Modeling two-state cooperativity in protein folding

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.Comment: 5 figure

Scalar, Vector and Tensor Harmonics on the Three-Sphere

Scalar, vector and tensor harmonics on the three-sphere were introduced originally to facilitate the study of various problems in gravitational physics. These harmonics are defined as eigenfunctions of the covariant Laplace operator which satisfy certain divergence and trace identities, and ortho-normality conditions. This paper provides a summary of these properties, along with a new notation that simplifies and clarifies some of the key expressions. Practical methods are described for accurately and efficiently computing these harmonics numerically, and test results are given that illustrate how well the analytical identities are satisfied by the harmonics computed numerically in this way.Comment: 14 pages, 9 figures, to appear in General Relativity and Gravitatio