Unbiased sampling of globular lattice proteins in three dimensions

Jesper Lykke Jacobsen (1, 2)

1 LPTMS - Laboratoire de Physique Théorique et Modèles Statistiques
2 SPhT - Service de Physique Théorique

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system.

Mots clés: lattice protein; hamiltonian walk; Monte Carlo

Domaines: Mécanique statistique [cond-mat.stat-mech]; Matière Molle [cond-mat.soft]; Biologie moléculaire

Jesper Lykke Jacobsen. Unbiased sampling of globular lattice proteins in three dimensions. 2007. ⟨hal-00172314⟩