Mathematical Biophysics/Mathematical Molecular Biosciences

 

(220) G. W. Wei, How can mathematicians contribute to molecular biosciences? (2017).

 

(219) Zachary F. Burton, Kristopher Opron, Guowei Wei and James H. Geiger, Ancient evolution of α/β protein folds and RNA synthesis systems was dominated by polymers, (2015).

 

(218) Kristopher Opron, Yin Cao, David Bramer, Kelin Xia and Guo-Wei Wei, Protein hinge prediction using machine learning with mainly flexibility-rigidity index features, (2015).

 

(217) Kelin Xia and Guo-Wei Wei, A review of geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular data (2016).

 

(216) Kedi Wu and Guo-Wei Wei, Comparison of multi-task convolutional neural network (MT-CNN) and a few other methods for toxicity prediction (2017).

 

(215) Bao Wang, Chengzhang Wang, Kedi Wu and Guo-Wei Wei, Feature functional theory - solvation predictor (FFT-SP) for the blind prediction of solvation free energy, (2016).

 

(213) Z. X. Cang, R. Q. Guo, Heedeok Hong and Guo-Wei Wei, Accurate prediction of membrane protein stability changes upon mutation, (2017).

 

(214) Z. X. Cang and Guo-Wei Wei, TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions, (2017).

 

(212) Z. X. Cang and Guo-Wei Wei, Topological fingerprints reveal protein-ligand binding mechanism, (2017).

 

(211) Z. X. Cang and Guo-Wei Wei, Element specific persistent homology for the analysis and prediction of protein folding stability upon mutation, (2017).

 

(210) Duc D Nguyen, Tian Xiao, Menglun Wang and Guo-Wei Wei, Rigidity strengthening is a vital mechanism for protein-ligand binding, (2017).

 

(209) Bao Wang, Zhixiong Zhao, Duc Nguyen and Guo-Wei Wei, Feature functional theory - binding predictor (FFT-BP) for the blind prediction of binding free energy, Theoretical Chemistry Account, accepted (2017).

 

(207) Duc D Nguyen, Bao Wang and Guo-Wei Wei, Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies, Journal of Computational Chemistry, 38, 941-948 (2017).

 

(206) Duan Chen and Guo-Wei Wei, A Review of Mathematical Modeling, Simulation and Analysis of Membrane Channel Charge Transport, Reference Module in Life Sciences, (2017).

 

(205) Yongcheng Zhou and Guo-Wei Wei, Variational Methods for Biomolecular Modeling, in Variational Methods in Molecular Modeling, Edited by Jianzhong Wu, Springer Science+Business Media Singapore, 181-221, (2017).

 

(204) Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong and Guo-Wei Wei, ESES: software for Eulerian solvent excluded surface, Journal of Computational Chemistry, 38, 446-466 (2017).

 

(203) Lin Mu, Kelin Xia and Guo-Wei Wei, Geometric and electrostatic modeling using molecular rigidity functions, Journal of Computational and Applied Mathematics, 313, 18-37 (2017).

 

(202) Duc D Nguyen and Guo-Wei Wei, The impact of surface area, volume, curvature and Lennard-Jones potential to solvation modeling, Journal of Computational Chemistry, 38, 2436 (2017).

(201) Guo-Wei Wei and Nathan A. Baker, Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: A review. In Many-Body Effects and Electrostatics in Biomolecules, edited by Qiang Cui, Markus Meuwly, and Pengyu Ren, Pan Stanford, 417-464, (2016).

 

(200) Guo-Wei Wei, Mathematical Molecular Bioscience and Biophysics, SIAM News, 49 (7), (2016).

 

(199) Bao Wang, Zhixiong Zhao and Guo-Wei Wei, Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies, Journal of Chemical Physics, 145, 124110 (2016).

 

(198) Duc D Nguyen, Kelin Xia and Guo-Wei Wei, Generalized flexibility-rigidity index, Journal of Chemical Physics, 144, 234106 (2016).

 

(197) Kristopher Opron, Kelin Xia, Zachary F. Burton and Guo-Wei Wei, Flexibility-Rigidity Index  for Protein-Nucleic Acid Flexibility and Fluctuation Analysis, Journal of Computational Chemistry, 37, 12831295 (2016).

 

(196) Zachary F. Burton, Kristopher Opron, Guowei Wei and James H. Geiger, A model for genesis of transcription systems, Transcription, 7, 1-13 (2016).

 

(195) Bao Wang and Guo-Wei Wei, Object-oriented persistent homology, Journal of Computational Physics, 305, 276-299 (2016).

 

(194) Zixuan Cang, Lin Mu, Kedi Wu, Kris Opron, Kelin Xia and Guo-Wei Wei, A topological approach to protein classification, Molecular based Mathematical Biology, 3, 140-162 (2015)

 

(193) Kelin Xia, Kristopher Opron and Guo-Wei Wei, Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM), Journal of Chemical Physics, 143, 204106 (2015).

 

(192) Bao Wang and Guo-Wei Wei, Parameter optimization in differential geometry based solvation models, Journal of Chemical Physics, 143, 134119 (2015).

 

(191) Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, Multiresolution persistent homology for excessively large biomolecular datasets, Journal of Chemical Physics, 143, 134103 (2015).

 

(190) Kristopher Opron, Kelin Xia, and Guo-Wei Wei, Communication: Capturing protein multiscale thermal fluctuations, Journal of Chemical Physics, 142, 211101 (2015).

 

(189) Jinkyoung Park, Kelin Xia and G.W. Wei, Atomic scale design and three-dimensional simulations of nanofluidic systems, Microfluidics and Nanofluidics, 19, 665-692 (2015).

 

(188) Kelin Xia and Guo-Wei Wei, Multidimensional persistence in biomolecular data, Journal of Computational Chemistry, 36, 1502-1520 (2015).

 

(187) Kelin Xia, Zhixiong Zhao and Guo-Wei Wei, Multiresolution topological simplification, Journal of Computational Biology, 22, 9, 1-5 (2015).

 

(185) Kelin Xia and Guo-Wei Wei, Persistent topology for cryo-EM data analysis, International Journal for Numerical Methods in Biomedical Engineering, 31, e02719 (2015).

 

(182) Kelin Xia, X. Feng, Yiying Tong and Guo-Wei Wei, Persistent homology for the quantitative prediction of fullerene stability, Journal of Computational Chemistry, 36, 408-422 (2015).

 

(178) Kelin Xia and Guo-Wei Wei, Persistent homology analysis of protein structure, flexibility and folding, International Journal for Numerical Methods in Biomedical Engineering, 30, 814-844 (2014).

 

(177) Kristopher Opron, Kelin Xia, and Guo-Wei Wei, Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis, Journal of Chemical Physics, 140(23), 234105, (2014).

 

(176) Kelin Xia and Guo-Wei Wei, Molecular nonlinear dynamics and protein thermal uncertainty quantification, Chaos, 24, 013103 (2014).

 

(174) Kelin Xia, Xin Feng, Zhan Chen, Yiying Tong and Guo-Wei Wei, Multiscale geometric modeling of macromolecules I: Cartesian representation, Journal of Computational Physics, 257, 912-936 (2014).

 

(173) Kelin Xia, and Guo-Wei Wei, A stochastic model for protein flexibility analysis, Physical Review E, 88, 062709 (2013).

 

(172) X. Feng, Kelin Xia, Zhan Chen, Yiying Tong and Guo-Wei Wei, Multiscale geometric modeling of macromolecules II: Lagrangian representation, Journal of Computational Chemistry, 34, 2100-2120 (2013).

 

(171) Kelin Xia, Kristopher Opron and Guo-Wei Wei, Multiscale multiphysics and multidomain models Flexibility and rigidity, Journal of Chemical Physics, 139, 194109 (2013).

 

(169) Michael Daily, Jaehun Chun, Alejandro Heredia-Langner, Guo-Wei Wei, and Nathan Baker, Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. Journal of Chemical Physics, 139, 204108 (2013).

 

(168) Guo-Wei Wei, Multiscale multiphysics and multidomain models I: Basic theory, Journal of Theoretical and Computational Chemistry, 12(8), 1341006, (2013)

 

(167) Jinkyoung Park and G.W. Wei, A molecular level prototype for mechanoelectrical transducers in mammalian hair cells, Journal of Computational Neuroscience, 35, 231-241, (2013).

 

(166) Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guo-Wei Wei, Nathan A. Baker, Parameterization of a geometric flow implicit solvation model, Journal of Computational Chemistry, 24, 687-695 (2013)

 

(165) Emil Alexov and Guo-Wei Wei, Preface: Special issue on modeling electrostatics in molecular biology (MEMB), Commun. Comput. Phys., 13(1) 1-5, (2013).

 

(164) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport I: Basic formulation, Communication in Computational Physics, 13, 285-324 (2013)

 

(163) Langhua Hu, Duan Chen and Guo-Wei Wei, High-order fractional partial differential equations for molecular surface construction, Molecular Based Mathematical Biology, 1-25 (2012).

 

(162) X. Feng, Kelin Xia, Yiying Tong and Guo-Wei Wei, Geometric modeling of organelles, subcellular structures and multiprotein complexes, International Journal for Numerical Methods in Biomedical Engineering, 28, 1198-1223 (2012).

 

(161) Zhan Chen, Shan Zhao, Jaehun Chun, Dennis G. Thomas, Nathan Baker, Peter Bates and Guo-Wei Wei, Variational approach for nonpolar solvation analysis, Journal of Chemical Physics, 137, 084101 (2012).

(160) Anita T. Layton and Guo-Wei Wei, Editorials: Interface methods for biological and biomedical problems, International Journal for Numerical Methods in Biomedical Engineering, 28, 289290, (2012)

(159) Duan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport --- Generalized correlation, Journal of Chemical Physics, 136, 134109 (2012)

 

(158) Guo-Wei Wei, Qiong Zheng, Zhan Chen, and Kelin Xia, Variational multiscale models for charge transport, SIAM Review. 54(4), 699-754 (2012)

 

(157) Yang Wang, Guo-Wei Wei and Siyang Yang, Selective extraction of entangled textures via adaptive PDE transform, Int. J. Biomed Imaging, Volume 2012 (2012), Article ID 958142 (2012).

 

(156) Langhua Hu and Guo-Wei Wei, Nonlinear Poisson equation for inhomogeneous media. Biophysical Journal, 103, 758766 (2012).

 

(155) Duan Chen, Zhan Chen and Guo-Wei Wei, Quantum dynamics in continuum models for proton transport II: Variational solvent-solute interface, International Journal for Numerical Methods in Biomedical Engineering, 28, 25-51 (2012)

 

(154) Qiong Zheng, Siyang Yang and Guo-Wei Wei, Molecular surface generation using PDE transform. International Journal for Numerical Methods in Biomedical Engineering, 28, 291-316 (2012)

 

(150) Zhan Chen and G. W. Wei, Differential geometry based salvation model III: Quantum formulation, Journal of Chemical Physics, 135, 194108 (2011).

 

(149) Qiong Zheng and Guo-Wei Wei, Poisson-Boltzmann-Nernst-Planck model. Journal of Chemical Physics, 134 (19), 194101, (2011) (It was the most downloaded in JCP in May 2011)

 

(146) Qiong Zheng, Duan Chen and Guo-Wei Wei, Second-order Poisson-Nernst-Planck solver for ion transport. Journal of Computational Physics, 230, 5239-5262 (2011)

 

(145) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based salvation model II: Lagrangian formulation (62 pages), Journal of Mathematical Biology, 63, 11391200, (2011).

 

(144) Weihua Geng and G.W. Wei, Multiscale molecular dynamics via the matched interface and boundary (MIB) method, Journal of Computational Physics, 230, 435-457 (2011).

(143) Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng and Guo-Wei Wei, MIBPB: A software package for electrostatic analysis, Journal of Computational Chemistry, 32, 756770 (2011).

 

(141) Zhan Chen, Nathan Baker and G. W. Wei, Differential geometry based solvation model I: Eulerian formulation, Journal of Computational Physics, 229, 8231-8258 (2010).

 

(140) Duan Chen and Guo-Wei Wei, Modeling and simulation of nano-electronic devices (44 pages), Journal of Computational Physics, 229, 4431-4460, (2010).

 

(139) Changjun Chen, Rishu Saxena, and Guo-Wei Wei, Differential geometry based multiscale model for virus capsid dynamics, Int. J. Biomed Imaging, Volume 2010, Article ID 308627, 9 pages (2010).

 

(138) Guo-Wei, Wei, Differential geometry based multiscale models, Bulletin of Mathematical Biology, volume 72, 1562-1622, (2010).

 

(136) G.W. Wei and G. Wang, Editoral: Special issue on recent advances in computational techniques for biomedical imaging, Commun. Numer. Methods Engng, 25, 581-582 (2009)

 

(135) P. Bates, Z. Chen, Y.H. Sun, G.W. Wei and S. Zhao, Geometric and potential driving formation and evolution of biomolecular surfaces, J. Math. Biol. 59, 193-231 (2009)

 

(133) Duan Chen, G.W. Wei, X. Cong and Ge Wang, Computational methods for optical molecular imaging, Commun. Numer. Methods Engng, 25, 1137-1161(2008).

 

(130) W.H. Geng, S.N. Yu and G.W. Wei, Treatment of charge singularities in implicit solvent models, J. Chem. Phys., 127, 114106 (20 pages) (2007). Also available at the Virtual Journal of Biological Physics Research October 1, 2007

 

(129) P. Bates, G.W. Wei and S. Zhao, Minimal molecular surfaces and their applications, J. Comput. Chem., ., 29, 380-391 (2008).

 

(128) S. N. Yu, W. H. Geng and G.W. Wei, Treatment of geometric singularities in implicit solvent models, J. Chem. Phys., 126, 244108 (13 pages) (2007). ). Also available at the Virtual Journal of Biological Physics Research July 1, 2007

 

(127) Y.C. Zhou, M. Feig and G.W. Wei, Highly accurate biomolecular electrostatics in continuum dielectric environments, J. Comput. Chem. 29, 87-97 (2008).

 

(124) G.W. Wei, Editoral: Recent advances in mathematical methods for the analysis of biomedical image, International Journal of Biomedical Imaging, vol. 2006, 70578, 1, (2006).

 

(121) Ge Wang, Haiou Shen Wenxiang Cong, Shan Zhao and G.W. Wei, Temperature modulated bioluminescence tomography, Optics Express, 14 (17) 7852-7871 (2006).

 

(MB2) P. W. Bates, G.W. Wei and Shan Zhao, The minimal molecular surface, arXiv:q-bio/0610038 [q-bio.BM] (2006).

 

(MB1) G. W. Wei, Yuhui Sun, Yongcheng Zhou and Michael Feig, Molecular multiresolution surfaces, arXiv:math-ph/0511001v1 1 Nov 2005.