Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design

Abstract

Simulations of virus-like particles needed for computer-aided vaccine design highlight the need for new algorithms that accelerate molecular dynamics. Such simulations via conventional molecular dynamics present a practical challenge due to the millions of atoms involved and the long timescales of the phenomena of interest. These phenomena include structural transitions, self-assembly, and interaction with a cell surface. A promising approach for addressing this challenge is multiscale factorization. The approach is distinct from coarse-graining techniques in that it (1) avoids the need for conjecturing phenomenological governing equations for coarse-grained variables, (2) provides simulations with atomic resolution, (3) captures the cross-talk between disturbances at the atomic and the whole virus-like particle scale, and (4) achieves significant speedup over molecular dynamics. A brief review of multiscale factorization method is provided, as is a prospective on its development.