Unbiased sampling of globular lattice proteins in three dimensions.
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)=262 144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system.
Jacobsen
Jesper Lykke
JL
LPTMS, UMR CNRS 8626, Université Paris Sud, 91405 Orsay, France.
D000465:Algorithms; D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
D011506:Proteins