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 $ α$-helices for a wide range of dielectric constant values $ (ε= 1,10,80), $ and that there is no noticeable difference between the distribution of energy minima in $ ϕψ$ space for different values of $ ε. $ Ultrametricity tests show that lower-energy $ (α$ -helical) $ ε=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 $ ε=10 $ and $ ε=80 $ energy minima. We analyze the distribution of lengths of $ α$-helical portions among the minimized configurations and find a persistence phenomenon for the $ ε=1 $ ones, in qualitative agreement with previous studies of critical lengths. Email contact: [e-mail]