124,008 research outputs found

    Modeling two-state cooperativity in protein folding

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    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

    Pollicott's Algorithm for Markovian Products of Positive Matrices

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    In a recent paper by M. Pollicott, an efficient algorithm was proposed, applying Ruelle's theory of transfer operators and Grothendieck's classical work on nuclear operators, to compute the Lyapunov exponent associated with the i.i.d. products of positive matrices. In this article, we generalise the result to Markovian products and correct some minor mistakes in Pollicott's original paper.Comment: 27 page