327 research outputs found
Thermodynamics and Kinetics of Folding of a Small Peptide
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
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 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
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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