Langevin dynamics simulation of polymer-assisted virus-like assembly

JP Mahalik and M Muthukumar, JOURNAL OF CHEMICAL PHYSICS, 136, 135101 (2012).

DOI: 10.1063/1.3698408

Starting from a coarse grained representation of the building units of the minute virus of mice and a flexible polyelectrolyte molecule, we have explored the mechanism of assembly into icosahedral structures with the help of Langevin dynamics simulations and the parallel tempering technique. Regular icosahedra with appropriate symmetry form only in a narrow range of temperature and polymer length. Within this region of parameters where successful assembly would proceed, we have systematically investigated the growth kinetics. The assembly of icosahedra is found to follow the classical nucleation and growth mechanism in the absence of the polymer, with the three regimes of nucleation, linear growth, and slowing down in the later stage. The calculated average nucleation time obeys the laws expected from the classical nucleation theory. The linear growth rate is found to obey the laws of secondary nucleation as in the case of lamellar growth in polymer crystallization. The same mechanism is seen in the simulations of the assembly of icosahedra in the presence of the polymer as well. The polymer reduces the nucleation barrier significantly by enhancing the local concentration of subunits via adsorbing them on their backbone. The details of growth in the presence of the polymer are also found to be consistent with the classical nucleation theory, despite the smallness of the assembled structures. (C) 2012 American Institute of Physics.

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