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
The entanglement quantification and classification of multipartite quantum states is an important research area in quantum information. In this paper, in terms of the reduced density matrices corresponding to all possible partitions of the entire system, a bounded entanglement measure is constructed for arbitrary-dimensional multipartite quantum states. In particular, for three-qubit quantum systems, we prove that our entanglement measure satisfies the relation of monogamy. Furthermore, we present a necessary condition for characterizing maximally entangled states using our entanglement measure.
Jianlian CuiDepartment of Mathematics, Tsinghua University,Chi-KwongLiDepartment of Mathematics, College of William and MaryNung-SingSzeDepartment of Applied Mathematics, The Hong Kong Polytechnic University
It is known that every complex square matrix with nonnega-tive determinant is the product of positive semi-definite matrices. There are characterizations of matrices that require two or five positive semi-definite matrices in the product. However, the characterizations of matrices that require three or four positive semi-definite matrices in the product are lacking. In this paper, we give a complete characterization of these two types of matrices. With these results, we give an algorithm to determine whether a square matrix can be expressed as the product of kpositive semi-definite matrices but not fewer, for k=1, 2, 3, 4, 5.
Jianlian CuiDepartment of Mathematics, Tsinghua UniversityChi-Kwong LiDepartment of Mathematics, College of William & Mary, WilliamsburgYiu-Tung PooncDepartment of Mathematics, Iowa State University, Ames
Linear Algebra and its Applications, 498, 160-180, 2016.6
Denote by Mnthe set of n ×ncomplex matrices. Let f:Mn→[0, ∞)be a continuous map such that f(μUAU∗) =f(A)for any complex unit μ, A ∈Mnand unitary U∈Mn, f(X) =0if and only if X=0and the induced map t →f(tX)is monotonically increasing on [0, ∞)for any rank onenilpotent X∈Mn. Characterization is given for surjective maps φon Mnsatisfying f(AB−BA) =f(φ(A)φ(B) −φ(B)φ(A)). The general theorem isthen used to deduce results on special cases when the function is the pseudo spectrum and the pseudo spectral radius.
Protein universe is a complex system with critical problem of protein evolution to be analyzed. Early studies have used geometric distances and polygenetic-trees to solve this problem. However, the traditional methods are bivariate, whose taxonomy classification relies on bivariate branching. This is not sufficient to describe the complex nature of protein universe. Therefore, we propose a novel approach on multivariate protein classification. The new method bases on the theory of information and network, can be used to analyze multivariate relationships of proteins. The new method is alignment-free and have wide-applications to both sequences and 3D structures. We demonstrate the new method on six protein examples, results show that the new method is efficient and can potentially be used for future protein classifications.