We carried out ab initio fragment molecular orbital calculations for vitamin D receptor (VDR) mutants at the RI-MP2/cc-pVDZ level, to elucidate the mechanism of hereditary vitamin D-resistant rickets caused by mutant VDR. We calculated the energies of interactions between the residues of the ligand binding pocket in the VDR and its ligands by using inter-fragment interaction energy analysis based on the fragment molecular orbital method. In all mutants, the interaction energies of Y147, F150, and Q273 were decreased. These results indicate that these residues are key to ligand recognition.
Next-generation sequencers (NGS) have made it possible to analyze entire genome sequence. NGS can be used for the identification of genes associated with a wide variety of diseases. We investigate RNAs encoded by intergenic regions to identify novel genes that are involved in respiratory diseases. The respiratory tracts of mice were exposed to lipopolysaccharide to establish a model of respiratory disease. RNA expression levels in the mouse exosome were analyzed by NGS to identify genes involved in the development of respiratory diseases. Several disease-related regions exhibited altered expression levels of intergenic RNAs.
Previously, we demonstrated that Cs1-xNaxMnII(CN)3 prussian blue analog exhibits high-efficient cesium adsorption, through the ion-exchange between cesium and sodium ions under applied voltage. In this study, we investigated the superexchange interaction between manganese atoms via cyano-ligand, by the use of chemical bonding rule.
GPU acceleration for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. We have developed a GPU-accelerated Fock matrix preparation routine without atomic operation and implemented it into the worker module of an OpenFMO program, which is parallelized in a master-worker programming model. The GPU-accelerated program shows 1.5× speedups from CPU only FMO-HF/6-31G (d) calculation with a direct SCF method for 642 atomic protein on 8 nodes of HA-PACS base cluster.
The local pseudopotential method (PS) has been implemented into real-space electronic structure calculations based on symmetric smoothed particle hydrodynamics (SSPH). As a simple example, we applied this SSPH to a simple atom such as H, He and Li. To evaluate SSPH with PS, the results are compared with those of the finite difference method (FD), the simple SSPH, and the usual atom calculation (AT). Similar results were obtained from both of FD and the simple SSPH. However, there are several differences between the results of the simple SSPH and that of AT. When we use SSPH with PS, the results can be controlled to those of AT, using appropriate parameters. We recognize that, in our previous study, the error between the simple SSPH and AT is mainly caused by the difference of the charge in the vicinity of the ion core. The discretization by the simple SSPH is not enough to describe the electronic structure, especially the Hartree term. Since the pseudopotential around the ion core is finite, this error reduces in our SSPH with PS. Our results show that SSPH with PS can be practically applied to electronic calculations, keeping high accuracy, SSPH with PS
We observed scattering light of the atomosphere by using a digital camera on Marishiten peak on Mt. Norikura at Sept 11, 2013. The RGB brightness, B/R and G/R ratio of the pixels were analized. The optical character of the black mist layer was discussed. We also observed the distribution of dilute particules in the atmosphere and the difference between zodiacal light and city light.
To establish a system for the early diagnosis of respiratory diseases, we developed a method for analyzing RNA sequence data obtained by next-generation sequencer identify genes showing altered expression as biomarkers of respiratory tract infection. The respiratory tracts of mice were exposed to lipopolysaccharide to establish a model of respiratory disease. Twenty-five genes exhibited significantly altered RNA expression following exposure. We identified non-coding RNAs in five regions that could be candidate biomarkers of respiratory diseases.
For small memory communications in the exascale computing, we are developing an Advanced Communication Primitives (ACP) library based on one-sided communication. ACP library uses Global Address (GA) data for identifying a logical address of a process. We estimated memory requirements of ACP library for four communication patterns of the OpenFMO application. The maximum memory requirement of GAs is about 1 MByte for the master process of master-worker communications. This result shows the memory requirement of GAs is considerably smaller than the available memory size of one process of exascale computer.
Photomechanical materials in which the shape change of a high polymer is extracted as motion by photoirradiation are attracting attention lately. Nevertheless, details of the complicated mechanism of this photoirradiation-induced shape change have yet to be elucidated. Using molecular dynamics and the Monte Carlo method, we have conducted molecular simulations for a case in which a straight chain oligomer is irradiated by photons. Thereby, we have investigated the interaction between an oligomer and photon as the first step in elucidating photoirradiation-induced shape change. Results show that the oligomer's light absorption and the Compton effect between a photon and an oligomer cause a chemical energy change and bring about shape change. Furthermore, short-wavelength ultraviolet radiation has been found to cause greater shape change than infrared radiation does.