Chapter 7 The “Programming Language” of Dynamic Self-Assembly

Abstract

Abstract We show how protein dynamic self-assembly processes map naturally onto a formal model of computing, the random access machine (RAM), which is equivalent to a Turing machine. Specifically, we show that many biological processes that do not appear to be information processing, such as synthesis of macromolecules, structural assembly, transport, disassembly, and degradation of molecules, actually do perform computation when viewed from the RAM perspective. With this view that dynamic self-assembly processes are performing computation, we then look at this relationship from two perspectives. First, if self-assembly processes in living systems are performing computation, what algorithms are they carrying out? We discuss examples of algorithms implemented by living systems at multiple hierarchy levels. Second, if we can understand the “programming language” of dynamic self-assembly, can we design programs to self-assemble novel structures or materials? We give example computer simulations of programmed dynamic self-assembly of nanostructures.