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Hibrid QM/MM methods applied to electronic transport simulations of graphene: applications to DNA sequencing and protein detection

Grant number: 13/02112-0
Support type:Regular Research Grants
Duration: June 01, 2013 - May 31, 2015
Field of knowledge:Physical Sciences and Mathematics - Physics - Condensed Matter Physics
Principal Investigator:Alexandre Reily Rocha
Grantee:Alexandre Reily Rocha
Home Institution: Instituto de Física Teórica (IFT). Universidade Estadual Paulista (UNESP). Campus de São Paulo. São Paulo , SP, Brazil
Assoc. researchers:Antonio José Roque da Silva ; Gustavo Troiano Feliciano ; Jeconias Rocha Guimarães ; Ralph Hendrik Scheicher ; Rodrigo Garcia Amorim


Our constant drive for the miniaturization of electronic devices, introduces both the perspective of new technologies and raises a number of important questions from the point of view of basic science. At the nanoscopic scale these systems behave in a fundamentally different manner and require a deeper understanding from a experimental as well as theoretical point of view. Considering the electronic transport, the mechanisms driving the effects observed at these scales are entirely quantum mechanical, which increase the complexity, but also opens up a wide range of new phenomena that can be explored. A deep knowledge of these mechanisms can lead to devices that can be applied in fields that range from electronics to biology.The aim of this project is to study, via computer simulations, the electronic transport properties of nanoscale systems based on graphene for applications in biotechnology. In particular two devices will be designed and simulated: a DNA sequencing device using graphene nanopores and a protein biosensor using functionalized graphene. In all cases the full structure of the biomolecules as well as the solvent will be taken into consideration. This way, effect which can influence a hypothetical working device will be included. This means that we intend to simulate, using atomistic methods, the electronic transport properties of systems containing tens of thousands of atoms. In order to accomplish this feat a methodology wich combines classical molecular dynamics and {\it ab initio} density functional theory methods will be used (in what is conventionally named QM/MM). This way it is possible to obtain the electronic structure of graphene and part of the biomolecule - the active region - using quantum mechanical methods that take into consideration the dynamical effects of the system, the solvent and the counter ions via a classical electrostatic potential. Thereafter we will join this tool with Non-equilibrium Green's functions which allows one to obtain the electronic transport properties of the system.This project thus combines the development of a tool for simulating electronic transport in biological systems, issues pertaining applied physics as one aims to develop nanoscopic devices and finally basic science questions associated with effects of solvents in nanoscopic systems. Therefere we have a number of interesting issues under the same umbrella in a proposal that aims to develop and simulate biomolecular-detection devices using graphene and a common methodology. (AU)

Scientific publications (4)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
ANDRADE-FILHO, T.; MARTINS, TIAGO CARVALHO; FERREIRA, FABIO FURLAN; ALVES, WENDEL ANDRADE; ROCHA, ALEXANDRE REILY. Water-driven stabilization of diphenylalanine nanotube structures. THEORETICAL CHEMISTRY ACCOUNTS, v. 135, n. 8 JUL 11 2016. Web of Science Citations: 13.
PRASONGKIT, JARIYANEE; FELICIANO, GUSTAVO T.; ROCHA, ALEXANDRE R.; HE, YUHUI; OSOTCHAN, TANAKORN; AHUJA, RAJEEV; SCHEICHER, RALPH H. Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene. SCIENTIFIC REPORTS, v. 5, DEC 4 2015. Web of Science Citations: 20.
FELICIANO, GUSTAVO T.; SANZ-NAVARRO, CARLOS; COUTINHO-NETO, MAURICIO DOMINGUES; ORDEJON, PABLO; SCHEICHER, RALPH H.; ROCHA, ALEXANDRE REILY. Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore. PHYSICAL REVIEW APPLIED, v. 3, n. 3 MAR 9 2015. Web of Science Citations: 29.
DO PRADO, VANIA MENDES; SEICEIRA, RAFAEL CARDOSO; PITALUGA, JR., ALTIVO; ANDRADE-FILHO, TARCISO; ALVES, WENDEL ANDRADE; ROCHA, ALEXANDRE REILY; FERREIRA, FABIO FURLAN. Elucidating the crystal structure of the antimalarial drug (+/-)-mefloquine hydrochloride: a tetragonal hydrated species. JOURNAL OF APPLIED CRYSTALLOGRAPHY, v. 47, n. 4, p. 1380-1386, AUG 2014. Web of Science Citations: 1.

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