Geometrical effects on folding of macromolecules

Abstract

Geometrical effects on folding of macromolecules are investigated using linear chains with tetrahedral structure and hard-core interactions among its monomers; extra self-avoidance, namely, nontopological neighbor, is also considered. Our results were obtained by exact calculations using chains with small number N of monomers (up to 16) and by Monte Carlo simulation, using the ensemble growth method (EGM), for larger N. For some cases we provide a comparative study using two types of lattice and three different models. The original number of angle choices, ζ=3 (coordination number), is shown to be effectively reduced to ζeff=2.760, and the radius of gyration and end-to-end distance, for finite chains (N⩽140), scales with the number of monomers as Nν, where ν≅2/3. This is significantly larger than the corresponding value for the self-avoiding walk model, ν≅0.6. The relative frequency of monomer pair contacts was obtained by the exact Gibbs ensemble, involving all possible configurations. The same calculation using the EGM reveals ergodic difficulties; its significance on the setting up of pathways for folding of macromolecules is discussed.