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Molecular dynamics simulation of the self-assembly of icosahedral virus

Abstract : Viruses are known for infecting all classes of living organisms on Earth, whether vegetal or animal. Virions consist of a nucleic acid genome protected by a single or multilayered protein shell called capsid, and in some cases by an envelope of lipids. The viral capsid is generally made of hundreds or thousands of proteins forming ordered structures. Half of all known viruses exhibit an icosahedral symmetry, the rest being helical, prolate or having a complex irregular structure. Recently, viral particles have attracted an increasing attention due to their extremely regular structure and their potential use for fabricating nanostructures with various functions. Therefore, understanding the assembly mechanisms underlying the production of viral particles is not only helpful to the development of inhibitors for therapeutic purpose, but it should also open new routes for the self-assembly of complex supramolecular materials. To date, numerous experimental and theoretical investigations on virus assembly have been performed. Through experimental investigations, a lot of information have been obtained on virus assembly, including the proper conditions required for the assembly and the kinetic pathways. Combining those information and theoretical methods, an initial understanding of the assembly mechanism of viruses has been worked out. However, information coming purely from experiments cannot give the whole picture, in particular at a microscopic scale. Therefore, in this thesis, we employed computer simulations, including Monte Carlo and molecular dynamics techniques, to probe the assembly of virus, with the expectation to gain new insights into the molecular mechanisms at play.
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  • HAL Id : tel-02353631, version 1

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Jingzhi Chen. Molecular dynamics simulation of the self-assembly of icosahedral virus. Biological Physics [physics.bio-ph]. Université Paris Saclay (COmUE), 2019. English. ⟨NNT : 2019SACLS326⟩. ⟨tel-02353631⟩

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