Evolutionary dynamics of incubation periods

The incubation period of a disease is the time between an initiating pathologic event and the onset of symptoms. For typhoid fever, polio, measles, leukemia and many other diseases, the incubation period is highly variable. Some affected people take much longer than average to show symptoms, leading to a distribution of incubation periods that is right skewed and often approximately lognormal. Although this statistical pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.Comment: 24 pages, 8 figures, 1 tabl

Stretching and folding versus cutting and shuffling: An illustrated perspective on mixing and deformations of continua

We compare and contrast two types of deformations inspired by mixing applications -- one from the mixing of fluids (stretching and folding), the other from the mixing of granular matter (cutting and shuffling). The connection between mechanics and dynamical systems is discussed in the context of the kinematics of deformation, emphasizing the equivalence between stretches and Lyapunov exponents. The stretching and folding motion exemplified by the baker's map is shown to give rise to a dynamical system with a positive Lyapunov exponent, the hallmark of chaotic mixing. On the other hand, cutting and shuffling does not stretch. When an interval exchange transformation is used as the basis for cutting and shuffling, we establish that all of the map's Lyapunov exponents are zero. Mixing, as quantified by the interfacial area per unit volume, is shown to be exponentially fast when there is stretching and folding, but linear when there is only cutting and shuffling. We also discuss how a simple computational approach can discern stretching in discrete data.Comment: REVTeX 4.1, 9 pages, 3 figures; v2 corrects some misprints. The following article appeared in the American Journal of Physics and may be found at http://ajp.aapt.org/resource/1/ajpias/v79/i4/p359_s1 . Copyright 2011 American Association of Physics Teachers. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the AAP

Experimental evidence of chaotic advection in a convective flow

Lagrangian chaos is experimentally investigated in a convective flow by means of Particle Tracking Velocimetry. The Fnite Size Lyapunov Exponent analysis is applied to quantify dispersion properties at different scales. In the range of parameters of the experiment, Lagrangian motion is found to be chaotic. Moreover, the Lyapunov depends on the Rayleigh number as ${\cal R}a^{1/2}$. A simple dimensional argument for explaining the observed power law scaling is proposed.Comment: 7 pages, 3 figur

Optimization of 125-mu m Heterogeneous Multi-Core Fibre Design Using Artificial Intelligence

We propose an automated heterogeneous trench-assisted multi-core fibre (MCF) design method. This method uses neural networks to speed up coating loss estimation by ∼ 10^{6} times and using particle swarm optimization (PSO) algorithm to explore the optimal MCF design under various objectives and properties constraints. The latter reduces the permutation evaluations by ten orders of magnitude compared with the brute force method. The artificial intelligence (AI)-based method is used to design MCFs on two objectives: minimizing crosstalk (XT) and maximizing effective mode area ( A_{eff} ). By optimizing XT with different A_{eff} and cutoff wavelength constraints combinations for 6-core fibres, we achieved −92.1 dB/km ultra-low XT for C+L band fibre and −64 dB/km for E+S+C+L-band fibre. Meanwhile, we explored the upper limit of A_{eff} given different bandwidth constraints resulting in a 6.82 relative core multiplicity factor. We performed capacity analysis of fibres for two transmission lengths. It is shown that bandwidth is the dominant factor while the increase brought by A_{eff} and the penalty caused by XT are relevantly small. Our fibres exceed the cutoff-limited capacity of the 7-core fibre in literature by 35.1% and 84.8% for 1200 km and 6000 km transmission respectively

Design Optimization of Uncoupled Six-core Fibers in Standard Cladding Diameter Using Artificial Intelligence

We report on ultra-wide-band and long-haul compatible 125µm six-core trench-assisted fiber designs. The AI-optimization process considers crosstalk, effective area, and bandwidth. We show that homogeneous cores can lead to low complexity yet high capacity fiber

Transport and diffusion in the embedding map

We study the transport properties of passive inertial particles in a $2-d$ incompressible flows. Here the particle dynamics is represented by the $4-d$ dissipative embedding map of $2-d$ area-preserving standard map which models the incompressible flow. The system is a model for impurity dynamics in a fluid and is characterized by two parameters, the inertia parameter $\alpha$, and the dissipation parameter $\gamma$. We obtain the statistical characterisers of transport for this system in these dynamical regimes. These are, the recurrence time statistics, the diffusion constant, and the distribution of jump lengths. The recurrence time distribution shows a power law tail in the dynamical regimes where there is preferential concentration of particles in sticky regions of the phase space, and an exponential decay in mixing regimes. The diffusion constant shows behaviour of three types - normal, subdiffusive and superdiffusive, depending on the parameter regimes. Phase diagrams of the system are constructed to differentiate different types of diffusion behaviour, as well as the behaviour of the absolute drift. We correlate the dynamical regimes seen for the system at different parameter values with the transport properties observed at these regimes, and in the behaviour of the transients. This system also shows the existence of a crisis and unstable dimension variability at certain parameter values. The signature of the unstable dimension variability is seen in the statistical characterisers of transport. We discuss the implications of our results for realistic systems.Comment: 28 pages, 14 figures, To Appear in Phys. Rev. E; Vol. 79 (2009

Walls Inhibit Chaotic Mixing

We report on experiments of chaotic mixing in a closed vessel, in which a highly viscous fluid is stirred by a moving rod. We analyze quantitatively how the concentration field of a low-diffusivity dye relaxes towards homogeneity, and we observe a slow algebraic decay of the inhomogeneity, at odds with the exponential decay predicted by most previous studies. Visual observations reveal the dominant role of the vessel wall, which strongly influences the concentration field in the entire domain and causes the anomalous scaling. A simplified 1D model supports our experimental results. Quantitative analysis of the concentration pattern leads to scalings for the distributions and the variance of the concentration field consistent with experimental and numerical results.Comment: 4 pages, 3 figure

Targeted mixing in an array of alternating vortices

Transport and mixing properties of passive particles advected by an array of vortices are investigated. Starting from the integrable case, it is shown that a special class of perturbations allows one to preserve separatrices which act as effective transport barriers, while triggering chaotic advection. In this setting, mixing within the two dynamical barriers is enhanced while long range transport is prevented. A numerical analysis of mixing properties depending on parameter values is performed; regions for which optimal mixing is achieved are proposed. Robustness of the targeted mixing properties regarding errors in the applied perturbation are considered, as well as slip/no-slip boundary conditions for the flow