Replica Exchange Monte Carlo Simulations for Folding of Di-Block Polyampholyte

Yuri YAMADA*, Yosuke UEDA and Yosuke KATAOKA

Department of Materials Chemistry, College of Engineering, Hosei University
3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan

(Received: September 29, 2004; Accepted for publication: June 9, 2005; Published on Web: September 7, 2005)

We studied the folding of di-block polyampholyte (PA) using Replica Exchange Monte Carlo (REMC) simulations. The PA is a chain-like molecule model that is one of the typical cases of the complex systems with a huge number of local minima in the phase space. The REMC is suggested to search a global minimum of such complex systems. The potential function of our model PA consists of the Coulombic, the elastic, and the softcore interactions. We performed some REMC and the conventional annealing MC calculations for a comparison. As a result, we found the lowest energy configuration of the di-block PA as a stretched double-helical structure. The double helix was obtained not only by the REMC but also by the conventional MC, however the superiority of the REMC was not clearly established. It is considered that this result is caused by the potential function and its parameters.

Keywords: Replica exchange method, Monte Carlo simulation, Polyampholyte, Folding

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