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Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a “molecular clock” to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either K<u or K>u. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K
u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

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In this paper we develop a leap-frog-type finite element method for modeling the electromagnetic wave propagation in metamaterials. The metamaterial model equations are represented by integrodifferential Maxwell’s equations, which are quite challenging to analyze and solve in that we have to solve a coupled problem with different partial differential equations given in different material regions. Our method is based on a mixed finite element method using edge elements, which can easily handle the tangential continuity of the electric field. Stability analysis and optimal error estimate are carried out for the proposed scheme. The scheme is implemented and confirmed to obey the proved optimal convergence rate by using a smooth analytical solution. Then the scheme is extended to model wave propagation in heterogeneous media composed of metamaterials and free space, and extensive numerical results (using a rectangular edge element, a triangular edge element, and mixed edge elements) demonstrate the effectiveness of our algorithm for modeling the exotic backward wave propagation phenomenon in metamaterials. To the best of our knowledge, this is the first paper with an exhaustive simulation of backward wave propagation in metamaterials using time-domain finite element methods.

Error reconciliation is an important technique for learning with error (LWE) and ring-LWE (RLWE)-based constructions. In this paper, we present a comparison analysis on two error reconciliation-based RLWE key exchange protocols: Ding et al. in 2012 (DING12) and Bos et al. in 2015 (BCNS15). We take them as examples to explain the core idea of error reconciliation, building key exchange over RLWE problem, implementation and real-world performance, and compare them comprehensively. We also analyse a LWE key exchange 'Frodo' that uses an improved error reconciliation mechanism in BCNS15. To the best of our knowledge, our work is the first to present at least 128-bit classic (80-bit quantum) and 256-bit classic (> 200-bit quantum) secure parameter choices for DING12 with efficient portable C/C++ implementations. Benchmark shows that our efficient implementation is 11× faster than BCNS15 and one key exchange execution only costs 0.07 ms on a four-year-old middle range CPU. Error reconciliation is 1.57× faster than BCNS15.