Viral capsid nanoindentation simulations using octree-type data structures

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.