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arXiv · 2508.15547

Nonequilibrium Dynamics of the Helix-Coil Transition in Polyalanine

Maximilian Conradi·Henrik Christiansen·Suman Majumder·Fabio Müller·Wolfhard Janke
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Abstract

In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At the start of the transition short $3_{10}$-helices form, seemingly leading to the molecule becoming more aspherical midway through the collapse. After the completed collapse, the formation of $\alpha$-helices seems to become the prevalent ordering mechanism leading to helical bundles, a structure representative for the equilibrium behavior of longer chains. The dynamics of this transition is explored in terms of the power-law scaling of two associated relaxation times as a function of the chain length.

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Maximilian Conradi, Henrik Christiansen, Suman Majumder, Fabio Müller, Wolfhard Janke. 2025-08-21. Nonequilibrium Dynamics of the Helix-Coil Transition in Polyalanine. https://doi.org/10.1063/5.0245056

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