First-principles calculation method for electron transport based on 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 metal electrodes. The results confirm that the leakage current through the (001)Si/SiO$_2$ model becomes much larger when the dangling-bond (DB) state is induced by a defect in the oxygen layer while that through the (001)Ge/GeO$_2$ model is insensitive to the DB state

Magnetic orderings in Al nanowires suspended between electrodes

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.Comment: 9 page

Sudden Suppression of Electron-Transmission Peaks in Finite-Biased Nanowires

Negative differential conductance (NDC) is expected to be an essential property to realize fast switching in future electronic devices. We here present a thorough analysis on electron transportability of a simple atomic-scale model consisting of square prisms, and clarify the detailed mechanism of the occurrence of NDC phenomenon in terms of the changes of local density of states upon applying bias voltages to the electrodes. Boosting up bias voltages, we observe sudden suppression of transmission peaks which results in NDC behavior in the current-voltage characteristic. This suppression is explained by the fact that when the bias voltage exceeds a certain threshold, the conduction channels contributing to the current flow are suddenly closed up to deny the electron transportation.Comment: 12 text pages, 6 figure

Real-space electronic-structure calculations with full-potential all-electron precision for transition-metals

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 Page

Texture-Modified Diets Need to be Improved

Purpose : The aim of this study is to compare the nutritional status of older adult inpatients consuming Texture-Modified Diets (TMD) to older adult inpatients consuming a regular diet. Methods : The study was designed as cross-sectional and was conducted in three large hospitals in northern Vietnam. The data for 344 older adult inpatients were collected in 2021 by dietitians. Results : The result showed 104 subjects were prescribed TMD. The textures of hospital diets have still not been adequately developed. In particular, the hospitals had not yet developed pureed meals. All older adult inpatients (74.7 ± 6.8 years old, 52.9% female) had 28.8% malnutrition by the GLIM criteria. The TMD group had a malnutrition prevalence two times higher than the regular diet group. Total energy intake from hospital meal and outside snacks in the regular diet group was higher than in the TMD group, about 150 kcal. Although energy provided from the hospital diet in both groups was similar, hospital meal wastage in the TMD group was higher than in the regular diet group. Conclusion : The older adult inpatients on TMD may have a nutritional status worse than those consuming a regular diet. Hospital diets need to be improved in texture and quality

Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

BACKGROUND: Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. RESULTS: In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. CONCLUSIONS: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions