TMSmesh swMATH ID: 14719 Software Authors: Chen M., Lu B. Description: TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique. Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review in B. Z. Lu et al. Commun. Comput. Phys. 2008, 3, 973−1009). In this paper, we present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface of biomolecules. The method computes the surface points by solving a nonlinear equation directly, polygonizes by connecting surface points through a trace technique, and finally outputs a triangulated mesh. TMSmesh has a linear complexity with respect to the number of atoms and is shown to be capable of handling molecules consisting of more than one million atoms, which is usually difficult for the existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes generated by TMSmesh are successfully tested in boundary element solutions of the Poisson−Boltzmann equation, which directly gives rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh and a set of representative PQR benchmark molecules are downloadable at our Web page http://lsec.cc.ac.cn/∼lubz/Meshing.html. Homepage: http://lsec.cc.ac.cn/~lubz/Meshing.html Related Software: APBS; MIBPB; tabipb; TetGen; TABI; AFMPB; PHG; PDB2PQR; VCMM; PAFMPB; Apbsmem; CHARMM; ParaView; UHBD; FEtk; SG; FFTSVD; NAMD; MolSurf; nuSMPBIC Cited in: 22 Documents Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation. Zbl 1393.65027Liu, Tiantian; Chen, Minxin; Lu, Benzhuo 2018 all top 5 Cited by 50 Authors 13 Lu, Benzhuo 4 Geng, Weihua 4 Zhang, Linbo 3 Xie, Yan 2 Alexov, Emil 2 Chen, Minxin 2 Gui, Sheng 2 Li, Hongliang 2 Liu, Tiantian 2 Tu, Bin 2 Xie, Dexuan 2 Zhang, Bo 2 Zhao, Shan 1 Bai, Shiyang 1 Chao, Zhen 1 Chen, Jiahui 1 Cheng, Jie 1 Debuhr, Jackson 1 Deng, Weishan 1 Faria, Luiz M. 1 Hazra, Tania 1 Huang, Jingfang 1 Jacob, Ferosh 1 Krasny, Robert 1 Li, Chuan 1 Li, Lin 1 Liu, Chun 1 Liu, Xuejiao 1 Ma, Zhaocan 1 Mayolo, Silvio 1 Mu, Lin 1 Niedzielski, Drake 1 Peng, Bo 1 Pérez-Arancibia, Carlos 1 Petukh, Marharyta 1 Pitsianis, Nikos P. 1 Qiao, Yu 1 Sterling, Thomas Lawrence 1 Sun, Xiaobai 1 Tang, Ming 1 Turc, Catalin 1 Ullah, Sheik Ahmed 1 Wang, Qin 1 Wang, Siwen 1 Wei, Guowei 1 Xia, Kelin 1 Xu, Jin 1 Yang, Ying 1 Zhang, Qianru 1 Zhong, Liuqiang all top 5 Cited in 11 Serials 4 Journal of Computational Physics 3 Computer Physics Communications 3 SIAM Journal on Scientific Computing 2 Journal of Computational and Applied Mathematics 2 Communications in Computational Physics 2 Molecular Based Mathematical Biology 1 Journal of Mathematical Biology 1 Journal of Statistical Physics 1 Advances in Computational Mathematics 1 Journal on Numerical Methods and Computer Applications 1 International Journal of Numerical Analysis and Modeling all top 5 Cited in 9 Fields 17 Numerical analysis (65-XX) 13 Biology and other natural sciences (92-XX) 11 Partial differential equations (35-XX) 9 Optics, electromagnetic theory (78-XX) 4 Computer science (68-XX) 3 Statistical mechanics, structure of matter (82-XX) 1 Integral equations (45-XX) 1 Mechanics of deformable solids (74-XX) 1 Quantum theory (81-XX) Citations by Year