IDEAS home Printed from https://ideas.repec.org/a/eee/matcom/v203y2023icp131-149.html
   My bibliography  Save this article

Viral capsid nanoindentation simulations using octree-type data structures

Author

Listed:
  • López-Ruiz, Jorge
  • Botello-Rionda, Salvador
  • Herrera-Guzmán, Rafael
  • Carrillo-Tripp, Mauricio

Abstract

Viruses affect all forms of life and their relevance cannot be overstated. The main structural component of a virus is a protein shell known as the capsid which protects and transports the genetic material allowing the virion to infect a cell. It is possible to study the physical properties of the capsid through computational simulations with the use of physico-mathematical models at different approximation levels. In this work, we describe a methodology to generate topologically and geometrically faithful mesh representations of viral capsids through a homogeneous volume discretization using hexahedrons (cubes). The current implementation leverages octree-type binary operations, computer graphics, and high performance computing techniques. This approach reduces the meshing time by orders of magnitude compared to previous strategies. We performed simulations of nanoindentation and shearing of four viral capsids using the octree-type meshes and the Finite Element Method, in order to evaluate their response. Our results show that the capsid material response is consistent in terms of isotropic–anisotropic structural features while it increases numerical accuracy.

Suggested Citation

  • López-Ruiz, Jorge & Botello-Rionda, Salvador & Herrera-Guzmán, Rafael & Carrillo-Tripp, Mauricio, 2023. "Viral capsid nanoindentation simulations using octree-type data structures," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 203(C), pages 131-149.
    • Handle: RePEc:eee:matcom:v:203:y:2023:i:c:p:131-149
    DOI: 10.1016/j.matcom.2022.06.017
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378475422002877
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.matcom.2022.06.017?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Ito, Yasushi & Cheng, Gary C. & Shih, Alan M. & Koomullil, Roy P. & Soni, Bharat K. & Sittitavornwong, Somsak & Waite, Peter D., 2011. "Patient-specific geometry modeling and mesh generation for simulating Obstructive Sleep Apnea Syndrome cases by Maxillomandibular Advancement," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 81(9), pages 1876-1891.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mohd Faruq Abdul Latif & Nik Nazri Nik Ghazali & M. F. Abdullah & Norliza Binti Ibrahim & Roziana M. Razi & Irfan Anjum Badruddin & Sarfaraz Kamangar & Mohamed Hussien & N. Ameer Ahammad & Azeem Khan, 2023. "Modelling the Upper Airways of Mandibular Advancement Surgery: A Systematic Review," Mathematics, MDPI, vol. 11(1), pages 1-16, January.
    2. Cheng, Gary C. & Koomullil, Roy P. & Ito, Yasushi & Shih, Alan M. & Sittitavornwong, Somsak & Waite, Peter D., 2014. "Assessment of surgical effects on patients with obstructive sleep apnea syndrome using computational fluid dynamics simulations," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 106(C), pages 44-59.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:matcom:v:203:y:2023:i:c:p:131-149. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/mathematics-and-computers-in-simulation/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.