tabipb swMATH ID: 43645 Software Authors: Geng, W. H.; Krasny, R. Description: tabipb: A treecode-accelerated boundary integral Poisson-Boltzmann solver. TABI (treecode-accelerated boundary integral) solves the linear Poisson-Boltzmann equation. The solver employs a well-conditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface, which is triangulated and the integral equations are discretized by centroid collocation. The linear system is solved by GMRES iteration and the matrix-vector product is carried out by a Cartesian terraced which reduces the cost from O(N^2) to O(N*logN), where N is the number elements. REFERENCE: W.H. Geng and R. Krasny, A treecode-accelerated boundary integral Poisson-Boltzmann solver for continuum electrostatics of solvated biomolecules, J. Comput. Phys. 247, 62-87 (2013) Homepage: https://sourceforge.net/projects/tabipb/ Related Software: TABI; MIBPB; APBS; PDB2PQR; CHARMM; TMSmesh; PBEQ-Solver; AFMPB; PyGBe; PAFMPB; Apbsmem; SDPBS; ESES; hlib; pvfmm; ScalFMM; Algorithm 967; ASKIT; VCMM; UHBD Cited in: 38 Documents Standard Articles 2 Publications describing the Software, including 2 Publications in zbMATH Year Computing electrostatic binding energy with the TABI Poisson-Boltzmann solver. Zbl 1510.81156Wilson, Leighton; Hu, Jingzhen; Chen, Jiahui; Krasny, Robert; Geng, Weihua 2022 A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules. Zbl 1349.78084Geng, Weihua; Krasny, Robert 2013 all top 5 Cited by 75 Authors 11 Geng, Weihua 6 Zhao, Shan 5 Krasny, Robert 4 Chen, Duan 4 Chen, Jiahui 4 Wang, Lei 2 Gan, Zecheng 2 Hu, Jingzhen 2 Lu, Benzhuo 2 Stamm, Benjamin 2 Tlupova, Svetlana 2 Xie, Dexuan 2 Zhang, Bo 1 Alexov, Emil 1 Argudo, David 1 Barba, Lorena A. 1 Borleske, George 1 Bramas, Bérenger 1 Cai, Wei 1 Cheng, Maggie Xiaoyan 1 Cheng, Yingda 1 Cheng, Yuhui 1 Cheruvu, Vani 1 Christlieb, Andrew J. 1 Cooper, Christopher D. H. 1 Corona, Eduardo 1 Debuhr, Jackson 1 Deng, Weishan 1 Fu, Jing 1 Grabe, Michael 1 Guo, Wei 1 Hassan, Muhammad 1 Holst, Michael J. 1 Huang, Jingfang 1 Ijaodoro, Idowu Esther 1 Jacob, Ferosh 1 Jiang, Yi 1 Kekenes-Huskey, Peter M. 1 Kohl, Ryan 1 Krishnamurthy, Mahesh 1 Lee, Arum 1 Li, Shuwang 1 Liao, Tao 1 Maday, Yvon 1 Marcoline, Frank V. 1 Mayolo, Silvio 1 McCammon, J. Andrew 1 McCulloch, Andrew D. 1 McGowan, Mark 1 Michailova, Anushka 1 Negi, Pawan 1 Niedzielski, Drake 1 Ong, Benjamin W. 1 Peng, Bo 1 Pitsianis, Nikos P. 1 Quan, Chaoyu 1 Ren, Kui 1 Sterling, Thomas Lawrence 1 Sun, Xiaobai 1 Tausch, Johannes 1 Tong, Yiying 1 Tsai, Yen-Hsi Richard 1 Veerapaneni, Shravan Kumar 1 Wang, Menglun 1 Wei, Guowei 1 Wilson, Leighton 1 Xie, Yang 1 Xu, Jin 1 Xu, Zhenli 1 Ying, Jinyong 1 Ying, Wenjun 1 Yu, Zeyun 1 Zhang, Yongjie Jessica 1 Zhao, Rundong 1 Zhong, Yimin all top 5 Cited in 15 Serials 13 Journal of Computational Physics 5 Molecular Based Mathematical Biology 4 Communications in Computational Physics 3 Computer Physics Communications 2 Advances in Applied Mathematics and Mechanics 2 Computational and Mathematical Biophysics 1 Computer Methods in Applied Mechanics and Engineering 1 Bulletin of Mathematical Biology 1 Journal of Computational and Applied Mathematics 1 Journal of Scientific Computing 1 SIAM Journal on Scientific Computing 1 Advances in Computational Mathematics 1 Communications in Information and Systems 1 European Series in Applied and Industrial Mathematics (ESAIM): Mathematical Modelling and Numerical Analysis 1 Science China. Mathematics all top 5 Cited in 15 Fields 25 Numerical analysis (65-XX) 19 Biology and other natural sciences (92-XX) 16 Optics, electromagnetic theory (78-XX) 9 Partial differential equations (35-XX) 4 Fluid mechanics (76-XX) 2 Computer science (68-XX) 2 Mechanics of deformable solids (74-XX) 2 Quantum theory (81-XX) 1 General and overarching topics; collections (00-XX) 1 Combinatorics (05-XX) 1 Potential theory (31-XX) 1 Integral equations (45-XX) 1 Differential geometry (53-XX) 1 Algebraic topology (55-XX) 1 Statistical mechanics, structure of matter (82-XX) Citations by Year