ARVO

ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations. For calculating the solvation energy of proteins, hydration effects, drug binding, molecular docking, etc., it is important to have efficient and exact algorithms for computing the solvent accessible surface area and the excluded volume of macromolecules.We present a Fortran package based on new exact analytical methods for computing volume and surface areas of overlapping spheres. In this procedure the surface area and volume are expressed as surface integrals of the second kind over closed regions. Using stereographic projections the surface integrals are transformed to a sum of double integrals which are reduced to curve integrals. The MPI Fortran version is described as well. The package is also useful for computing the percolation probability of continuum percolation models. (Source: http://cpc.cs.qub.ac.uk/summaries/)


References in zbMATH (referenced in 13 articles , 1 standard article )

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  1. Buša, Ján; Hayryan, Shura; Hu, Chin-Kun; Skřivánek, Jaroslav; Wu, Ming-Chya: CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins (2010)
  2. Choi, Juhwan; Ryu, Han Sik; Kim, Chang Wan; Choi, Jin Hwan: An efficient and robust contact algorithm for a compliant contact force model between bodies of complex geometry (2010)
  3. Misiołek, Gerard; Preston, Stephen C.: Fredholm properties of Riemannian exponential maps on diffeomorphism groups (2010)
  4. Huang, Peijie; Gu, Yuanting; Wu, Xiaolong; Chen, Yanyun; Wu, Enhua: Time-varying clustering for local lighting and material design (2009)
  5. Dimov, Ivan T.; Penzov, Anton A.; Stoilova, Stanislava S.: Parallel Monte Carlo sampling scheme for sphere and hemisphere (2007)
  6. Buša, Ján; Džurina, Jozef; Hayryan, Edik; Hayryan, Shura; Hu, Chin-Kun; Plavka, Ján; Pokorný, Imrich; Skřivánek, Jaroslav; Wu, Ming-Chya: ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations (2005)
  7. Hansen, Olaf: A fast collocation method for the radiosity equation, based on the hierarchical algorithm of Hanrahan and Salzman: the 1D case (2005)
  8. Wu, Enhua; Wang, Wenping: Interleaving radiosity (2002)
  9. Jin, Xiaogang; Wan, Huagen; Peng, Qunsheng: Geometric deformations based on 3D volume morphing (2001)
  10. Szirmay-Kalos, L.; Márton, G.: Worst-case versus average case complexity of ray-shooting (1998)
  11. Pellegrini, M.: Monte Carlo approximation of form factors with error bounded a priori (1997)
  12. Brunet, Pere (ed.); Jansen, Frederik W. (ed.): Photorealistic rendering in computer graphics. Proceedings of the 2nd Eurographics Workshop on Rendering, held in May 1991 at the University of Catalunya in Barcelona, Spain (1994)
  13. Pellegrini, M.: Ray shooting on triangles in 3-space (1993)