The authors' group has developed the program named DC-DFTB-K for the on-the-fly quantum mechanical molecular dynamics (MD) simulation of huge systems using the density-functional tight binding (DFTB) method. The combination with the divide-and-conquer (DC) method enables linear-scaling calculation of DFTB energy and its derivatives. Due to the massively parallel implementation, the program can treat systems containing one million atoms on the K computer. In this paper, the recent extension of DC-DFTB-MD technique is outlined together with the illustrative application to chemical reaction dynamics in lithium-ion device.
We applied a method for calculating indefinite integrals developed for atomic structure calculations to mathematical functions defined by integrals and obtained highly accurate results. The method is simple and has wide applicability. Examples of application are, elementary transcendental functions such as exponential, logarithmic, and arctangent functions, then error function, Fresnel integrals, exponential, cosine, and sine integrals, and incomplete gamma functions.
Isotropic NMR shielding constants σiso were calculated for hydrogen, carbon, nitrogen, oxygen, fluorine and phosphorous atoms in small molecules by using numerical basis functions, which were based on AOs of Discrete Variational Xα (DV-Xα) method and were modified to London atomic orbitals to avoid the gauge-origin-dependence when magnetic field exists. In DV-Xα method AOs are prepared by solving the Hartree-Fock-Slater (HFS) equation substantially equivalent to that used to calculate MOs and are very accurate around each nucleus. However, σisos calculated in the default condition of DV-Xα method don't agree well to experimental ones. By optimizing AOs in a reasonable way, σisos were highly improved and agreed with experimental ones far better than results by Hartree-Fock (HF) method having conventional basis functions. The usefulness of MOs constructed with optimized numerical basis functions was clearly demonstrated.
Electronic structure calculation is necessary for metal nanoparticles composed of more than 1000 atoms to understand the intrinsic physical and chemical properties of nanoparticles. In this study, we analyzed the parallel performance of electronic structure calculation for metal nanoparticles by using the Vienna Ab-initio Simulation Package (VASP) program with large-scale computational resources. We found that VASP is suitable for the large-scale electronic structure calculation because the parallelization efficiency improved with increasing metal nanoparticle size (Pd405, Pd807, and Pd1289).
The role of water in the protein-ligand binding site was investigated from the viewpoint of enthalpic bridging between human coagulation factor Xa (fXa) and four ligands. Ligand-constrained MD simulation was done for identifying hydration sites and representative water molecules were arranged at the sites. The calculated fXa-ligand interaction energy while considering these explicit water molecules as parts of fXa shows excellent correlation to the experimental binding affinity, while the energy with considering them as implicit solvent does not correlate. This result indicates that the representative water molecules at the hydration sites should be explicitly considered when protein-ligand interaction energy is analyzed, and ligand-constrained MD simulation is a powerful tool to identify these hydration sites.
The author is confident that knowledge of electronic materials and molecular simulation will become indispensable for future students of electrical and electronic engineering majors.This paper presents an approach for an introductory lesson on molecular simulation just inaugurated by the author. Specifically, the first step of molecular simulation was incorporated into the lecture "The Basic Theory of Optical Property." This lesson was taught using spreadsheets (Excel; Microsoft Corp.), which are familiar and easily used software for students. Comments by students after the lesson included the following; "Abstract contents were well understood through exercises," and "The significance of simulations was abundantly clear." Consequently, the author believes that effects anticipated from this lesson (the objective of this lesson) were attained to a good degree.
We performed theoretically to reproduce site-selective X-ray emission spectroscopy (XES) spectra of acetic acid and methyl formate in the liquid phase at two oxygen K-edge (OC=O and OOH,OCH3) to observe the intermolecular interaction dependence of XES spectra. Structure sampling as a cluster model was performed from a snapshot of molecular dynamics simulation. Relative intensities of XES with core-hole excited state dynamics simulation were calculated using density functional theory. We found that theoretical XES spectra were well reproduced experimentally.
The interatomic potential for a wide composition range of sodium silicate glasses was proposed by first-principles calculation. Point charge was set for each glass composition on the basis of population analysis of the alkali silicate crystals by using the density functional theory. The potential parameters were obtained from the energy surface of the SiO2+ model by using the molecular orbital method. The molecular dynamics simulation using the new interatomic potential showed improved structures of sodium silicate glasses.
Chiral dinuclear zinc(II) complexes [Zn2(R-bppmp)(MeCO2)2]BPh4 (1R) and [Zn2(S-bppmp)(MeCO2)2]BPh4 (1S) were previously reported to hydrolyze peptide bonds, and the activity of 1S was two times larger than that of 1R. In order to clarify the reason for the difference in activity, substrate incorporation modes were investigated on the basis of Density Functional Theory (DFT) method. Consequently, in the case of 1S, the most stable isomer was found to be suitable in incorporating the substrate in a stable form. As for the case of 1R, the most stable isomer was found to be not suitable, whereas the second most stable isomer was found to be suitable in incorporating the substrate in a stable form.
GPU acceleration of four-center (4C) inter-fragment Coulomb interaction term (IFC) for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. FMO calculation has two time-consuming steps: Fock matrix construction and IFC calculation, and in our previous letter, it was reported that the former is successfully accelerated with our GPU-enable code. The 4C-IFC calculation is the core part of the latter and its code is similar to that of Fock matrix construction. In this letter, we briefly describe the GPU-accelerated 4C-IFC calculation routine, and report a performance benchmark for GPU-accelerated FMO calculation. The GPU-accelerated program shows 3.3× speedups from CPU only FMO-HF/6-31G (d) calculation for 642 atomic protein on 8 nodes of HA-PACS base cluster.
The maximum entropy method (MEM) is one of the key techniques for spectral analysis. The main feature is to describe spectra in low frequency with short time-series data. We adopted MEM to analyze the spectrum from the dipole moment obtained by the time-dependent density functional theory (TDDFT) calculation in real time, which is intensively studied and applied to computing optical properties. In the MEM analysis, we proposed that we use the concatenated data set made from several-times repeated raw data and the phase shift. We have applied this technique to the spectral analysis of the TDDFT dipole moment of oligo-fluorene with n=8. As a result, higher resolution can be obtained without any peak shift due to the phase jump. The peak position is in good agreement with that of FT with just raw data. The efficiency and the characteristic feature of this technique are presented in this paper.
Under nuclear power plant accident, by the ventilation of containment vessel, suspended particulate matter (SPM) is emitted; it attracts radioactive compounds, and the plume diffuses in air. It soaks into the human body. We are required to run away from the invisible plumes. The routes do not exist at any time. We recognize status soon, and should select priority persons to escape from there. We code a real-time plume tracer, which reads 4D-winds of Meso Scale Model (MSM), calculates time-development of plumes. The precision for reach time of plumes is 3–5 min, inner 8 km points from emission.
We have launched a project called "Maizo"-chemistry, which is aimed toward molecular- and reaction discovery based on big data of quantum mechanical global reaction route mappings. The global reaction data includes equilibrium structures (EQs), dissociation channels (DCs), and transition structures (TSs), which are automatically calculated by a global search on a potential energy surface using the GRRM (global reaction route mapping) method. Applications to molecular- and synthesis design are an important part of the project. Machine learning and visualization techniques as well as chemoinformatics methods are essential to acquire useful information from the large reaction data space. We describe here a software system, RMapViewer, which we have developed to visualize and analyze the GRRM outputs.
We have applied alchemical free energy calculation of theophylline with an RNA aptamer with one or more ligand docking poses. We find that the predicted binding affinity strongly depends on the anchor's position at the receptor using only distance restraints; it means that a ligand is trapped at the other metastable states during the decoupling process. We also demonstrate that the binding affinity of a fragment-like molecule such as theophylline to the receptor is obtained by phase space decomposition with orientational restraints.