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Soft Matter and Biological Physics
Eur. Phys. J. E 2, 285-288

Characterization of heteropolymer collapse

Ø. Skjaeveland - K. Sneppen

NORDITA, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denemark
sneppen@nbivms.nbi.dk

Received 28 October 1999

Abstract
This paper proposes a method to enumerate and characterize the multidimensional rearrangement that a heteropolymer collapse represents. We follow the collapse using Langevin dynamics, and analyze folding pathways by measuring how matches to the final state develop, when viewed from each monomer in the polymer. The method is illustrated by following one specific heteropolymer, which was selected to have repeatable dynamical access to its final state. For this heteropolymer we found a nucleation event that precedes the correctly folded state.

PACS
45.50.-j Dynamics and kinematics of a particle and a system of particles - 87.14.Ee Proteins - 87.15.-v Biomolecules: structure and physical properties

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