Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells

Abstract

A general phase-plot is proposed for discrete particle shells that allows for thermal fluctuations of the shell geometry and of the inter-particle connectivities. The phase plot contains a first-order melting transition, a buckling transition and a collapse transition and is used to interpret the thermodynamics of microbiological shells.

Physics of viral dynamics

“…All-atom MD simulations of viruses 147 – 149 — which have also been used to study the permeability of poliovirus capsids to water 150 and the binding of ions to HIV-1 capsids 146 , for example — indicate that mutated capsids may collapse because of thermal fluctuations 151 . Relatedly, Brownian dynamics simulations of a coarse-grained representation of capsids revealed that they can melt, crumple or collapse under the action of thermal fluctuations, depending on the materials properties of the shell 152 (Fig. 4e ).…”

Buckling of thermalized elastic sheets

“…Note that this is different from spherical shells, where thermal fluctuations effectively reduce the critical buckling pressure [85][86][87][88]. Note also that the applied external load could affect the renormalization of the bending rigidity as was previously demonstrated for sheets under tension [59,63,[89][90][91].…”

Machine-learning a virus assembly fitness landscape

“…The output is an integer (which we treat as a real number) between 0 and 2000, which we can normalise into � 2 [0, 1] � by dividing by 2000. The algorithm used by [14] is thus a map f : v 2 12 3 À !� 2 ½0; 1� : ð1Þ…”

“…The thermodynamics of PS binding and of the number of CP bonds formed then translates into assembly efficiency. This in turn is taken as a proxy for fitness (all other things being equal)-or at least the contribution to the fitness that results from assembly considerations [11][12][13].…”

“…While not ideal, cluster computation was limited; the simulation allows to capture the more generic features whilst the above cross-validation suggests that the error is small [9]. Nevertheless a brute-force simulation has been performed on the 3 12 = 531, 441 possible input values and the efficiency value extracted. This gives us a database of some half a million known cases of the form (2).…”