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

The triangle-free graphs with rank 6

The rank of a graph G is defined to be the rank of its adjacency matrix A(G). In this paper we characterize all connected triangle-free graphs with rank 6

Minimality of p-adic rational maps with good reduction

A rational map with good reduction in the field $\mathbb{Q}\_p$ of $p$-adic numbers defines a $1$-Lipschitz dynamical system on the projective line $\mathbb{P}^1(\mathbb{Q}\_p)$ over $\mathbb{Q}\_p$. The dynamical structure of such a system is completely described by a minimal decomposition. That is to say, $\mathbb{P}^1(\mathbb{Q}\_p)$ is decomposed into three parts: finitely many periodic orbits; finite or countably many minimal subsystems each consisting of a finite union of balls; and the attracting basins of periodic orbits and minimal subsystems. For any prime $p$, a criterion of minimality for rational maps with good reduction is obtained. When $p=2$, a condition in terms of the coefficients of the rational map is proved to be necessary for the map being minimal and having good reduction, and sufficient for the map being minimal and $1$-Lipschitz. It is also proved that a rational map having good reduction of degree $2$, $3$ and $4$ can never be minimal on the whole space $\mathbb{P}^1(\mathbb{Q}\_2)$.Comment: 21 page