Brasi

Dados do Trabalho de Conclusão
UNIVERSIDADE FEDERAL DO ABC
NANOCIÊNCIAS E MATERIAIS AVANÇADOS (33144010006P9)

Simulating DNA sequencing in graphene nanopores: a QM/MM study to include dynamical and environmental eects
EKATERINA FILATOVA
DISSERTAÇÃO
21/02/2014

Determining the DNA sequence in the human genome in a fast, cheap and reliable way can be the key to predicting a number of genetic disorders. The cost of sequencing a whole genome, from scratch, has been dramatically reduced over the years. The National Institutes of Health proposed the "US$1000 genome challenge" in 2004, which would be the target cost for sequencing one entire human genome. The technologies inspired by this challenge are expected to be a new step in modern medicine. One of the promissing technologies is DNA sequencing using graphene nanopores. In such a device the transverse current is measured while the DNA strand passes through a graphene nanopore. In principle, this device could signi cantly reduce the time and the cost of DNA sequencing in comparison with the existing methods, as one could envision a single-step process where a full strand is sequenced in one go. In our project we proposed to simulate such a device. We were interested to see whereas dierent kind of pores help in stabilizing the bases. The second problem that we have adressed were if the transverse current changes when dierent nucleobases are inside the pore. In order to calculate electronic transport the system needed to be treated quantum mechanically. At the same time we were interested in dynamics of the DNA inside the pore and the eects of the water and ions. For this purporses we used a combination of density functional theory coupled to classical molecular dynamics to simulate the electronic structure of a graphene sheet as a DNA strand passes through a nanopore drilled in the sheet. The eects of the solvent and of counter-ions were included in the simulation via the classical part of the simulation (using QM/MM approach) whereas the rest is simulated quantum mechanically (using DFT). From dierent snapshots of the simulation we used the Non-equilibrium Greens functions methodology to calculate the electronic transport properties of this system. Our results show that pore termination and the presence of water tend to signi - cantly alter the results. In particular, dierent pores, either hydrogen or nitrogen lead to signi cantly dierent charge transfer eects. Water molecules, either classically or quantum-mechanically described tend to screen this charge transfer. From the transport point of view we also observe signi cant changes due to pore termination, but we also note that there is not enough distinction between bases in either case.

DNA, QM/MM
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107
INGLES
UFABC

Contexto
NANOCIÊNCIAS E MATERIAIS AVANÇADOS
SIMULAÇÃO E MODELAGEM
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Banca Examinadora
Orientador:
Alexandre Reily Rocha
O orientador principal compôs a banca do discente?
Sim
Nome Categoria
ROBERTO RIVELINO DE MELO MORENO Participante Externo
MAURICIO DOMINGUES COUTINHO NETO Participante Externo

Financiadores
Financiador - Programa Fomento Número de Meses
UNIVERSIDADE FEDERAL DO ABC - Pró reitoria de Pós Graduação 5
CONS NAC DE DESENVOLVIMENTO CIENTIFICO E TECNOLOGICO - Bolsa de Mestrado no País GM 18

Vínculo
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Não
Setor Bancário Norte, Quadra 2, Bloco L, Lote 06,
CEP 70040-020 - Brasília, DF CNPJ 00889834/0001-08 -
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