Evolution of Protein Interactions

A local optimisation method has been applied to the problem of folding and interaction between protein-like structures. These are composed of a randomly selected sequence of amino acids that are linked together to form linear polymers in three dimensions. The objective function chosen for optimisation is the potential energy given by a toy protein model. Convergence is reached as soon as the value for the objective function falls below a xed value given by an equilibrium temperature, Teq. Structures fold to minimise their objective function at a given rate, Frate, ranging from global optimisation of the whole structure to linear minimisation at every amino acid. The interaction between diierent structures is also modelled and optimised giving a whole range of local repulsion/attraction behaviours.

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