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Doctoral Thesis
DOI
10.11606/T.43.1998.tde-21022014-174534
Document
Author
Full name
Marta Maria Cassiano
Institute/School/College
Knowledge Area
Date of Defense
Published
São Paulo, 1998
Supervisor
Committee
Bisch, Paulo Mascarello (President)
Areas, Jose Alfredo Gomes
Freitas, Luiz Carlos Gomide
Ortmans, Isabelle
Ruggiero, José Roberto
Title in Portuguese
Dinâmica de Biomoléculas em Água: Simulações com Representação Explícita do Solvente
Keywords in Portuguese
Biologia molecular
Matéria condensada
Abstract in Portuguese
O programa THOR de dinâmica e mecânica molecular foi aprimorado com a introdução de técnicas que permitem a modelagem de sistemas biomoleculares na presença do solvente representado explicitamente. Essas técnicas incluem o emprego de condições de contorno periódicas, raio de corte, potencial eletrostático modificado e método shake para vínculos de distância. Além disso, a técnica da lista de vizinhos foi implementada devido ao grande aumento no número de átomos do sistema, pela inclusão explícita do solvente. Alguns sistemas foram modelados e a influência do solvente sobre suas propriedades conformacionais foi analisada, respondendo às expectativas baseadas em previsões teóricas e evidências experimentais.
Title in English
Dynamics Biomolecules Water Simulations Explicit Representation Solvent
Keywords in English
Condensed matter
Molecular biology
Abstract in English
The computational package THOR for molecular mechanic and dynamics simulation was improved by the introduction of techniques for modeling of biomolecular systems with explicit representation of solvent molecules. Those techniques include the application of periodic boundary conditions, the use of a cut-off sphere for the potential, with modifications in the electrostatic potential, and the utilization of the method shake to impose distance constraints. Furthermore, a neighbours list was implemented, due to the high number of atoms to be dealt with when the solvent is explicity represented. Simulations were performed on some systems of biological interest, and the influence of the solvent on their conformational properties was analysed. The results are in good agreement with theoretical previsions and experimental data.
 
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39942CassianoMaria.pdf (928.41 Kbytes)
Publishing Date
2014-02-24
 
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