Journal of Biological Physics

, Volume 44, Issue 2, pp 147–162 | Cite as

Molecular dynamics study of T = 3 capsid assembly

  • D. C. Rapaport
Original Paper


Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T = 3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters. There are also no incorrectly assembled clusters. The simulations reveal details of intermediate structures along the growth pathway, information that is relevant for interpreting experiment.


Self-assembly Virus Capsid Simulation 


Compliance with Ethical Standards

Conflict of interests

The author declares that there is no conflict of interest.


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© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of PhysicsBar-Ilan UniversityRamat-GanIsrael

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