We provide a refinement of the Poincaré inequality on the torus $\mathbb{T}^{d}$ : there exists a set $\mathcal{B} \subset \mathbb{T} ^{d}$ of directions such that for every $\alpha \in \mathcal{B}$ there is a $c_{\alpha } > 0$ with $$\begin{aligned} \|\nabla f\|_{L^{2}(\mathbb{T}^{d})}^{d-1} \| \langle \nabla f, \alpha \rangle \|_{L^{2}(\mathbb{T}^{d})} \geq c_{\alpha }\|f\| _{L^{2}(\mathbb{T}^{d})}^{d} \quad \mbox{for all}~f\in H^{1}\bigl( \mathbb{T}^{d}\bigr)~ \mbox{with mean 0.} \end{aligned}$$ The derivative $\langle \nabla f, \alpha \rangle $ does not detect any oscillation in directions orthogonal to $\alpha $ , however, for certain $\alpha $ the geodesic flow in direction $\alpha $ is sufficiently mixing to compensate for that defect. On the two-dimensional torus $\mathbb{T}^{2}$ the inequality holds for $\alpha = (1, \sqrt{2})$ but is not true for $\alpha = (1,e)$ . Similar results should hold at a great level of generality on very general domains.

In this paper we propose a finite element time-domain method for modeling the optical black holes (OBHs) coupled with the perfectly matched layer (PML) technique. Stability analysis is carried out for the proposed scheme. Simulations of cylindrical, elliptical and square black holes demonstrate that our method is quite effective in modeling OBHs in time domain. To our best knowledge, this is the first OBHs simulation realized by the finite element time-domain method.

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.

We construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.

No abstract uploaded!