Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem

Maxim N. Chernodub (1, 2) , Martin Lundgren (3) , Antti J. Niemi (1, 3)

1 LMPT - Laboratoire de Mathématiques et Physique Théorique
2 Department of Physics and Astronomy [Ghent]
3 Department of Physics and Astronomy [Uppsala]

We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three known nontrivial phases of polymers: At low temperatures the model is in a collapsed phase, at medium temperatures it is in a random walk phase, and at high temperatures it enters the self-avoiding random walk phase. By investigating the temperature dependence of the specific energy we confirm that the transition between the collapsed phase and the random walk phase is a phase transition, while the random walk phase and self-avoiding random walk phase are separated from each other by a cross-over transition. We also compare the predictions of the model to a phenomenological elastic energy formula, proposed by Huang and Lei to describe folded proteins.

Mots clés: Protein folding; phase structure; effective model

Domaines: Mécanique statistique [cond-mat.stat-mech]; Biophysique [physics.bio-ph]

Maxim N. Chernodub, Martin Lundgren, Antti J. Niemi. Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2011, 83, pp.011126. ⟨10.1103/PhysRevE.83.011126⟩. ⟨hal-00512014⟩