We have developed an efficient simulation tool 'GOLLUM' for the computation of electrical, spin and thermal transport characteristics of complex nanostructures. The new multi-scale, multi-terminal tool addresses a number of new challenges and functionalities that have emerged in nanoscale-scale transport over the past few years. To illustrate the flexibility and functionality of GOL-LUM, we present a range of demonstrator calculations encompassing charge, spin and thermal transport, corrections to density functional theory such as local density approximation +U (LDA+U) and spectral adjustments, transport in the presence of non-collinear magnetism, the quantum Hall effect, Kondo and Coulomb blockade effects, finite-voltage transport, multi-terminal transport, quantum pumps, superconducting nanostructures, environmental effects, and pulling curves and conductance histograms for mechanically-controlled breakjunction experiments.New J. Phys. 16 (2014) 093029 J Ferrer et al that non-equilibrium transport codes are quite difficult to handle, in part because of their complex input data structures, which can create a steep learning curve, and also because they carry very heavy computational demands. As a consequence, we have devised the new code GOLLUM to be more user friendly, with simple and easy to understand input and output structures, and with no accuracy parameters to tune. We present now a short summary of the features and functionalities of the two programs to better appreciate their differences. SMEAGOL is a non-equilibrium Green's function (NEGF) program that computes the charge and spin transport properties of two-terminal junctions subject to a finite voltage bias. SMEAGOL cannot read a user-defined tight-binding Hamiltonian. Instead, it reads the meanfield Hamiltonian from the program SIESTA [27] and is tightly bound to the old versions of it. SMEAGOL can read from SIESTA Hamiltonians carrying non-collinear spin arrangements as well as the spin-orbit interaction. SIESTA and SMEAGOL have indeed been used successfully to simulate the magnetic anisotropies of atomic clusters [28][29][30] as well as the spin transport functionalities of several atomic chains and molecular junctions subjected to strong spin-orbit interaction [31,32]. However, SMEAGOL does not profit from other recent density functionals. Examples are the van der Waals family of functionals or those based on the local density approximation + U (LDA+U) approach.GOLLUM is a program that computes the charge, spin and electronic contribution to the thermal transport properties of multi-terminal junctions. In contrast to NEGF codes, GOLLUM is based on equilibrium transport theory, which means that it has a simpler structure, is faster, and consumes less memory. The program has been designed for user-friendliness and takes a considerable leap towards the realization of ab initio multi-scale simulations of conventional and more sophisticated transport functionalities.The simpler interface of GOLLUM allows it to read model tight-binding Hamiltonians. Fur...

To demonstrate the potential of nanopores in bilayer graphene for DNA sequencing, we computed the current-voltage characteristics of a bilayer graphene junction containing a nanopore and found that they change significantly when nucleobases are transported through the pore. To demonstrate the sensitivity and selectivity of example devices, we computed the probability distribution PX(β) of the quantity β representing the change in the logarithmic current through the pore due to the presence of a nucleobase X (X = adenine, thymine, guanine, or cytosine). We quantified the selectivity of the bilayer-graphene nanopores by showing that PX(β) exhibits distinct peaks for each base X. To demonstrate that such discriminating sensing is a general feature of bilayer nanopores, the well-separated positions of these peaks were shown to be present for different pores, with alternative examples of electrical contacts.

Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives. Furthermore, the ordering of the binding energies within the anthracene and pyrene series does not simply follow the electron affinities of the substituents. Energy barriers to rotation or displacement on the graphene surface are much lower than binding energies for adsorption and therefore at room temperature, although the molecules are bound to the graphene, they are almost free to move along the graphene surface. Binding energies can be increased by incorporating electrically inert side chains and are sensitive to the conformation of such chains. © 2014 AIP Publishing LLC.

ut. 8., Hungary Experimental correlation analysis and first-principles theory are used to probe the structure and evolution of Ag-CO-Ag single-molecule junctions, both before the formation, and after the rupture of the junctions. Two dimensional correlation histograms and conditional histograms demonstrate that prior to the single-molecule bridge configuration the CO molecule is already bound parallel to the Ag single-atom contact. This molecular precursor configuration is accompanied by the opening of additional conductance channels compared to the single-channel transport in pure Ag monoatomic junctions. To investigate the post-rupture evolution of the junction we introduce a cross-correlation analysis between the opening and the subsequent closing conductance traces. This analysis implies that the molecule is bound rigidly to the apex of one electrode, and so the same single-molecule configuration is re-established as the junction is closed. The experimental results are confirmed by ab initio simulations of the evolution of contact geometries, transmission eigenvalues and scattering wavefunctions.

We demonstrate a self-contained methodology for predicting conductance histograms of atomic and molecular junctions. Fast classical molecular-dynamics simulations are combined with accurate density functional theory calculations predicting both quantum transport properties and molecular-dynamics force field parameters. The methodology is confronted with experiments on atomic-sized indium nanojunctions. Beside conductance histograms the distribution of individual channel transmission eigenvalues is also determined by fitting the superconducting subgap features in the I-V curves. The remarkable agreement in the evolution of the channel transmissions demonstrates that the simulated ruptures are able to reproduce a realistic statistical ensemble of contact configurations, whereas simulations on selected ideal geometries show strong deviations from the experimental observations.