Valley filters using graphene blister defects from first principles.

Valleytronics, which makes use of the two valleys in graphenes, attracts considerable attention and a valley filter is expected to be the central component in valleytronics. We propose the application of the graphene valley filter using blister defects to the investigation of the valley-dependent transport properties of the Stone-Wales and blister defects of graphenes by density functional theory calculations. It is found that the intervalley transition from theKvalley to theK'valleys is completely suppressed in some defects. Using a large bipartite honeycomb cell (BHC) including several carbon atoms in a cell and replacing atomic orbitals with molecular orbitals in the tight-binding model, we demonstrate analytically and numerically that the symmetry between the A and B sites of the BHC contributes to the suppression of the intervalley transition. In addition, the universal rule for the atomic structures of the blisters suppressing the intervalley transition is derived. Furthermore, by introducing additional carbon atoms to graphenes to form blister defects, we can split the energies of the states at which resonant scattering occurs on theKandK'channel electrons. Because of this split, the fully valley-polarized current will be achieved by the local application of a gate voltage.

Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation.

Single-molecule measurements of biomaterials bring novel insights into cellular events. For almost all of these events, post-translational modifications (PTMs), which alter the properties of proteins through their chemical modifications, constitute essential regulatory mechanisms. However, suitable single-molecule methodology to study PTMs is very limited. Here we show single-molecule detection of peptide phosphorylation, an archetypal PTM, based on electrical measurements. We found that the phosphate group stably bridges a nanogap between metal electrodes and exhibited high electrical conductance, which enables specific single-molecule detection of peptide phosphorylation. The present methodology paves the way to single-molecule studies of PTMs, such as single-molecule kinetics for enzymatic modification of proteins as shown here.

Highly Reproducible Formation of a Polymer Single-Molecule Junction for a Well-Defined Current Signal.

Single-molecule devices attract much interest in the development of nanoscale electronics. Although a variety of functional single molecules for single-molecule electronics have been developed, there still remains the need to implement sophisticated functionalization toward practical applications. Given its superior functionality encountered in macroscopic materials, a polymer could be a useful building block in the single-molecule devices. Therefore, a molecular junction composed of polymer has now been created. Furthermore, an automated algorithm was developed to quantitatively analyze the tunneling current through the junction. Quantitative analysis revealed that the polymer junction exhibits a higher formation probability and longer lifetime than its monomer counterpart. These results suggest that the polymer provides a unique opportunity to design both stable and highly functional molecular devices for nanoelectronics.

Electrical Matching at Metal/Molecule Contacts for Efficient Heterogeneous Charge Transfer.

In a metal/molecule hybrid system, unavoidable electrical mismatch exists between metal continuum states and frontier molecular orbitals. This causes energy loss in the electron conduction across the metal/molecule interface. For efficient use of energy in a metal/molecule hybrid system, it is necessary to control interfacial electronic structures. Here we demonstrate that electrical matching between a gold substrate and π-conjugated molecular wires can be obtained by using monatomic foreign metal interlayers, which can change the degree of d-π* back-donation at metal/anchor contacts. This interfacial control leads to energy level alignment between the Fermi level of the metal electrode and conduction molecular orbitals, resulting in resonant electron conduction in the metal/molecule hybrid system. When this method is applied to molecule-modified electrocatalysts, the heterogeneous electrochemical reaction rate is considerably improved with significant suppression of energy loss at the internal electron conduction.

Self-energy matrices for electron transport calculations within the real-space finite-difference formalism.

The self-energy term used in transport calculations, which describes the coupling between electrode and transition regions, is able to be evaluated only from a limited number of the propagating and evanescent waves of a bulk electrode. This obviously contributes toward the reduction of the computational expenses in transport calculations. In this paper, we present a mathematical formula for reducing the computational expenses further without using any approximation and without losing accuracy. So far, the self-energy term has been handled as a matrix with the same dimension as the Hamiltonian submatrix representing the interaction between an electrode and a transition region. In this work, through the singular-value decomposition of the submatrix, the self-energy matrix is handled as a smaller matrix, whose dimension is the rank number of the Hamiltonian submatrix. This procedure is practical in the case of using the pseudopotentials in a separable form, and the computational expenses for determining the self-energy matrix are reduced by 90% when employing a code based on the real-space finite-difference formalism and projector-augmented wave method. In addition, this technique is applicable to the transport calculations using atomic or localized basis sets. Adopting the self-energy matrices obtained from this procedure, we present the calculation of the electron transport properties of C_{20} molecular junctions. The application demonstrates that the electron transmissions are sensitive to the orientation of the molecule with respect to the electrode surface. In addition, channel decomposition of the scattering wave functions reveals that some unoccupied C_{20} molecular orbitals mainly contribute to the electron conduction through the molecular junction.

[Visualization of Anterolateral Ligament of the Knee Using 3D Reconstructed Variable Refocus Flip Angle-Turbo Spin Echo T2 Weighted Image].

Anterolateral ligament (ALL) is one of the lateral structures in the knee that contributes to the internal rotational stability of tibia. ALL has been referred to in some recent reports to re-emphasize its importance. We visualized the ALL on 3D-MRI in 32 knees of 27 healthy volunteers (23 male knees, 4 female knees; mean age: 37 years). 3D-MRIs were performed using 1.5-T scanner [T(2) weighted image (WI), SPACE: Sampling Perfection with Application optimized Contrast using different flip angle Evolutions] in the knee extended positions. The visualization rate of the ALL, the mean angle to the lateral collateral ligament (LCL), and the width and the thickness of the ALL at the joint level were investigated. The visualization rate was 100%. The mean angle to the LCL was 10.6 degrees. The mean width and the mean thickness of the ALL were 6.4 mm and 1.0 mm, respectively. The ALL is a very thin ligament with a somewhat oblique course between the lateral femoral epicondyle and the mid-third area of lateral tibial condyle. Therefore, the slice thickness and the slice angle can easily affect the ALL visualization. 3D-MRI enables acquiring thin-slice imaging data over a relatively short time, and arbitrary sections aligned with the course of the ALL can later be selected.

First-principles calculation method for electron transport based on the grid Lippmann-Schwinger equation.

We develop a first-principles electron-transport simulator based on the Lippmann-Schwinger (LS) equation within the framework of the real-space finite-difference scheme. In our fully real-space-based LS (grid LS) method, the ratio expression technique for the scattering wave functions and the Green's function elements of the reference system is employed to avoid numerical collapse. Furthermore, we present analytical expressions and/or prominent calculation procedures for the retarded Green's function, which are utilized in the grid LS approach. In order to demonstrate the performance of the grid LS method, we simulate the electron-transport properties of the semiconductor-oxide interfaces sandwiched between semi-infinite jellium electrodes. The results confirm that the leakage current through the (001)Si-SiO_{2} model becomes much larger when the dangling-bond state is induced by a defect in the oxygen layer, while that through the (001)Ge-GeO_{2} model is insensitive to the dangling bond state.

Numerical solver for first-principles transport calculation based on real-space finite-difference method.

We propose an efficient procedure to obtain Green's functions by combining the shifted conjugate orthogonal conjugate gradient (shifted COCG) method with the nonequilibrium Green's function (NEGF) method based on a real-space finite-difference (RSFD) approach. The bottleneck of the computation in the NEGF scheme is matrix inversion of the Hamiltonian including the self-energy terms of electrodes to obtain the perturbed Green's function in the transition region. This procedure first computes unperturbed Green's functions and calculates perturbed Green's functions from the unperturbed ones using a mathematically strict relation. Since the matrices to be inverted to obtain the unperturbed Green's functions are sparse, complex-symmetric, and shifted for a given set of sampling energy points, we can use the shifted COCG method, in which once the Green's function for a reference energy point has been calculated the Green's functions for the other energy points can be obtained with a moderate computational cost. We calculate the transport properties of a C(60)@(10,10) carbon nanotube (CNT) peapod suspended by (10,10)CNTs as an example of a large-scale transport calculation. The proposed scheme opens the possibility of performing large-scale RSFD-NEGF transport calculations using massively parallel computers without the loss of accuracy originating from the incompleteness of the localized basis set.

First-principles study of spin-dependent transport through graphene/BNC/graphene structure.

: First-principles study on the electronic structure and transport property of the boron nitride sheet (BNC) structure, in which a triangular graphene flake surrounded by a hexagonal boron nitride sheet, is implemented. As the graphene flake becomes small and is more isolated by the boron nitride region, the magnetic ordering of the flake increases. When the BNC structure is connected to the graphene electrodes, the spin-polarized charge-density distribution appears only at the triangular graphene flake region, and the electronic structure of the graphene electrode is not spin polarized. First-principles transport calculation reveals that the transport property of the BNC structure is spin dependent.

Real-space calculations for electron transport properties of nanostructures.

Recent developments in the fabrication and investigation of conductors of atomic dimensions have stimulated a large number of experimental and theoretical studies on these nanoscale devices. In this paper, we introduce examples presenting the efficiencies and advantages of a first-principles transport calculation scheme based on the real-space finite-difference (RSFD) formalism and the overbridging boundary-matching (OBM) method. The RSFD method does not suffer from the artificial periodicity problems that arise in methods using plane-wave basis sets or the linear dependence problems that occur in methods using atomic basis sets. Moreover, the algorithm of the RSFD method is suitable for massively parallel computers and, thus, the combination of the RSFD and OBM methods enables us to execute first-principles transport calculations using large models. To demonstrate the advantages of this method, several applications of the transport calculations in various systems ranging from jellium nanowires to the tip and surface system of scanning tunneling microscopy are presented.

Mechanism of atomic-scale passivation and flattening of semiconductor surfaces by wet-chemical preparations.

Atomic arrangements of Si(001), Si(110) and 4H-SiC(0001) surfaces after wet-chemical preparations are investigated with scanning tunneling microscopy. Their passivated structures as well as the surface formation mechanisms in aqueous solutions are discussed. On both Si(001) and Si(110) surfaces, simple 1 × 1 phases terminated by H atoms are clearly resolved after dilute HF dipping. Subsequent etching with water produces the surfaces with 'near-atomic' smoothness. The mechanisms of atomic-scale preferential etching in water are described in detail together with first-principles calculations. Furthermore, 4H-SiC(0001), which is a hard material and where it is difficult to control the surface structure by solutions, is flattened on the atomic scale with Pt as a catalyst in HF solution. After a mechanism is proposed based on electroless oxidation, the flattened surface mainly composed of a 1 × 1 phase is analyzed. The obtained results will be helpful from various scientific and technological viewpoints.

Time-saving first-principles calculation method for electron transport between jellium electrodes.

We present a time-saving simulator within the framework of the density functional theory to calculate the transport properties of electrons through nanostructures suspended between semi-infinite electrodes. By introducing the Fourier transform and preconditioning conjugate-gradient algorithms into the simulator, a highly efficient performance can be achieved in determining scattering wave functions and electron-transport properties of nanostructures suspended between semi-infinite jellium electrodes. To demonstrate the performance of the present algorithms, we study the conductance of metallic nanowires and the origin of the oscillatory behavior in the conductance of an Ir nanowire. It is confirmed that the s-d(z²) channel of the Ir nanowire exhibits the transmission oscillation with a period of two-atom length, which is also dominant in the experimentally obtained conductance trace.

First-principles study of magnetic ordering of an Al infinite single-row atomic wire.

In this paper we present a detailed analysis of the atomic and spin-electronic structure of an Al infinite single-row atomic wire (Al-ISAW). Our work is based on ab initio self-consistent field calculations within the local density approximation, and we predict structural transformations during elongation using the norm-conserving (NC) and projector augmented-wave (PAW) pseudopotentials. The results obtained by the NC pseudopotential are in good agreement with those obtained by the PAW pseudopotential. We confirm that the Al-ISAW shows a metal-insulator transition and fractures when elongated beyond the equilibrium length. Then, a wire with antiferromagnetic ordering is found to be the lowest energetically. We find that the magnitude of spin polarization in the vicinity of nuclei is marginal and does not play an important role in the Peierls instability. The present results show that the NC pseudopotential can give an accurate physical picture of the atomic and spin-electronic structures of the Al-ISAW.

First-principles study of electron-conduction properties of C60 bridges.

The electron-conduction properties of fullerene-based nanostructures suspended between electrodes are examined by first-principles calculations based on the density functional theory. The electron conductivity of the C60-dimer bridge is low owing to the constraint of the junction of the molecules. When the fullerenes are doped electrons by being inserted Li atoms into the cages, the unoccupied state around the junction is filled and the conductivity can be significantly improved.

Relationship between the geometric structure and conductance oscillation in nanowires.

A theoretical analysis of the electron transport properties of plain and bumpy jellium nanowires suspended between semi-infinite jellium electrodes is carried out, and the possibility of the experimental observation of the conductance oscillation with a period longer than the two-atom length is discussed. In both the nanowires, the transmission trace as a function of the nanowire length exhibits oscillatory behaviour. The period of the oscillation of the plain nanowire corresponds to π divided by the Bloch wavenumber of the electrons in the nanowire region. However, the period of the oscillation of the bumpy nanowire results in the least common multiple of π divided by the Bloch wavenumber and the geometric period of the nanowire. Our result indicates that the conductance oscillation with a period longer than the two-atom length can be experimentally observed if nanowires without any defects are formed in experiments.

First-principles study of the electronic structures and dielectric properties of the Si/SiO(2) interface.

A first-principles study of the electronic structures and dielectric properties of Si/SiO(2) interfaces is implemented. Comparing the interfaces with and without defects, we explore the relationship between the defects and the dielectric properties, and also discuss the effect of the defects on the leakage current between the gate electrode and silicon substrate. We found that the electrons around the Fermi level percolate into the SiO(2) layers, which reduces the effective oxide thickness and is expected to enhance the leakage current. The dangling bonds largely affect the dielectric properties of the interface and the termination of dangling bonds by hydrogen atoms is successful in suppressing the increase of the dielectric constant.

A path-integration calculation method based on the real-space finite-difference scheme.

We propose a new path-integration calculation method to treat the time evolution of a wavefunction within the framework of the real-space finite-difference formalism, and also develop an effective scheme to compute the scattering wavefunction for an incident electron with arbitrary energy, in which an impulse wavefunction is adopted as an initial state of the time evolution. In this method, once the time evolution of the initial impulse wavefunction is calculated, all of the solutions in the scattering problem can be derived by means of Fourier analysis of the time-evolved wavefunction, which leads to a reduction of the calculation time. In order to test the applicability of our newly developed simulation procedures, we implemented simulations for the one-dimensional scattering problem. Each simulation showed the usefulness of the present scheme by yielding the steady scattering states in agreement with exact ones.

Order-N first-principles calculation method for self-consistent ground-state electronic structures of semi-infinite systems.

We present an efficient and highly accurate first-principles calculation method with linear system-size scaling to determine the self-consistent ground-state electron-charge densities of nanostructures suspended between semi-infinite bulks by directly minimizing the energy functional. By making efficient use of the advantages of the real-space finite-difference method, we can impose arbitrary boundary conditions on models and employ spatially localized orbitals. These advantages enable us to calculate the ground-state electron-charge densities in semi-infinite systems. Examples of electronic structure calculations for a one-dimensional case and a conductance calculation for sodium nanowires are presented. The calculated electronic structure of the one-dimensional system agrees well with the exact analytical solution, and the conduction properties of the sodium nanowires are consistent with experimental and other theoretical results. These results imply that our procedure enables us to accurately compute self-consistent electronic structures of semi-infinite systems.

First-principles study of electron-conduction properties of helical gold nanowires.

Multishell helical gold nanowires (HGNs) suspended between semi-infinite electrodes are found to exhibit peculiar electron-conduction properties by first-principles calculations based on the density functional theory. Our results that the numbers of conduction channels in the HGNs and their conductances are smaller than those expected from a single-atom row nanowire verify the recent experiment. In addition, we obtained a more striking result that, in the cases of thin HGNs, distinct magnetic fields are induced by the electronic current helically flowing around the shells. This finding indicates that the HGNs can be good candidates for nanometer-scale solenoids.