Study of the Influence of Localized Vibrational Modes in Charge Transport Properties at Nanoscale Systems.

In molecular and atomic devices the interaction between electrons and ionic vibrations has an important role in electronic transport. The electron-phonon coupling can cause the loss of the electron's phase coherence, the opening of new conductance channels and the suppression of purely elastic ones. From the technological viewpoint phonons might restrict the efficiency of electronic devices by energy dissipation, causing heating, power loss and instability. The state of the art in electron transport calculations consists in combining ab initio calculations via Density Functional Theory (DFT) with Non-Equilibrium Green's Function formalism (NEGF). In order to include electron-phonon interactions, one needs in principle to include a self-energy scattering term in the open system Hamiltonian which takes into account the effect of the phonons over the electrons and vice versa. Nevertheless this term could be obtained approximately by perturbative methods. In the First Born Approximation one considers only the first order terms of the electronic Green's function expansion. In the Self-Consistent Born Approximation, the interaction self-energy is calculated with the perturbed electronic Green's function in a self-consistent way. In this work we describe how to incorporate the electron-phonon interaction to the SMEAGOL program (Spin and Molecular Electronics in Atomically Generated Orbital Landscapes), an ab initio code for electronic transport based on the combination of DFT + NEGF. This provides a tool for calculating the transport properties of materials' specific system, particularly in molecular electronics. Preliminary results will be presented, showing the effects produced by considering the electron-phonon interaction in nanoscale devices

Functionalized nanopore-embedded electrodes for rapid DNA sequencing

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Green's Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.Comment: 12 pages, 5 figure

Stretching of BDT-gold molecular junctions: thiol or thiolate termination?

It is often assumed that the hydrogen atoms in the thiol groups of a benzene-1,4-dithiol dissociate when Au-benzene-1,4-dithiol-Au junctions are formed. We demonstrate, by stability and transport properties calculations, that this assumption can not be made. We show that the dissociative adsorption of methanethiol and benzene-1,4-dithiol molecules on a flat Au(111) surface is energetically unfavorable and that the activation barrier for this reaction is as high as 1 eV. For the molecule in the junction, our results show, for all electrode geometries studied, that the thiol junctions are energetically more stable than their thiolate counterparts. Due to the fact that density functional theory (DFT) within the local density approximation (LDA) underestimates the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital by several electron-volts, and that it does not capture the renormalization of the energy levels due to the image charge effect, the conductance of the Au-benzene-1,4-dithiol-Au junctions is overestimated. After taking into account corrections due to image charge effects by means of constrained-DFT calculations and electrostatic classical models, we apply a scissor operator to correct the DFT energy levels positions, and calculate the transport properties of the thiol and thiolate molecular junctions as a function of the electrodes separation.Comment: 14 pages, 13 figures, to appear in Nanoscal

Finite-size correction scheme for supercell calculations in Dirac-point two-dimensional materials

Modern electronic structure calculations are predominantly implemented within the super cell representation in which unit cells are periodically arranged in space. Even in the case of non-crystalline materials, defect-embedded unit cells are commonly used to describe doped structures. However, this type of computation becomes prohibitively demanding when convergence rates are sufficiently slow and may require calculations with very large unit cells. Here we show that a hitherto unexplored feature displayed by several 2D materials may be used to achieve convergence in formation- A nd adsorption-energy calculations with relatively small unit-cell sizes. The generality of our method is illustrated with Density Functional Theory calculations for different 2D hosts doped with different impurities, all of which providing accuracy levels that would otherwise require enormously large unit cells. This approach provides an efficient route to calculating the physical properties of 2D systems in general but is particularly suitable for Dirac-point materials doped with impurities that break their sublattice symmetry

Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems : A QM/MM-NEGF Approach

The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green's function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent

Theoretical and computational aspects of electronic transport at the nanoscale

THESIS 8084The problem of electronic transport in systems comprising only a handful of atoms is one of the most exciting branches of nanoscience. The aim of this work is to address the issue of non-equilibrium transport at the nanoscale. At first, we lay down the theoretical framework based on Keldysh\u27s non-equilibrium Green function formalism. We show how this formalism relates to the Landauer-Buttiker formalism for the linear regime and how the current through a nanoscopic system can be related to a rate equation for which a steady state solution can be found. This formalism can be applied with different choices of Hamiltonian. In this work we choose to work with the Hamiltonian obtained from density functional theory which provides an accurate description of the electronic structure of nanoscopic systems. The combination of NEGFs and D FT results in Smeagol, a state-of-the-art tool for calculating materials-specific electronic transport properties of molecular devices as well as interfaces and junctions