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Thermodynamics and structural properties of a confined HP protein determined by Wang-Landau simulation...

by Busara Pattanasiri, Ying Wai Li, David Landau, Thomas Wuest, Wannapong Triampo
Publication Type
Conference Paper
Journal Name
Journal of Physics: Conference Series
Publication Date
Page Number
012071
Volume
454
Conference Name
Conference on Computational Physics (CCP) 2012
Conference Location
Kobe, Japan
Conference Date
-

We used Wang-Landau sampling with inventive Monte Carlo moves to study the influence of surface characteristics on physical behavior of a hydrophobic-polar (HP) lattice protein model confined between two attractive surfaces. Three types of surfaces, namely, surfaces that attract: (a) all monomers; (b) only P monomers; or (c) only H monomers, have been considered. After obtaining the densities of states, we then found the thermodynamic and structural quantities, such as specific heat, number of surface contacts, and number of hydrophobic interaction pairs. A few conformational “transitions”, e.g., debridging process and hydrophobic core formation, can be identified based on an analysis of these quantities. Depending on the surface types, these transitions take place at different temperatures, while the ground state configurations show structural variations. These scenarios are confirmed by snapshots of typical states of the systems.