scholarly journals Uncovering Signals from the Coronavirus Genome

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 973
Author(s):  
Enrique Canessa

A signal analysis of the complete genome sequenced for coronavirus variants of concern—B.1.1.7 (Alpha), B.1.135 (Beta) and P1 (Gamma)—and coronavirus variants of interest—B.1.429–B.1.427 (Epsilon) and B.1.525 (Eta)—is presented using open GISAID data. We deal with a certain new type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases. Our method provides additional information to conventional similarity comparisons via alignment methods and Fourier Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of complete genomics sequences according to its progression along the nucleotide bases position. The present new method could be useful for the bioinformatics surveillance and dynamics of coronavirus genome variants.

2020 ◽  
Author(s):  
Kathryn Primerose Drake

This dissertation addresses problems that arise in a diverse group of fields including cosmology, electromagnetism, and graphic design. While these topics may seem disparate, they share a commonality in their need for fast and accurate algorithms which can handle large datasets collected on irregular domains. An important issue in cosmology is the calculation of the angular power spectrum of the cosmic microwave background (CMB) radiation. CMB photons offer a direct insight into the early stages of the universe's development and give the strongest evidence for the Big Bang theory to date. The Hierarchical Equal Area isoLatitude Pixelation (HEALPix) grid is used by cosmologists to collect CMB data and store it as points on the sphere. HEALPix also refers to the software package that analyzes CMB maps and calculates their angular power spectrums. Refined analysis of the CMB angular power spectrum can lead to revolutionary developments in understanding the curvature of the universe, dark matter density, and the nature of dark energy. In the first paper, we present a new method for performing spherical harmonic analysis for HEALPix data, which is a vital component for computing the CMB angular power spectrum. Using numerical experiments, we demonstrate that the new method provides better accuracy and a higher convergence rate when compared to the current methods on synthetic data. This paper is presented in Chapter 2. The problem of constructing smooth approximants to divergence-free (div-free) and curl-free vector fields and/or their potentials based only on discrete samples arises in science applications like fluid dynamics and electromagnetism. It is often necessary that the vector approximants preserve the div-free or curl-free properties of the field. Div/curl-free radial basis functions (RBFs) have traditionally been utilized for constructing these vector approximants, but their global nature can make them computationally expensive and impractical. In the second paper, we develop a technique for bypassing this issue that combines div/curl-free RBFs in a partition of unity (PUM) framework, where one solves for local approximants over subsets of the global samples and then blends them together to form a div-free or curl-free global approximant. This method can be used to approximate vector fields and their scalar potentials on the sphere and in irregular domains in ℝ2 and ℝ3. We present error estimates and demonstrate the effectiveness of the method on several test problems. This paper is presented in Chapter 3. The issue of reconstructing implicit surfaces from oriented point clouds has applications in computer aided design, medical imaging, and remote sensing. Utilizing the technique from the second paper, we introduce a novel approach to this problem by exploiting a fundamental result from vector calculus. In our method, deemed CFPU, we interpolate the normal vectors of the point cloud with a curl-free RBF-PUM interpolant and extract a potential of the reconstructed vector field. The zero-level surface of this potential approximates the implicit surface of the point cloud. Benefits of this method include its ability to represent local sharp features, handle noise in the normal vectors, and even exactly interpolate a point cloud. We demonstrate in the third paper that our method converges for known surfaces and also show how it performs on various surfaces found in the literature. This paper is presented in Chapter 4.


Gene ◽  
2018 ◽  
Vol 673 ◽  
pp. 239-250 ◽  
Author(s):  
Rui Dong ◽  
Ziyue Zhu ◽  
Changchuan Yin ◽  
Rong L. He ◽  
Stephen S.-T. Yau

2011 ◽  
Vol 2 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Cui-Ping Wei ◽  
Xijin Tang

In this paper the ranking method for intuitionistic fuzzy numbers is studied. The authors first define a possibility degree formula to compare two intuitionistic fuzzy numbers. In comparison with Chen and Tan’s score function, the possibility degree formula provides additional information for the comparison of two intuitionistic fuzzy numbers. Based on the possibility degree formula, the authors give a possibility degree method to rank intuitionistic fuzzy numbers, which is used to rank the alternatives in multi-criteria decision making problems.


2003 ◽  
Vol 17 (03) ◽  
pp. 91-94 ◽  
Author(s):  
BAILIN HAO ◽  
JI QI ◽  
BIN WANG

We present a brief review of a series of on-going work on bacterial phylogeny. We propose a new method to infer relatedness of prokaryotes from their complete genome data without using sequence alignment, leading to results comparable with the bacteriologist's systematics as reflected in the latest 2001 edition of Bergey's Manual of Systematic Bacteriology.1 We only touch on the mathematical aspects of the method. The biological implications of our results will be published elsewhere.


2018 ◽  
Vol 32 (20) ◽  
pp. 1850217
Author(s):  
Peng Kong ◽  
Zhengzheng Wei ◽  
Tao Hu ◽  
Yi Tang

Using nonequilibrium molecular dynamics simulations, we investigate thermal rectification in mass-graded lattices with a new type on-site potential which has a physical picture of the double-well. By adjusting the ratio of harmonic on-site potential and anharmonic on-site potential, we could obtain the optimal heat transport and the best thermal rectification. In addition, we observe the reversal thermal rectification by changing the ratio of on-site potential and analyzes the mechanism of thermal rectification through the power spectrum. At last, we also study the heat flux and thermal rectification in a different case of average temperature and mass gradient.


2014 ◽  
Vol 875-877 ◽  
pp. 1377-1381
Author(s):  
Jian Dong Yang ◽  
Feng Xiang Li ◽  
Hui Yan

This paper analyzes the existing problems of acting lapping pressure in lapping internal holes of main cylinder of brake-pump with solid abrasives, proposes a new type of solid abrasives supporting method, namely, three supportting points acting lapping pressure method. The method improves pressure distribution between solid abrasives and the surface of the machined workpiece,which is favorable to increase cylindricity of machined hole.Through actual machining process, new method is demonstrated increasing cylindricity accuracy of machined holes of main cylinder significantly.


1994 ◽  
Vol 358 ◽  
Author(s):  
Kunji Chen ◽  
Xuexuan Qu ◽  
Xinfan Huang ◽  
Zhifeng Li ◽  
Duan Feng

ABSTRACTWe report a new method for synthesizing Ge nano-crystallites embedded in SiNy film matrices. On the basis of the effect of the reactant precursors and preferential chemical bonding of Si-N and Ge-Ge, thin films with Ge clusters embedded in SiNy matrices have been prepared in the PECVD system with reactant gases of SiH4, GeH4 and NH3 mixed in the hydrogen plasma. The as-deposited films were then crystallized by Ar ion laser annealing or thermal annealing technique to form nanometer-sized Ge crystallites.The composition and microstructures of these new type of sample were characterized by infrared absorption spectra, transmission electron microscopy, X-ray diffraction and Raman scattering spectra. The results indicated that the average size of Ge crystallites was estimated to be 2-20 nm depending on the deposition and annealing parameters and can be controlled by a designed manner.


2012 ◽  
Vol 268-270 ◽  
pp. 841-844
Author(s):  
Li Rong Wan ◽  
Xing Hua Wang ◽  
Jian Liang Li ◽  
Bin Zhang ◽  
Xian Peng Li

Simulation analysis on the hydraulic system of shearer's cutting part was established based on the research of fluid simulation technology. The hydraulic model was built using the AMESim software. By verifying the results, a new method about the rigorous analysis of holistic dynamic property of the hydraulic system is developed and a new way to design new type mining machinery and improve its capabilities is provided.


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