See also Computer simulation
Ehud Shapiro (2012), A mechanical Turing machine: blueprint for a biomolecular computer. page 
The mechanical computer is similar to the ribosome in several other respects. Both operate on two polymers simultaneously, and their basic cycle consists of processing an incoming molecule that matches the currently held molecules on the first polymer, elongating the second polymer and moving sideways. Like the ribosome in the living cell, the computer requires supporting devices similar in function to aminoacyl-tRNA synthetases to load bare transition molecules with correct alphabet monomers, and a device similar in function to proteases to decompose the trace polymer and make its components available for reuse. However, unlike the ribosome, which only ‘reads’ the messenger RNA in one direction, the computer edits the tape polymer and may move in either direction. (p. 500)
[…]
Perhaps the most important property of the mechanical computer is that it is reactive: it can have an ongoing, program-controlled, interaction with its environment. This capability is a result of the biologically inspired architecture of the computer rather than inherited from the theoretical Turing machine, which was conceived as a ‘batch’ computing device that receives its input at the beginning of the computation and produces an output if and when the computation ends. The ribosome, for example, suspends the construction of a polypeptide chain when a required amino acid is unavailable. Similarly, our computer can be ‘programmed’ to suspend until a specific molecule is available. The availability of such a control molecule can be tied to other relevant environmental conditions, thus triggering a computation only when these conditions prevail. (p. 501)
[…]
Molecular machines such as DNA polymerase, RNA polymerase and the ribosome are most naturally understood as simple finite-state transducers, a special case of the Turing machine. (p. 502)
~
SHAPIRO, Ehud, 2012. A mechanical Turing machine: blueprint for a biomolecular computer. Interface Focus. 6 August 2012. Vol. 2, no. 4, p. 497–503. DOI 10.1098/rsfs.2011.0118.
> We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may ‘compute’ synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.