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 $\varphi \psi$ 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: [email protected]

arXiv commentSaclay-T93/025 Email: [email protected]

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