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Numerical encoding plays an important role in DNA sequence analysis via computational methods, in which numerical values are associated with corresponding symbolic characters. After numerical representation, digital signal processing methods can be exploited to analyze DNA sequences. To reflect the biological properties of the original sequence, it is vital that the representation is one-to-one. Chaos Game Representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane that allows the depiction of the DNA sequence in the form of image. Using CGR, a biological sequence can be transformed one-to-one to a numerical sequence that preserves the main features of the original sequence. In this research, we propose to encode DNA sequences by considering 2D CGR coordinates as complex numbers, and apply digital signal processing methods to analyze their evolutionary relationship. Computational experiments indicate that this approach gives comparable results to the state-of-the-art multiple sequence alignment method, Clustal Omega, and is significantly faster. The MATLAB code for our method can be accessed from: www.mathworks.com/matlabcentral/fileexchange/57152

In this paper, we construct a new suboptimal filter by deriving the Ito's stochastic differential equations of the estimation of higher order central moments satisfy and imposing some conditions to form a closed system. The essentially infinite-dimensional cubic sensor problem has been investigated in detail numerically to illustrate the reasonableness of the imposed conditions, and the numerical experiments support our discussion. A 2-dimensional polynomial filtering problem has also been experimented.

The singular parabolic problem $u_t-\triangle u=\l{\frac{1+\d|\nabla u|^2}{(1-u)^2}}$ on a bounded domain $\O$ of $\Rn$ with Dirichlet boundary condition, models the Microelectromechanical systems (MEMS) device with fringing field. In this paper, we focus on the quenching behavior of the solution to this equation. We first show that there exists a critical value $\l_\d^*>0$ such that if $0<\l<\l_\d^*$, all solutions exist globally; while for $\l>\l_\d^*$, all the solution will quench in finite time. The estimate of the quenching time in terms of large voltage $\l$ is investigated. Furthermore, the quenching set is a compact subset of $\O$, provided $\O$ is a convex bounded domain in $\mathbb{R}^n$. In particular, if the domain $\O$ is radially symmetric, then the origin is the only quenching point. We not only derive the one-side estimate of the quenching rate, but also further study the refined asymptotic behavior of the finite quenching solution.

In this paper we derive the stochastic differentials of the conditional central moments of the nonlinear filtering problems, especially those of the polynomial filtering problem, and develop a novel suboptimal method by solving this evolution equation. The basic idea is to augment the state of the original nonlinear system by including the original states' conditional central moments such that the augmented states form a so-called bilinear system after truncating. During our derivation, it is clear to see that the stochastic differentials of the conditional central moments of the linear filtering problem (i.e., $f$, $g$ and $h$ are all at most degree one polynomials) form a closed system automatically without truncation. This gives one reason for the existence of optimal filtering for linear problems. On the contrary, the conditional central moments form an infinite dimensional system, in general. To reduce it to a closed-form, we let all the high enough central moments to be zero, as one did in the Carleman approach \cite{GMP}. Consequently, a novel suboptimal method is developed by dealing with the bilinear system. Numerical simulation is performed for the cubic sensor problem to illustrate the accuracy and numerical stability.