of-equilibrium system.
Recent experiments have indicated that many biological systems self-organise near their critical point, which hints at a common design principle. While it has been suggested that information transmission is optimized near the critical point, it remains unclear how information transmission depends on the dynamics of the input signal, the distance over which the information needs to be transmitted, and the distance to the critical point. Here we employ stochastic simulations of a driven 2D Ising system and study the instantaneous mutual information and the information transmission rate between a driven input spin and an output spin. The instantaneous mutual information varies non-monotonically with the temperature, but increases monotonically with the correlation time of the input signal. In contrast, the information transmission rate exhibits a maximum as a function of the input correlation time. Moreover, there exists an optimal temperature that maximizes this maximum information transmission rate. It arises from a tradeoff between the necessity to respond fast to changes in the input so that more information per unit amount of time can be transmitted, and the need to respond to reliably. The optimal temperature lies above the critical point, but moves towards it as the distance between the input and output spin is increased.
Computable Information Density (CID), the ratio of the length of a losslessly compressed data file to that of the uncompressed file, is a measure of order and correlation in both equilibrium and nonequilibrium systems. Here we show that correlation lengths can be obtained by decimation - thinning a configuration by sampling data at increasing intervals and recalculating the CID. When the sampling interval is larger than the systems correlation length, the data becomes incompressible. The correlation length and its critical exponents are thus accessible with no a-priori knowledge of an order parameter or even the nature of the ordering. The correlation length measured in this way agrees well with that computed from the decay of two-point correlation functions $g_{2}(r)$ when they exist. But the CID reveals the correlation length and its scaling even when $g_{2}(r)$ has no structure, as we demonstrate by cloaking the data with a Rudin-Shapiro sequence.
In this paper we raise the question of how to compress sparse graphs. By introducing the idea of redundancy, we find a way to measure the overlap of neighbors between nodes in networks. We exploit symmetry and information by making use of the overlap in neighbors and analyzing how information is reduced by shrinking the network and using the specific data structure we created, we generalize the problem of compression as an optimization problem on the possible choices of orbits. To find a reasonably good solution to this problem we use a greedy algorithm to determine the orbit of symmetry identifications, to achieve compression. Some example implementations of our algorithm are illustrated and analyzed.
A polymer chain pinned in space exerts a fluctuating force on the pin point in thermal equilibrium. The average of such fluctuating force is well understood from statistical mechanics as an entropic force, but little is known about the underlying force distribution. Here, we introduce two phase space sampling methods that can produce the equilibrium distribution of instantaneous forces exerted by a terminally pinned polymer. In these methods, both the positions and momenta of mass points representing a freely jointed chain are perturbed in accordance with the spatial constraints and the Boltzmann distribution of total energy. The constraint force for each conformation and momentum is calculated using Lagrangian dynamics. Using terminally pinned chains in space and on a surface, we show that the force distribution is highly asymmetric with both tensile and compressive forces. Most importantly, the mean of the distribution, which is equal to the entropic force, is not the most probable force even for long chains. Our work provides insights into the mechanistic origin of entropic forces, and an efficient computational tool for unbiased sampling of the phase space of a constrained system.
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