Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine

It is commonly agreed that a chemical assembly of molecules can be considered alive if it can ingest resources and convert them into building blocks; has the ability to grow and self-reproduce; and can evolve. In the design proposed by Rasmussen and Chen (Science 2004, 303, 963) the assembly or protocell could be as simple as a small micellar surfactant aggregate acting as a container, anchoring an informational molecule to its exterior and incorporating a metabolism within the oily interior. We present several examples of modeling such a system with molecular dynamics computer simulations. © 2008 Wiley Periodicals, Inc. Complexity, 2008. This article was submitted as an invited paper resulting from the “Understanding Complex Systems” conference held at the University of Illinois-Urbana Champaign, May 2006.