Simulating electronic transport using QM/MM and adaptive Monte Carlo methods: applications to DNA Chips

• Grant number: 15/26862-4
• Support Opportunities: Scholarships abroad - Research
• Start date: September 01, 2016
• End date: July 31, 2017
• Field of knowledge: Physical Sciences and Mathematics - Physics - Condensed Matter Physics
• Principal Investigator: Alexandre Reily Rocha
• Grantee: Alexandre Reily Rocha
• Host Investigator: Heather J. Kulik
• Host Institution: Instituto de Física Teórica (IFT). Universidade Estadual Paulista (UNESP). Campus de São Paulo. São Paulo , SP, Brazil
• Institution abroad: Massachusetts Institute of Technology (MIT), United States

Abstract

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. Graphene, a two-dimensional honeycomb arrangement of carbon atoms could be the material of the future. With remarkable electronic properties it might be the scaffold of a number of new devices. This is particularly true in the field of biological sensors whereby one uses changes in a material's properties to detect biomolecules.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 we plan to design and simulate an all-electronic DNA-chip.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. We will also address the problem of diffusion of quantum mechanical water molecules in the first solvation layer using a Monte Carlo method combined with QM/MM. Thereafter we join this tool with Non-equilibrium Green's functions for the calculation of the electronic transport properties of the system. point of view. 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 we plan to design and simulate an all-electronic DNA-chip.In order to accomplish this feat a methodology wich combines classical molecular dynamics and ab initio density functional theory methods will be used (in what is conventionallynamed 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 takeinto consideration the dynamical effects of the system, the solvent and the counter ions, via a classical electrostatic potential. We will also address the problem of diffusion of quantum mechanical water molecules in the first solvation layer using a Monte Carlo method combined with QM/MM. Thereafter we join this tool with Non-equilibrium Green's functions for the calculation of the electronic transport properties of the system.

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)

DE SOUZA, FABIO A. L.; AMORIM, RODRIGO G.; PRASONGKIT, JARIYANEE; SCOPEL, WANDERLA L.; SCHEICHER, RALPH H.; ROCHA, ALEXANDRE R.. Topological line defects in graphene for applications in gas sensing. Carbon, v. 129, p. 803-808, APR 2018. (16/01343-7, 15/26862-4)

ROCHA, C. G.; ROCHA, A. R.; VENEZUELA, P.; GARCIA, J. H.; FERREIRA, M. S.. Finite-size correction scheme for supercell calculations in Dirac-point two-dimensional materials. SCIENTIFIC REPORTS, v. 8, JUN 19 2018. (16/01343-7, 15/26862-4)

GARCIA-BASABE, YUNIER; ROCHA, ALEXANDRE R.; VICENTIN, FLAVIO C.; VILLEGAS, CESAR E. P.; NASCIMENTO, REGIANE; ROMANI, ERIC C.; DE OLIVEIRA, EMERSON C.; FECHINE, GUILHERMINO J. M.; LI, SHISHENG; EDA, GOKI; et al. Ultrafast charge transfer dynamics pathways in two-dimensional MoS2-graphene heterostructures: a core-hole clock approach. Physical Chemistry Chemical Physics, v. 19, n. 44, p. 29954-29962, NOV 28 2017. (12/24227-1, 15/26862-4, 12/50259-8, 11/11973-4)

FERREIRA, M. S.; ROCHA, C. G.; LAWLOR, J. A.; VENEZUELA, P.; AMORIM, R. G.; ROCHA, A. R.. Commensurability effect on the electronic structure of carbon nanostructures: Impact on supercell calculations in nanotubes. EPL, v. 117, n. 2, JAN 2017. (15/26862-4, 11/11973-4)