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Parallel High-Performance Computing Algorithm to Generate FEM-Compliant Volumetric Mesh Representations of Biomolecules at Atomic Scale

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Supercomputing (ISUM 2019)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1151))

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Abstract

The computational study of biomolecules has been undermined by the lack of models that accurately represent the structure of big complexes at the atomic level. In this work, we report the development of an algorithm to generate a volumetric mesh of a biomolecule, of any size and shape, based on its atomic structure. Our mesh generation tool leverages the octree algorithm properties with parallel high-performance computing techniques to produce a discretized hexahedral model faster than previous methods. The reported algorithm is memory efficient and generates volumetric meshes suitable to be used directly in Finite Element Analysis. We tested the algorithm by producing mesh models of different biomolecule types and complex size, and also performed numerical simulations for the largest case. The Finite Element results show that our mesh models reproduce experimental data.

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References

  1. Gibbons, M.M., Klug, W.S.: Nonlinear finite-element analysis of nanoindentation of viral capsids. Phys. Rev. E 75(3), 031901:1–031901:11 (2007). https://doi.org/10.1103/PhysRevE.75.031901

  2. Anton, A., Wouter, R., Gijs, W., Klaus, S.: Elucidating the mechanism behind irreversible deformation of viral capsids. Biophys. J. 97, 2061–2069 (2009)

    Article  Google Scholar 

  3. Roos, W.H., Bruinsma, R., Wuite, G.J.L.: Physical virology. Nat. Phys. 6, 733 (2010)

    Article  Google Scholar 

  4. George, P.L., Hecht, F., Saltel, É.: Fully automatic mesh generator for 3D domains of any shape. IMPACT Comput. Sci. Eng. 2, 187–218 (1990)

    Article  Google Scholar 

  5. Frey, P.J., George, P.L.: Mesh Generation: Application to Finite Elements, 2nd edn. Hermes Sciences ltd., Hyderabad (2008)

    Book  Google Scholar 

  6. Cheng, S.W., Dey, T.K., Shewchuk, J.R.: Delaunay Mesh Generation. Chapman and HALL/CRC, Cambridge (2013)

    MATH  Google Scholar 

  7. Paul, G., Houman, B.: Delaunay Triangulation and Meshing. Application to Finite Elements. Hermes (1998). ISBN 2-86601-692-0

    Google Scholar 

  8. Weatherill, N.P.: Delaunay triangulation in computational fluid dynamics. Comput. Math Appl. 24, 129–150 (1992)

    Article  Google Scholar 

  9. Hardwick, J.C. Implementation and evaluation of an efficient 2D parallel Delaunay triangulation algorithm. In: Proceedings of the 9th Annual Symposium on Parallel Algorithms and Architectures (1997)

    Google Scholar 

  10. Cigoni, P., Montani, C., Perego, R., Scopigno, R.: Parallel 3D delaunay triangulation. Eurographics Association (1993)

    Google Scholar 

  11. Joachim, S.: An advancing front 2D/3D mesh generator based on abstract rules. Comput. Vis. Sci. 1, 41–52 (1997)

    Article  Google Scholar 

  12. Michael, S., Arthur, O., Juan-Claude, S.: Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38, 305–320 (1996)

    Article  Google Scholar 

  13. Ho-Lun, C., Shi, X.: Quality mesh generation for molecular skin surface using restricted union of balls. J. Comput. Geom. Theory Appl. 42, 196–206 (2009)

    Article  MathSciNet  Google Scholar 

  14. Yu, Z., Holst, M.J., Cheng, Y., McCammon, J.A.: Feature preserving adaptive mesh generation for molecular shape modeling and simulation. J. Mol. Graph. Modell. 26, 1370–1380 (2008)

    Article  Google Scholar 

  15. Alonzo-Velázquez, J., Botello Rionda, S., Herrera-Guzmán, R., Carrillo-Tripp, M.: CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties. Int. J. Numer. Methods Biomed. Eng. 34, e2991 (2018)

    Article  Google Scholar 

  16. Vargas Felix, M., Botello-Rionda, S.: FEMT, open source tools for solving large systems of equations in parallel. Acta universitaria (2012)

    Google Scholar 

  17. OpenMP Architecture Review Board: OpenMP application programing interface OpenMP (2018)

    Google Scholar 

  18. Frisken, S.F., Perry, R. N.: Simple and efficient traversal methods for quadtrees and octrees. Mitsubishi Electric Research Laboratories (2002)

    Google Scholar 

  19. Michel, J.P., et al.: Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. Proc. Nat. Acad. Sci. 103, 6184–6189 (2006)

    Article  Google Scholar 

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Correspondence to Jorge López .

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López, J., Botello, S., Herrera, R., Carrillo-Tripp, M. (2019). Parallel High-Performance Computing Algorithm to Generate FEM-Compliant Volumetric Mesh Representations of Biomolecules at Atomic Scale. In: Torres, M., Klapp, J. (eds) Supercomputing. ISUM 2019. Communications in Computer and Information Science, vol 1151. Springer, Cham. https://doi.org/10.1007/978-3-030-38043-4_25

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  • DOI: https://doi.org/10.1007/978-3-030-38043-4_25

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-38042-7

  • Online ISBN: 978-3-030-38043-4

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