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.

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.

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.

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.

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.