Simulação computacional do modelo HP generalizado para proteínas

• Ano de defesa: 2016
• Autor(a) principal: Santos, Fabrício de Sá Hora
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: por
• Instituição de defesa: Universidade Federal de Mato Grosso; Brasil; Instituto de Física (IF); UFMT CUC - Cuiabá; Programa de Pós-Graduação em Física
• Palavras-chave em Português: Monte Carlo; HP; PERM; Transições de fase; CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA; Phase transitions
• Link de acesso: http://ri.ufmt.br/handle/1/2502

We consider a generalized hydrophobic-polar model for proteins on square and cubic lat- tices. Besides the attraction between nonbonded hydrophobic monomers, the present model also takes into account an interaction between hydrophobic and polar units. By using the pruned-enriched Rosenbluth method (PERM), we investigate a specific poly- mer sequence composed of 42 monomers that has been proposed to simulate the physical properties of the parallel β-helix of pectate lyase C. For each temperature, the total number of generated chains varies from 106 to 107 . Physical observables such as speci- fic heat, total energy, end-to-end distance, radius of gyration, and the average number of hydrophobic-hydrophobic and hydrophobic-polar contacts, are evaluated for different values of the parameter s, which corresponds to the ratio between the hydrophobic-polar and the hydrophobic-hydrophobic contact energies. Eventually, a pseudo-phase diagram in the space of temperature and the ratio of contact energy scales is constructed.