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Doctoral Thesis
DOI
https://doi.org/10.11606/T.59.2010.tde-27012011-185248
Document
Author
Full name
Rafael Bertolini Frigori
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
Ribeirão Preto, 2010
Supervisor
Committee
Alves, Nelson Augusto (President)
Chahine, Jorge
Oliveira, Mario Jose de
Ruggiero, José Roberto
Silva, Fernando Luis Barroso da
Title in Portuguese
Simulações microcanônicas de proteínas
Keywords in Portuguese
Agregação
Enovelamento
Inequivalência de Ensembles
Monte Carlo
Proteínas
Simulações Microcanônicas
Transições de Fase
Abstract in Portuguese
Transições de fase termodinâmicas são usualmente estudadas por meio do ensemble canônico e estão associadas a sistemas macroscópicos. Entretanto, tem-se tornado cada vez mais frequente e importante o estudo de sistemas físicos pequenos, cujos alcances característicos das interações equivalem aos tamanhos dos sistemas. Nestes casos pode haver inequivalência entre grandezas físicas obtidas nos ensembles canônico e microcanônico. Encontramos inúmeros exemplos destes sistemas em diversas áreas da Física. Na área de matéria condensada temos, por exemplo, o modelo Blume-Capel com interações de alcance infinito. Neste modelo as soluções exatas canônica e microcanônica são inequivalentes. Este modelo é investigado nesta tese por meio de um ensemble interpolante, conhecido como gaussiano estendido, como uma aplicação teórica preliminar. Adicionalmente, empregamos o arcabouço mecânico-estatístico no estudo de certas biomoléculas com ampla importância biológica: proteínas. Atualmente o estudo do comportamento termodinâmico destas moléculas tem ficado restrito quase que exclusivamente a abordagem via ensemble canônico. Neste trabalho analisamos os resultados da etapa microcanônica de simulações multicanônicas procurando obter aspectos físicos de biomoléculas como os domínios Src SH3 (pdb: 1NLO) e as Príons humanas (pdb: 1HJM). Caracterizamos com esta abordagem as transições de fase de enovelamento e de agregação destes sistemas. Os resultados obtidos são interpretados à luz da termoestatística microcanônica, oferecendo um ponto de vista fenomenológico alternativo à abordagem usual.
Title in English
Microcanonical Simulations of Proteins
Keywords in English
Aggregation
Ensemble Inequivalence.
Folding
Microcanonical Simulations
Monte Carlo
Phase Transitions
Proteins
Abstract in English
Thermodynamic phase transitions are usualy studied by the canonical ensemble and they are associated to macroscopic systems. However, it is becoming more frequent and important the study of small physical systems: whose characteristic interaction-lengths are equivalent to system sizes. In these cases there can happen inequivalences among quantities computed im the canonical and microcanonical ensembles. There are inumerous examples of that systems in various areas of physics. In the field of condensed matter there is for instance the Blume-Capel model with infinite-range interactions. The canonical and microcanonical exact solutions of this model are inequivalents. That model is investigated on this thesis through an interpolating ensemble, known as the extended gaussian, as a preliminar theoretical application. Additionally, we have employed the statistic-mechanical framework to study some biomolecules of large biological interest: proteins. Nowadays the study of the thermodynamic behavior of that molecules has been restricted almost only to the canonical approach. However, in this work we have analysed by the microcanonical step of multicanonical simulations the physical aspects of biomolecules as the domain Src SH3 (pdb: 1NLO) and the human Prions (pdb: 1HJM). Thus, we characterize with this approach the phase transitions of folding and aggregation of that systems. The results obtained are interpretated under the light of the microcanonical thermostatistics, offering an alternative phenomenological viewpoint.
 
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Tese_RBFrigori.pdf (3.40 Mbytes)
Publishing Date
2011-03-04
 
WARNING: The material described below relates to works resulting from this thesis or dissertation. The contents of these works are the author's responsibility.
  • Frigori, R B, Rizzi, L G, and Alves, N A. The extended Gaussian ensemble and metastabilities in the Blume Capel model [doi:10.1088/1742-6596/246/1/012018]. Journal of Physics. Conference Series [online], 2010, vol. 246, p. 012018-7.
  • FRIGORI, R B, RIZZI, L G, and ALVES, N A. The extended Gaussian ensemble and metastabilities in the Blume–Capel model [doi:10.1088/1742-6596/246/1/012018]. Journal of Physics: Conference Series [online], 2010, vol. 246, p. 012018.
  • Frigori, R. B., Rizzi, L. G., and ALVES, N. A. Extended gaussian ensemble solution and tricritical points of a system with long-range interactions [doi:10.1140/epjb/e2010-00161-y]. The European Physical Journal. B, Condensed Matter Physics [online], 2010, vol. 75, p. 311-318.
  • FRIGORI, R. B., RIZZI, L. G., and ALVES, N. A.. Extended gaussian ensemble solution and tricritical points of a system with long-range interactions [doi:10.1140/epjb/e2010-00161-y]. The European Physical Journal B [online], 2010, vol. 75, n. 3, p. 311-318.
  • FRIGORI, Rafael B., RIZZI, Leandro G., and ALVES, Nelson A.. Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity [doi:10.1063/1.4773007]. The Journal of Chemical Physics [online], 2013, vol. 138, n. 1, p. 015102.
  • Frigori, R. B., e Alves, N A. Agregação de IAPP e a Diabetes-II sob a perspectiva de simulações microcanônicas. In Encontro de Física 2011, Foz do Iguaçu, 2011. Encontro de Física 2011., 2011. Resumo. Dispon?vel em: http://www.sbf1.sbfisica.org.br/eventos/enf/2011/sys/resumos/R1273-1.pdf.
  • Frigori, R. B., e Alves, N A. Microcanonical simulations of protein folding and aggregation. In XXXIII Encontro Nacional de Física da Matéria Condensada, Águas de Lindóia, 2010. XXXIII Encontro Nacional de Física da Matéria Condensada., 2010. Resumo. Dispon?vel em: http://www.sbf1.sbfisica.org.br/eventos/enfmc/xxxiii/sys/resumos/44.pdf.
  • Frigori, R. B., Rizzi, L. G., e Alves, N A. Extended Gaussian ensemble for the mean-field Blume-Capel model. In XI Latin American Workshop on Nonlinear Phenomena (LAWNP 09), Buzios, 2009. LAWNP'09 ABSTRACT BOOK., 2009. Resumo. Dispon?vel em: http://lawnp09.fis.puc-rio.br/abstracts_book.pdf.
  • Frigori, R. B., Rizzi, L. G., e ALVES, N. A. Extended Gaussian ensemble and phase transition in systems with long-range interactions. In XXXII Encontro Nacional de Física da Matéria Condensada, Águas de Lindóia, 2009. XXXII ENCONTRO NACIONAL DE FÍSICA DA MATÉRIA CONDENSADA., 2009. Resumo. Dispon?vel em: http://www.sbf1.sbfisica.org.br/eventos/enfmc/xxxii/prog/xxxii_enfmc_abstracts.pdf.
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