We use molecular dynamics (MD) simulations and related theoretical and computational methods to investigate the self-assembly, phase behavior and interaction networks of a range of soft-matter biological systems. In MD simulations, a complex molecular assembly is modeled by a set of interacting particles, whose evolution in time and space is calculated by numerical integration of Newton’s second law. The method is rigorously based on the laws of statistical mechanics, and allows calculation of bulk thermodynamic properties while simultaneously providing atomic-scale resolution of molecular behavior that cannot directly be obtained from analytical measurements alone.

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