Structural and ultrametric properties of twenty(L-alanine)

Abstract

We study local energy minima of twenty(L-alanine). The minima are generated using high-temperature Molecular Dynamics and Chain-Growth Monte Carlo simulations, with subsequent minimization. We find that the lower-energy configurations are $ \alpha $-helices for a wide range of dielectric constant values $ (\epsilon = 1,10,80), $ and that there is no noticeable difference between the distribution of energy minima in $ \phi \psi $ space for different values of $ \epsilon . $ Ultrametricity tests show that lower-energy $ (\alpha $ -helical) $ \epsilon =1 $ configurations form a set which is ultrametric to a certain degree, providing evidence for the presence of fine structure among those minima. We put forward a heuristic argument for this fine structure. We also find evidence for ultrametricity of a different kind among $ \epsilon =10 $ and $ \epsilon =80 $ energy minima. We analyze the distribution of lengths of $ \alpha $-helical portions among the minimized configurations and find a persistence phenomenon for the $ \epsilon =1 $ ones, in qualitative agreement with previous studies of critical lengths. Email contact: [e-mail]