Biomolecular surface construction by PDE transform.

International Journal for Numerical Methods in Biomedical Engineering
Qiong ZhengGuo-Wei Wei

Abstract

This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some b...Continue Reading

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Citations

Jan 21, 2014·Computational & Theoretical Chemistry·Changhao WangRay Luo
Dec 11, 2013·The Journal of Chemical Physics·Kelin XiaGuo-Wei Wei
Feb 9, 2012·International Journal of Biomedical Imaging·Yang WangSiyang Yang
Feb 15, 2013·International Journal for Numerical Methods in Biomedical Engineering·Fabio GibiinoMaria Filomena Santarelli
Dec 6, 2012·International Journal for Numerical Methods in Biomedical Engineering·Xin FengGuo-Wei Wei
Feb 28, 2014·International Journal for Numerical Methods in Biomedical Engineering·Wufeng Tian, Shan Zhao
Jun 7, 2014·International Journal for Numerical Methods in Biomedical Engineering·Kelin Xia, Guo-Wei Wei
Apr 9, 2015·International Journal for Numerical Methods in Biomedical Engineering·Kelin Xia, Guo-Wei Wei
May 20, 2015·Frontiers in Molecular Biosciences·Lin LiEmil Alexov
Nov 11, 2014·Journal of Theoretical & Computational Chemistry·Guo-Wei Wei
Dec 26, 2015·Journal of Computational Physics·Bao Wang, Guo-Wei Wei
Oct 9, 2016·Journal of Computational Chemistry·Duc D Nguyen, Guo-Wei Wei
Jan 5, 2017·Journal of Computational Chemistry·Beibei LiuGuo-Wei Wei
Feb 19, 2019·Journal of Computational Chemistry·Haixin WeiRuxi Qi
Jun 3, 2015·Journal of Computational Chemistry·Kelin Xia, Guo-Wei Wei
Dec 20, 2013·Molecular Based Mathematical Biology·Tao LiaoJ Andrew McCammon
Mar 1, 2012·International Journal for Numerical Methods in Biomedical Engineering·Anita T Layton, Guowei Wei
Aug 10, 2020·Bulletin of Mathematical Biology·Rundong ZhaoGuo-Wei Wei
Jul 3, 2013·Journal of Computational Chemistry·Xin FengGuo-Wei Wei

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