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

Conference · Tue Jan 01 00:00:00 EST 2013

OSTI ID:1092237

Pattanasiri, Busara ^[1]; Li, Ying Wai ^[2]; Landau, David P ^[3]; Wuest, Thomas ^[4]; Triampo, Wannapong ^[1]

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1. Mahidol University, Bangkok 10400, Thailand
2. ORNL
3. University of Georgia, Athens, GA
4. Swiss Federal Research Institute, Switzerland

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 1092237
• Resource Relation: Conference: Conference on Computational Physics (CCP) 2012, Kobe, Japan, 20121014, 20121018
• Country of Publication: United States
• Language: English