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Sandwich-molecular wires consisting of europium and cyclooctatetraene (Cot) were grown in situ on the moiré of graphene with Ir(110). The moiré templates a uniaxial alignment of monolayer EuCot nanowire carpets and multilayer films with the EuCot wire axis along the [001] direction of the Ir substrate. Using angle-resolved photoemission spectroscopy, we investigate the band structure of the wire carpet films. While π-derived bands were not observed experimentally, we find a flat band 1.85 eV below the Fermi energy. Using density-functional theory and X-ray photoelectron spectroscopy and replacing europium through barium in the sandwich-molecular wires, it is concluded that the flat band is derived from Eu 4f states weakly mixed with Eu 5d states and slightly overlapping with Cot π states. X-ray magnetic circular dichroism is employed to characterize the magnetic properties of the EuCot wire carpet films at low temperatures. Clear evidence for an easy-axis magnetization along the wires is found.

The organometallic on-surface synthesis of the eight-membered sp2 carbon-based ring cyclooctatetraene (C8H8, Cot) with the neighboring rare-earth elements ytterbium and thulium yields fundamentally different products for the two lanthanides, when conducted on graphene (Gr) close to the charge neutrality point. Sandwich-molecular YbCot wires of more than 500 Å length being composed of an alternating sequence of Yb atoms and upright-standing Cot molecules result from the on-surface synthesis with Yb. In contrast, repulsively interacting TmCot dots consisting of a single Cot molecule and a single Tm atom result from the on-surface synthesis with Tm. While the YbCot wires are bound through van der Waals interactions to the substrate, the dots are chemisorbed to Gr via the Tm atoms being more electropositive compared to Yb atoms. When the electron chemical potential in Gr is substantially raised (n-doping) through backside doping from an intercalation layer, the reaction product in the synthesis with Tm can be tuned to TmCot sandwich-molecular wires rather than TmCot dots. By use of density functional theory, it is found that the reduced electronegativity of Gr upon n-doping weakens the binding as well as the charge transfer between the reaction intermediate TmCot dot and Gr. Thus, the assembly of the TmCot dots to long TmCot sandwich-molecular wires becomes energetically favorable. It is thereby demonstrated that the electron chemical potential in Gr can be used as a control parameter in an organometallic on-surface synthesis to tune the outcome of a reaction.

A single-crystal sheet of graphene is synthesized on the low-symmetry substrate Ir(110) by thermal decomposition of C$_2$H$_4$ at 1500 K. Using scanning tunneling microscopy, low-energy electron diffraction, angle-resolved photoemission spectroscopy, and ab initio density functional theory the structure and electronic properties of the adsorbed graphene sheet and its moir\'e with the substrate are uncovered. The adsorbed graphene layer forms a wave pattern of nm wave length with a corresponding modulation of its electronic properties. This wave pattern is demonstrated to enable the templated adsorption of aromatic molecules and the uniaxial growth of organometallic wires. Not limited to this, graphene on Ir(110) is also a versatile substrate for 2D-layer growth and makes it possible to grow epitaxial layers on ureconstructed Ir(110)., Comment: 34 pages, 14 figures

From macroscopic heavy-duty permanent magnets to nanodevices, the precise control of the magnetic properties in rare-earth metals is crucial for many applications used in our daily life. Therefore, a detailed understanding and manipulation of the 4f-metals' magnetic properties are key to further boosting the functionalization and efficiency of future applications. We present a proof-of-concept approach consisting of a dysprosium-iridium surface alloy in which graphene adsorption allows us to tailor its magnetic properties. By adsorbing graphene onto a long-range ordered two-dimensional dysprosium-iridium surface alloy, the magnetic 4f-metal atoms are selectively lifted from the surface alloy. This selective skyhook effect introduces a giant magnetic anisotropy in dysprosium atoms as a result of manipulating its geometrical structure within the surface alloy. Introducing and proving this concept by our combined theoretical and experimental approach provides an easy and unambiguous understanding of its underlying mechanism. Our study sets the ground for an alternative path on how to modify the crystal field around 4f-atoms and therefore their magnetic anisotropies.

The local dimerization and dedimerization of C60 molecules in a C60 thin film using a scanning tunneling microscopy (STM) [M. Nakaya et al. Adv. Mater. 22, 1622 (2010)] are promising techniques for realizing ultradense data storages. However, the detailed mechanism of the reversible topochemical reactions has not been clarified yet. Based on the density functional theory we explain the mechanism in terms of charging and electric-field effects on the molecules. The total-energy calculations reveal that when the C60 molecules in the surface layer are negatively charged, the dimerization is promoted and inter-layer dimers composed of two C60 molecules in different layers are formed dominantly over in-plane dimers. When the thin-film surface is positively charged or the inter-layer dimers are exposed to a strong electric field, a C60 monomer pair becomes more stable than a C60 dimer, and the dedimerization is promoted. These results predict competition between the dimerization and dedimerization of a negatively charged C60 binary system in a strong electric field, which is indeed confirmed by our STM experiments. In addition, the dedimerization induced in the electric field is discussed from the viewpoints of the intermolecular donor-acceptor interaction and the charge-dipole relaxation of a C60 binary system.

The computational cost of calculating the self-energy matrices used in first-principles transport-property calculations is proportional to the cube of the lateral length of electrodes. Therefore, the clarification of transport properties is difficult because the system size increases when the transition region structure becomes complicated owing to lattice defects such as adatoms, substitutional doping, vacancies, and lattice distortions. In this study we propose an improved procedure to calculate the self-energy matrices in the electrodes to reduce computational costs of electron-transport calculations without degrading the accuracy. This procedure accurately reproduces the self-energy matrices of the supercell-structured electrodes from the generalized Bloch states of the primitive unit cell. Furthermore, we carry out electron-transport calculations on fluorine-adsorbed graphene sheets connected to semi-infinite graphene electrodes and find the dependence of the electron transmission on the symmetry of the arrangement of adatoms perpendicular to the transport direction.

Large scale electronic structure calculations require modern high performance computing (HPC) resources and, as important, mature HPC applications that can make efficient use of those. Real-space grid-based applications of Density Functional Theory (DFT) using the Projector Augmented Wave method (PAW) can give the same accuracy as DFT codes relying on a plane wave basis set but exhibit an improved scalability on distributed memory machines. The projection operations of the PAW Hamiltonian are known to be the performance critical part due to their limitation by the available memory bandwidth. We investigate on the utility of a 3D factorizable basis of Hermite functions for the localized PAW projector functions which allows to reduce the bandwidth requirements for the grid representation of the projector functions in projection operations. Additional on-the-fly sampling of the 1D basis functions eliminates the memory transfer almost entirely. For an quantitative assessment of the expected memory bandwidth savings we show performance results of a first implementation on GPUs. Finally, we suggest a PAW generation scheme adjusted to the analytically given projector functions., Comment: 11 pages, 10 figures, conference contribution at PASC19

The oligothiophene molecule family has a tunable energy gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) as the function of the number of thiophene units. This tunability is of great use to controlling carrier injection at the molecule/electrode interface in molecule-based electronic devices. We investigate quaterthiophene (4T) and septithiophene (7T) molecules adsorbed on Cu(111) surfaces by scanning tunneling microscopy and spectroscopy (STM and STS) at room temperature. Both oligothiophene molecules form one-dimensional (1D) chain structures on Cu(111), and each molecule in the 1D structures is observed as a row of bright ovals corresponding to thiophene units. Observed features of 4T and 7T molecules differ from those expected from the HOMO and LUMO of the free-standing molecules, and density-functional calculations of a 4T molecule together with a Cu(111) surface reproduce the experimental STM images as they reflect characteristic spatial distribution of adsor...

A complex band structure describes the dispersion relation not only of propagating bulk states but also of evanescent ones, both of which are together referred to as generalized Bloch states and are important for understanding the electronic nature of solid surfaces and interfaces. On the basis of the real-space finite-difference formalism within the framework of the density functional theory, we formulate the Kohn-Sham equation for generalized Bloch wave functions as a generalized eigenvalue problem without using any Green's function matrix. By exploiting the sparseness of the coefficient matrices and using the Sakurai-Sugiura projection method, we efficiently solve the derived eigenvalue problem for the propagating and slowly decaying/growing evanescent waves, which are essential for describing the physics of surface/interface states. The accuracy of the generalized Bloch states and the computational efficiency of the present method in solving the eigenvalue problem obtained are compared with those by other methods using the Green's function matrix. In addition, we propose two computational techniques to be combined with the Sakurai-Sugiura projection method and achieve further improvement in the accuracy and efficiency. Complex band structures are calculated with the present method for single- and multiwall carbon nanotubes, and the interwall hybridization and branch points of evanescent electronic states observed in the imaginary parts of the band structures are also discussed.

The wave-function-matching (WFM) technique for first-principles transport-property calculations was bettered by S\o{}rensen et al. so as to exclude rapidly decreasing evanescent waves [S\o{}rensen et al., Phys. Rev. B 77, 155301 (2008)]. In their method, the translational invariance of the transmission probability is not preserved when moving the matching planes between electrode and transition regions, and the sum of transmission and reflection probabilities does not agree with the number of transport channels in the transition region. The lack of the translational invariance is caused by the overlap of the layers between the electrode and transition regions. We reformulate the WFM method by removing the layer overlap, and the translational invariance of the transmission probability becomes preserved. On the other hand, the error in the sum of transmission and reflection probabilities is attributed to using pseudoinverses that is accompanied by the exclusion of rapidly decreasing evanescent waves. We introduce a formulation to calculate the transmission/reflection probability without the pseudoinverses, resulting in that the sum of the transmission and reflection probabilities exactly agrees with the number of channels, and the accuracy is largely improved. In addition, we prove that the accuracy in the transmission probability obtained by our WFM technique is comparable to that obtained by a nonequilibrium Green's function method. Furthermore, we carry out electron transport calculations on two-dimensional graphene sheets embedded with B-N line defects sandwiched between a pair of semi-infinite graphene electrodes and find the dependence of the electron transmission on the transverse momentum perpendicular to the transport direction.

When a solid polymer water electrolyzer (SPWE) is operated under high-pressure conditions, a large pressure difference occurs between the anode and cathode. This causes crossover of produced gas, especially hydrogen gas, leading to a decrease in the production efficiency of an SPWE. As a countermeasure against gas crossover, water should be supplied into the cathode channel, as well as into the anode channel, because the water flow will facilitate the drainage of hydrogen gas outside of the cell, resulting in decreased crossover and increased efficiency of the SPWE. This countermeasure is evaluated by observing SPWE operation at a pressure of 2 MPa, with a visualization of hydrogen bubbles in the cathode channel. The evaluation revealed that supplying water into the cathode channel increases the efficiency by several percent at 0.33 A/cm 2 . Further, the visualization of the hydrogen bubbles revealed an enhancement in the separation of hydrogen bubbles from the surface of the current supplier. This suggests that additional water flow can increase the hydrogen production efficiency through promoting bubble detachment.

Functionalized naphthalene diimides (NDIs) are attractive candidates as small molecule acceptors for various molecular electronic applications due to their reversible two-step one-electron reductions at relatively low potentials. Here, we utilize low-temperature scanning tunneling microscopy (STM) to study the spatial extent and the electronic structure of 2,7-dibenzyl 1,4,5,8-naphthalenetetracarboxylic diimide (BNTCDI) adsorbed on the Pt(111) surface. We succeeded to map in real space the electronic structure of this three-dimensional (3D) molecule with orbital resolution, and thus were able to image an in-plane π-nodal plane located at the benzyl side arms. Furthermore, on the basis of the comparison of voltage dependent STM images and ab initio density functional theory simulations, we are able to explain the STM features of BNTCDI in terms of a convolution between its 3D shape and electronic structure. Importantly, for this weakly coupled molecule on the Pt(111) substrate, the intramolecular N···H–C hydrogen bonds (i) stabilize the protruding π-systems of the benzyl groups perpendicular to the flat NDI core and (ii) open an effective transport path around Fermi energy.

We propose an efficient computational method for evaluating the self-energy matrices of electrodes to study ballistic electron transport properties in nanoscale systems. To reduce the high computational cost incurred in large systems, a contour integral eigensolver based on the Sakurai-Sugiura method combined with the shifted biconjugate gradient method is developed to solve exponential-type eigenvalue problem for complex wave vectors. A remarkable feature of the proposed algorithm is that the numerical procedure is very similar to that of conventional band structure calculations. We implement the developed method in the framework of the real-space higher-order finite difference scheme with nonlocal pseudopotentials. Numerical tests for a wide variety of materials validate the robustness, accuracy, and efficiency of the proposed method. As an illustration of the method, we present the electron transport property of the free-standing silicene with the line defect originating from the reversed buckled phases., Comment: 36 pages, 13 figures, 2 tables

In this article, we briefly overview our experimental and theoretical studies aimed to investigate the electronic structure and the transport properties of several carboxylates chemisorbed on the Cu(110) surface. In particular, we have theoretically explored the possibility to chemically functionalize a carboxylate–Cu(110) system to specifically tune its electronic structure. Experimentally, it could be proven that the transport properties of the carboxylate–Cu(110) interface indeed revealed specific features in the d spectra corresponding to the used functionalization process. Moreover, the d spectra can be used to identify specific adsorption geometries or conformations of carboxylates on Cu(110). Furthermore, transport calculations for molecules with different anchoring groups between two Cu(110) electrodes are also discussed. Schematic view of a STM tip probing a carboxylate molecule chemisorbed on the Cu(110) surface with the corresponding energy level alignment in the case of a zero bias voltage.

We present details of our effective computational methods based on the real-space finite-difference formalism to elucidate electronic and magnetic properties of the two-dimensional (2D) materials within the framework of the density functional theory. The real-space finite-difference formalism enables us to treat truly 2D computational models by imposing individual boundary condition on each direction. The formulae for practical computations under the boundary conditions specific to the 2D materials are derived and the electronic band structures of 2D materials are demonstrated using the proposed method. Additionally, we introduce other first-principles works on the MoS2 monolayer focusing on the modulation of electronic and magnetic properties originating from lattice defects., 39 pages, 8 figures, 1 table

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.

Adsorption and electronic structure of octithiophene (8T) molecules on Cu(III) and Au(III) surfaces are investigated using scanning tunneling microscopy (STM) and spectroscopy (STS) at room temperature. We find a large difference in adsorption behavior of 8T molecules on the two surfaces. At the initial stage of adsorption, 8T molecules are stabilized in the form of molecular chain on a terrace of Cu(III), whereas neither such chain structure nor isolated 8T molecules have been observed on a terrace of Au(III). By increasing the amount of adsorbed molecules, a disordered monolayer film is formed on Cu(III) while a well-ordered monolayer film is formed on Au(III). From the spectroscopic investigations using bias-dependent STM images and STS spectra and by comparing the data with theoretical calculations, it is found that the electronic property of 8T molecules in the molecular chain on Cu(III) is different from that of a free-standing 8T molecule while that in the monolayer film on Au(III) keeps original character of the free-standing 8T molecule. The present study shows that adsorption of 8T molecules on Cu(III) results in a formation of adsorption-induced states near the Fermi level.

The initial stage of the adsorption of octithiophene (8T) molecules on a Cu(111) surface is investigated using a scanning tunneling microscope at room temperature. We find a characteristic molecular chain structure of 8T molecules on a terrace of the Cu(111) surface, which has not been reported so far for adsorption of oligothiophene molecules on metal surfaces. Up to the adsorption of 0.26 monolayer (ML), 8T molecules in the molecular chain align with their long axis parallel to the Cu direction. With increasing coverage, there appear 8T molecules that align with their long axis parallel to the Cu direction. The appearance of different molecular orientations is understood by the decrease of the number of the adsorption sites for extending the molecular chains. Fragments of 8T molecules, such as single thiophene molecules, are also observed in this work. They are trapped only at the step edges of the Cu(111) surface at the beginning and later trapped in a small Cu(111) region surrounded by 8T molecules.

Key to single-molecule electronics is connecting functional molecules to each other using conductive nanowires. This involves two issues: how to create conductive nanowires at designated positions, and how to ensure chemical bonding between the nanowires and functional molecules. Here, we present a novel method that solves both issues. Relevant functional molecules are placed on a self-assembled monolayer of diacetylene compound. A probe tip of a scanning tunneling microscope is then positioned on the molecular row of the diacetylene compound to which the functional molecule is adsorbed, and a conductive polydiacetylene nanowire is fabricated by initiating chain polymerization by stimulation with the tip. Since the front edge of chain polymerization necessarily has a reactive chemical species, the created polymer nanowire forms chemical bonding with an encountered molecular element. We name this spontaneous reaction "chemical soldering". First-principles theoretical calculations are used to investigate the structures and electronic properties of the connection. We demonstrate that two conductive polymer nanowires are connected to a single phthalocyanine molecule. A resonant tunneling diode formed by this method is discussed.

Using a density-functional electronic structure calculation method, the electronic structure of an isolated C 60 molecule are calculated under consideration of finite external electric fields, and changes in electron density induced by the external electric fields are investigated in detail. Main finding of this study is that field-induced change in the electron density of an isolated C 60 molecule significantly differs depending on molecular orientation relative to electric field direction, even though the field-induced total dipole moment of a whole molecule hardly shows such orientational dependence. Moreover, such orientational dependence also arises both in total energy and in dielectric constant. These orientational dependence would affect the chemical reactivity and orientational preference of rotating C 60 molecules in a gas phase under finite external electric fields.

We present a theoretical study on stable orientations of photoinduced C 60 dimers in a C 60 monolayer film, on the basis of first-principles calculations within the framework of the density functional theory. Using Tersoff and Hamann’s tunnel current theory, current images of scanning tunneling microscopy (STM) for a C 60 dimer in several different orientations are reproduced from the spatial distribution of the wave functions of an isolated C 60 dimer. Comparing the resultant current images with experimentally obtained STM images, in consequence, two stable orientations of C 60 dimers are determined: one is that a C–C double bond shared by two adjacent hexagons faces to vacuum, and the other is that a C–C single bond shared by a hexagon and an adjacent pentagon faces to vacuum. These orientations are supported by empirical total-energy calculations.

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.

We examined the clinical data of patients treated with oxaliplatin to determine the risk factors of oxaliplatin-related hypersensitivity reaction (HSR). In addition, we evaluated the efficacy of rechallenging patients with HSRs with oxaliplatin using prophylactic agents or desensitization procedures.This study consisted of 162 patients with colorectal cancer (88 men and 74 women) who were treated consecutively at the outpatient chemotherapy department at University Hospital, Kyoto Prefectural University of Medicine. Patients underwent chemotherapy, including oxaliplatin, between March 2006 and June 2012. We analyzed the patients' clinical backgrounds (eg, age, sex, performance status, disease stage, and allergic history) to uncover any connections to the development of HSR to oxaliplatin. In addition, we rechallenged 10 patients who had oxaliplatin-related HSR using prophylactic agents or desensitization procedures.Of 162 patients, 28 (17.2%) developed oxaliplatin-related HSRs (16, 2, 9 and 1 patient had grade 1, 2, 3, and 4 HSRs, respectively). The total cumulative dose of oxaliplatin at the onset of the HSR was 301 to 1126 mg/m(2) (median, 582 mg/m(2)), and the first reactions developed in these patients after 5 to 17 infusions of oxaliplatin (median, 8 infusions). Logistic regression analysis indicated that sex (male: odds ratio = 3.624; 95% CI, 1.181-11.122; P = 0.024) and eosinophil count in peripheral blood (odds ratio = 35.118; 95% CI, 1.058-1166.007; P = 0.046) were independent variables for oxaliplatin-related HSRs. Rechallenging patients with prophylactic agents was successful in 2 (28.6%) of 7 patients who successfully completed their treatment. On the other hand, all 3 patients rechallenged with oxaliplatin using a desensitization protocol successfully completed their treatment without new HSRs.In this retrospective study, we observed that being male and having higher counts of peripheral eosinophil could be predictors for HSR to oxaliplatin. In addition, this study confirms that oxaliplatin desensitization protocol allows patients who developed HSRs to continue with their treatment. However, the optimum desensitization protocol for oxaliplatin administration in terms of tolerability and efficacy needs to be defined.

Using the first-principles real-space finite-difference method, we have theoretically examined optimized structures and electronic energy levels of three peanut-shaped C120 molecules (C60 dimers), namely, P55-, P56-, and P66-C120 molecules. Our calculations show that as the number of eight-membered rings included in each C120 molecule increases, the total energy becomes large and the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) energy gap becomes small. For the P56-C120 molecule, the LUMO is found to be localized at one C60 component, while for the other molecules, the LUMOs are extended over the entire molecule. This fact is understood from the symmetry/asymmetry in the atomic configuration of the three C120 molecules.

We present first-principles calculations of electron conduction properties of monatomic sodium wires suspended between semi-infinite crystalline electrodes, using the overbridging boundary-matching method. We find that the conductances oscillate depending on the number of atoms in the wire, Natom. Furthermore, the values of conductances are � 3 G0 (G0 = 2e 2 =h) for the closed packed structure and � 1 G0 for singlerow wires, which is in agreement with the experimental results of the conductance histogram.

First-principles calculations of electron-transport properties for a single-row atomic wire of Na under the application of a finite bias voltage are presented. Calculations are carried out by a density functional Green-function approach based on the Lippmann-Schwinger equation and the Landauer-Buttiker formula to evaluate the conductance. The model consists of a linear wire, a pair of jellium electrodes and two pyramidal clusters as the interface between the linear wire and the jellium electrode. As a result of the calculations, we found that the voltage drop is generated neither in the pyramidal clusters nor in the jellium electrodes, but in the linear wire. The conductance of Na atomic wire evaluated from the electron transmission is about 84% of the quantized unit 2e2⁄h, and this low conductance is caused by partial reductions of the transmission in some parts of the incident energies. The main reason for this reduction is that the spatial distributions of some states responsible for electron transport become discontinuous around the linear wire in the case of applying a finite bias voltage.

Generalized Bloch wave functions of bulk structures, which are composed of not only propagating waves but also decaying and growing evanescent waves, are known to be essential for defining the open boundary conditions in the calculations of the electronic surface states and scattering wave functions of surface and junction structures. Electronic complex band structures being derived from the generalized Bloch wave functions are also essential for studying bound states of the surface and junction structures, which do not appear in conventional band structures. We present a novel calculation method to obtain the generalized Bloch wave functions of periodic bulk structures by solving a generalized eigenvalue problem, whose dimension is drastically reduced in comparison with the conventional generalized eigenvalue problem derived by Fujimoto and Hirose [Phys. Rev. B 67, 195315 (2003)]. The generalized eigenvalue problem derived in this work is even mathematically equivalent to the conventional one, and, thus, we reduce computational cost for solving the eigenvalue problem considerably without any approximation and losing the strictness of the formulations. To exhibit the performance of the present method, we demonstrate practical calculations of electronic complex band structures and electron transport properties of Al and Cu nanoscale systems. Moreover, employing atom-structured electrodes and jellium-approximated ones for both of the Al and Si monatomic chains, we investigate how much the electron transport properties are unphysically affected by the jellium parts.

We present a fast and stable numerical technique to obtain the self-energy terms of electrodes for first-principles electron-transport calculations. Although first-principles calculations based on the real-space finite-difference method are advantageous for execution on massively parallel computers, large-scale transport calculations are hampered by the computational cost and numerical instability of the computation of the self-energy terms. Using the orthogonal complement vectors of the space spanned by the generalized Bloch waves that actually contribute to transport phenomena, the computational accuracy of transport properties is significantly improved with a moderate computational cost. To demonstrate the efficiency of the present technique, the electron-transport properties of a Stone-Wales (SW) defect in graphene and silicene are examined. The resonance scattering of the SW defect is observed in the conductance spectrum of silicene since the $\sigma^\ast$ state of silicene lies near the Fermi energy. In addition, we found that one conduction channel is sensitive to a defect near the Fermi energy, while the other channel is hardly affected. This characteristic behavior of the conduction channels is interpreted in terms of the bonding network between the bilattices of the honeycomb structure in the formation of the SW defect. The present technique enables us to distinguish the different behaviors of the two conduction channels in graphene and silicene owing to its excellent accuracy., Comment: 28 pages

A theoretical analysis of a relation between atomic and spin-electronic structures for the ground state of single-row aluminum nanowires suspended between Al(001) electrodes is demonstrated using first-principles molecular-dynamics simulations. We obtain a unusual result that a 3-aluminum-atom nanowire sandwiched between the electrodes does not manifest magnetic ordering although an isolated aluminum trimer molecule in a straight line is spin-polarized. On the other hand, a 5-atom nanowire exhibits ferromagnetic ordering, where three central atoms form a spin-polarized trimer. Moreover, in the case of an 8-atom nanowire, the middle atoms in the nanowire form two spin-polarized trimers with antiferromagnetic ordering., 9 pages

Adsorption and electronic structure of octithiophene (8T) molecules on Cu(III) and Au(III) surfaces are investigated using scanning tunneling microscopy (STM) and spectroscopy (STS) at room temperature. We find a large difference in adsorption behavior of 8T molecules on the two surfaces. At the initial stage of adsorption, 8T molecules are stabilized in the form of molecular chain on a terrace of Cu(III), whereas neither such chain structure nor isolated 8T molecules have been observed on a terrace of Au(III). By increasing the amount of adsorbed molecules, a disordered monolayer film is formed on Cu(III) while a well-ordered monolayer film is formed on Au(III). From the spectroscopic investigations using bias-dependent STM images and STS spectra and by comparing the data with theoretical calculations, it is found that the electronic property of 8T molecules in the molecular chain on Cu(III) is different from that of a free-standing 8T molecule while that in the monolayer film on Au(III) keeps original character of the free-standing 8T molecule. The present study shows that adsorption of 8T molecules on Cu(III) results in a formation of adsorption-induced states near the Fermi level.

In this first-principles study, we present density-functional calculations of the electronic structures and electron transport properties of organic molecular junctions with several anchoring groups containing atoms with different electronegativities, i.e., benzenediboronate (BDB), benzenedicarboxylate (BDC), and dinitrobenzene (DNB) molecular junctions sandwiched between two Cu(110) electrodes. The electronic-structure calculations exhibit a significant difference in the density of states not only at the anchoring groups but also at the aromatic rings of the molecular junctions, suggesting that the electron transport is specific for each system. Our transport calculations show that the BDB and DNB molecular junctions have finite electron transmissions at the zero-bias limit while the BDC molecular junction has a negligible electron transmission. Moreover, for the BDB and DNB systems, the electron transmission channels around the Fermi energy reveal fingerprint features, which provide specific functionalities for the molecular junctions. Therefore, our theoretical results demonstrate the possibility to precisely tune the electron transport properties of molecular junctions by engineering the anchoring groups at the single-atom level.

Liposomal-encapsulated superoxide dismutase (L-SOD) was prepared with a view to prolonging the half-life and pharmacodynamic action time. Presome® was adopted as a phospholipid in the preparation of L-SOD.L-SOD was sterilized through polycarbonate membrane filters having pore diameters of 0.2 μm and 0.4μm. The liposomal particle size, as measured by the dynamic light scattering method, was 198±40 nm. Effective SOD encapsulation efficiency was approximately 25.8%.Immediately after the i.v. injection of L-SOD into rats, blood levels of SOD decreased in a bi-exponential manner; the half-lives of the α-and β-phases were 16.6 minutes and 7.8 hours, respectively.AUC and MRT increased as compared with the i. v. injection of r-hSOD (free SOD), The SOD-activity in plasma was on a low level.These results suggested that still more L-SOD was trapped in the reticulo-endothelial system (RES), involving such organs as in the liver and spleen.In an effect to increase the SOD activity in plasma and prolong the circulation time of liposomes in blood, we prepared L-SOD modified with polyethyleneglycol derivatives (L-SOD/PEG. DOPE; L-SOD/PEG·DMG).After the i. v. injection of L-SOD/PEG·DOPE and L-SOD/PEG·DMG into rats, the SOD activity in plasma became higher and also the circulation time of liposomes in blood became longer as compared with the L-SOD i. v. injection.

We present an improvement of the Lippmann-Schwinger equation method, which calculates electron-scattering wave functions of a nanoscale conductor suspended between a pair of electrodes. The improvement eliminates the numerical collapse which frequently occurs while solving the Lippmann-Schwinger equation for long conductor systems and originates from evanescent wave components of the retarded Green's function of the Lippmann-Schwinger equation. We introduce regularization and ratio expression into the Green's function matrix and discover that the resultant Green's function does not suffer from the numerical collapse without increasing computational cost. As a performance test, we carry out electron transport calculations of Al monoatomic linear chains with a length of up to 75.6 bohrs. The numerical test demonstrates that the improved Lippmann-Schwinger equation method is applicable to long conductor systems with no numerical collapse and adequate computational accuracy.

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.

Density functional calculations of the atomic configuration of electron-beam irradiated C${}_{60}$ thin films were implemented. By examining the electronic structure and electron-transport properties of C${}_{60}$ clusters, we found that a rhombohedral C${}_{60}$ polymer with $s{p}^{3}$-bonded dumbbell-shaped connections at the molecule junction is a semiconductor with a narrow band gap. In addition, the polymer changes to exhibit metallic behavior by forming $s{p}^{2}$-bonded peanut-shaped connections. Conductance below the Fermi level increases and the peak of the conductance spectrum arising from the ${t}_{u1}$ states of the C${}_{60}$ molecule becomes obscure after the connections are rearranged. The present rhombohedral polymer, including the [$2+2$] four-membered rings and peanut-shaped connections, is a candidate for representing the structure of the metallic C${}_{60}$ polymer at the initial stage of electron-beam irradiation.

We have developed a method using a scanning tunneling microscope (STM) probe tip to control the chain polymerization of diacetylene compounds in a self-ordered layer, thereby creating conjugated polydiacetylene nanowires. When a small amount of phthalocyanine was deposited on a molecular layer of diacetylene compound, we found adsorbed and stabilized phthalocyanine single molecules. The initiation of chain polymerization on the diacetylene molecular row to which the single phthalocyanine molecule was adsorbed was also demonstrated.

We have developed an efficient computational scheme utilizing the real-space finite-difference formalism and the projector augmented-wave (PAW) method to perform precise first-principles electronic-structure simulations based on the density functional theory for systems containing transition metals with a modest computational effort. By combining the advantages of the time-saving double-grid technique and the Fourier filtering procedure for the projectors of pseudopotentials, we can overcome the egg box effect in the computations even for first-row elements and transition metals, which is a problem of the real-space finite-difference formalism. In order to demonstrate the potential power in terms of precision and applicability of the present scheme, we have carried out simulations to examine several bulk properties and structural energy differences between different bulk phases of transition metals, and have obtained excellent agreement with the results of other precise first-principles methods such as a plane wave based PAW method and an all-electron full-potential linearized augmented plane wave (FLAPW) method., Comment: 29 Pages