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Master's Dissertation
DOI
https://doi.org/10.11606/D.60.2017.tde-04052017-093725
Document
Author
Full name
Pablo Andrei Silva
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
Ribeirão Preto, 2017
Supervisor
Committee
Caliri, Antonio (President)
Silva, Fernando Luis Barroso da
Araujo, Alexandre Suman de
Title in Portuguese
Simulação computacional distribuída: aplicação a problemas de folding de heteropolímeros
Keywords in Portuguese
Computação distribuída
Folding
Proteínas
Abstract in Portuguese
Nesta dissertação apresentamos o desenvolvimento de ferramentas computacionais dedicadas a racionalizar processos que envolvem simulações Monte Carlo e análises de suas aplicações; são evocados conceitos pertinentes às principais áreas envolvidas (computação, tecnologia da informação, matemática e física). São introduzidas e discutidas técnicas de simulação computacional distribuída e o método Monte Carlo, com ênfase à aplicação em heteropolímeros. Exemplos ilustrativos de aplicação da ferramenta também são providos, mediante simulações e análise dos resultados de três tipos de cadeias heteropoliméricas em rede regular: cadeia polar (todos monômeros polares); cadeia hidrofóbica (todos monômeros apolares); cadeia com mescla de monômeros polares e apolares (modelo HP). O propósito motivador deste trabalho é o estudo do problema de folding de heteropolímeros, o que inclui proteínas. Contudo, a ferramenta em questão, poderá ser generalizada e aplicada a praticamente todos os tipos de polímeros lineares em rede, pois o usuário poderá definir e implementar o modelo de cadeia que desejar
Title in English
Distributed computer simulation: Application on folding of heteropolymers problems
Keywords in English
Distributed computing
Folding
Proteins
Abstract in English
We present the development of computational tools dedicated to streamlining processes involving Monte Carlo simulations and analysis of some applications. Relevant concepts to the main areas involved (computation, information technology, mathematics and physics) are evoked. We introduce and discuss techniques of distributed computer simulation and Monte Carlo method with emphasis on heteropolymers. Illustrative examples of the application of the tool are also provided through simulations and analysis of results from three types of polymeric chains: polar chain (all polar monomers); hydrophobic chain (all nonpolar monomers); and a chain with mixture of polar and nonpolar monomers (HP model). The motivating purpose of this work is the study of the folding problem of heteropolymers, which includes proteins. However, the tool in question, can be generalized and applied to virtually all types of linear polymers network, once users can define and implement the chain models they want
 
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Publishing Date
2017-07-28
 
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