327 research outputs found

    Thermodynamics and Kinetics of Folding of a Small Peptide

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    We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at suitable temperatures. The results of these canonical simulations are compared with that of a generalized-ensemble simulation. Our work demonstrates that concepts of folding which were developed in the past for minimalist models hold also for this peptide when simulated with an all-atom force field

    Configuration Space for Random Walk Dynamics

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    Applied to statistical physics models, the random cost algorithm enforces a Random Walk (RW) in energy (or possibly other thermodynamic quantities). The dynamics of this procedure is distinct from fixed weight updates. The probability for a configuration to be sampled depends on a number of unusual quantities, which are explained in this paper. This has been overlooked in recent literature, where the method is advertised for the calculation of canonical expectation values. We illustrate these points for the 2d2d Ising model. In addition, we proof a previously conjectured equation which relates microcanonical expectation values to the spectral density.Comment: Various minor changes, appendix added, Fig. 2 droppe

    Yang-Lee zeros and the helix-coil transition in a continuum model of polyalanine

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    We calculate the Yang-Lee zeros for characteristic temperatures of the helix-coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm-Bragg theory and supports recent claims that polyalanine exhibits a true phase transition. New estimates for critical exponents are presented and the relation of our results to the Lee-Yang theorem is discussed.Comment: 15 pages and 5 figure
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