@Article{CiCP-24-810,
author = {Olivares-Quiroz , Luis and A. González-Olvera , Marcos},
title = {Minimum Energy Conformations of Self-Interacting Polymer Chains via Multipopulation Genetic Algorithms (MpGA)},
journal = {Communications in Computational Physics},
year = {2018},
volume = {24},
number = {3},
pages = {810--829},
abstract = {<p style="text-align: justify;">Identification of stable three-dimensional conformations in proteins and peptides
that correspond to minima in potential and free energy hypersurfaces has been
under intense scrutiny over the past decades since the paradigm structure-function
was proposed [1]. This classical paradigm states that most of biologically active conformations
in proteins and peptides can be associated with global minima energy states
on the energy hypersurface of the polypeptide chain [2, 3]. In this work we discuss the
onset of macroscopic minimum-energy conformations on small interacting peptides
composed by only two types of residues: hydrophobic (A) or polar (B). Based on a
previous work in 2D [4], we consider here an interacting three dimensional potential $V$ =$V_1$+$V_2$ where $V_1$ corresponds to a intramolecular bending potential between adjacent
residues whereas $V_2$ is a Lennard-Jones (LJ) type intermolecular potential with
both an attractive and repulsive part. In addition, the $V_2$ term can switch to repulsive
or attractive depending on the type of pair interaction AA, AB or BB considered. As a
novel approach to the standard geometric-based minimization methods [5–7], we propose
a Multipopulation Genetic Algorithm (MpGA) as a minimization algorithm [8].
The central advantage of this approach is a wider search on the energy hypersurface. In
order to test the validity of our method, we reproduced in excellent agreement the results
previously obtained in 2D by [4]. Our results show that in three dimensions our
method enlarges the number of stable macroscopic conformations found for a given
polypeptide. As an example of the role played by the interacting pairs AB, AA and BB, we discuss as well the case of small diblock polymers and quantify the degree of compactness
expected in the three dimensional structure as function of the composition of
the chain.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.OA-2017-0217},
url = {http://global-sci.org/intro/article_detail/cicp/12282.html}
}