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Protein collapse can be viewed as a dynamical phase transition, during whichnew scales and collective variables become excited while the old ones recedeand fade away. This causes formidable computational bottle-necks in approachesthat are based on atomic scale scrutiny. Here we consider an effectivedynamical Landau theory to model the folding process at biologically relevanttime and distance scales. We reach both a substantial decrease in the executiontime and improvement in the accuracy of the final configuration, in comparisonto more conventional approaches. As an example we inspect the collapse of HP35chicken villin headpiece subdomain, where there are detailed molecular dynamicssimulations to compare with. We start from a structureless, unbend anduntwisted initial configuration. In less than one second of wall-clock time ona single processor personal computer we consistently reach the native statewith 0.5 Angstrom root mean square distance (RMSD) precision. We confirm thatour folding pathways are indeed akin those obtained in recent atomic levelmolecular dynamics simulations. We conclude that our approach appears to havethe potential for a computationally economical method to accurately understandtheoretical aspects of protein collapse.

Soliton driven relaxation dynamics and universality in protein collapse