Conformation-based molecular computing: Simulation and implementation

The conformational dynamics of proteins is a computational resource that fuses milieu signals in a nonlinear fashion. Proteins can be regarded as immense processing networks of nuclei and electrons that can serve as molecular modules providing high complexity basis functions. The possibility for reproducing the nonlinearity of proteins in a highly precise manner by specifying their discrete amino acid sequences opens up the possibility of realizing computing technology based on complex elementary components.; Response surface methodology can be used to elicit computational functionality from enzyme dynamics. We have analyzed the response (in the form of NADH accumulation) of the enzyme porcine mitochondrial malate dehydrogenase with respect to MgCl ₂, CaCl₂ and citrate concentration from the perspective of different signal encodings.; To study enzymatic signal processing in a device context two table-top prototype implementations of enzymatic pattern processors have been built. These prototypes were employed in conjunction with malate dehydrogenase to perform the linearly inseparable exclusive-or operation. This shows that proteins can execute signal processing operations that are more complex than those performed by individual threshold elements.; The essential requirement for the implementation of an algorithmically complex computer architecture is that there exist no simple rule that would allow derivation of the response of the architecture from the response of individual components. Using a significantly enhanced version of a simulation software previously implemented by us to study the interaction of conformational, kinetic (reaction-diffusion), structural, and dynamic (force) interactions that multienzyme systems can self-organize to yield novel response behavior.; We view the results reported as a stepping stone towards architectures of high algorithmic complexity that can transform difficult pattern grouping problems into simpler tasks manageable by conventional techniques. Devices of this type could serve as molecular co-processors that provide computational synergies for digital machines.