Volume And Issue List
Journal of Computer Chemistry, Japan
- Vol.13(2014)
- Vol.12(2013)
- Vol.11(2012)
- Vol.10(2011)
- Vol.9(2010)
- Vol.8(2009)
- Vol.7(2008)
- Vol.6(2007)
- Vol.5(2006)
- Vol.4(2005)
- Vol.3(2004)
- Vol.2(2003)
- Vol.1(2002)

Predecessor

JCPE Journal

Journal of Chemical Software

Journal of Computer Chemistry, Japan Vol. 13(2014) No. 6
Special Issue: Selected Papers from the Annual Autumn Meeting 2014

Foreword

My Dream as the Chemist

Katsuhiko OKUYAMA

Released: December 31, 2014

foreword_13_6

Full Text PDF[295K]

Letters (Selected Paper)

The Tube Length Dependence of Electronic Structures in Armchair Carbon Nanotubes - From the Standpoint of Topological Characteristics -
(SCCJ Annual Meeting 2014 Autumn Poster Award Article)

Dai NORIKAWA, Yasushi NOMURA, Noriyuki MIZOGUCHI

Released: December 31, 2014

p.293-294

[in Japanese]

A Solution of 3d-Ising Model with Boundary

Hideyuki NARUMI, Haruo HOSOYA

Released: December 31, 2014

p.295-296

[in Japanese]

Theoretical Study for Inner-Shell Double-Core-Hole States

Osamu TAKAHASHI, Kiyoshi UEDA

Released: December 31, 2014

p.297-298

[in Japanese]

Development of NGS data Analysis Program for RNA-Seq

Taiju MIKOSHI, Yoshihito FUKANO, Yuki MIYAZAWA, Kenji YAMAGISHI

Released: December 31, 2014

p.299-300

[in Japanese]

Creation of a Web Page for Learning "Dangerous Drugs" by Jmol Molecular Visualization

Yoshio HONMA

Released: December 31, 2014

p.301-302

[in Japanese]

Structure Development of a hA_2AAR Antagonist with StarDrop/Nova Function

Sumie TAJIMA, Yasuo INOUE

Released: December 31, 2014

p.303-304

[in Japanese]

Analysis of Interactions between Mutant Vitamin D Receptor and Its Ligands: Fragment Molecular Orbital Study

Hisae YOSHIDA, Mitsuru HARUKI, Kenji YAMAGISHI

Released: December 31, 2014

p.305-307

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.

Structural Stability of Halogenated Protein: Fragment Molecular Orbital Study

Jumpei TAKANOHASHI, Sousuke KOHASHI, Takeshi ISHIKAWA, Kensaku SAKAMOTO, Kenji YAMAGISHI

Released: December 31, 2014

p.308-309

[in Japanese]

Establishment of Next-Generation Sequencer Data Analysis Methods and Exploration of Novel Gene Candidates

Yuki MIYAZAWA, Yoshihito FUKANO, Taiju MIKOSHI, Toshio INOUE, Syuichirou MARUOKA, Kazumichi KURODA, Yasuhiro GON, Shu HASHIMOTO, Kenji YAMAGISHI

Released: December 31, 2014

p.310-311

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.

Molecular Orbital Calculation Study of Rreaction in the Refractories Containing Fumed Silica

Koichi TAKANO, Nozomu UCHIDA

Released: December 31, 2014

p.312-313

[in Japanese]

Effective Usage of the Maximum Entropy Method in Optical Spectrum Analysis of Real-Time TDDFT

Mitsuki TOOGOSHI, Satoru KANO, Yasunari ZEMPO

Released: December 31, 2014

p.314-316

[in Japanese]

Structural Analysis of Iron(III) Complexes Relevant to Carcinogenicity

Keita ABE, Hiroshi SAKIYAMA, Yuzo NISHIDA

Released: January 06, 2015

p.317-318

[in Japanese]

A Theoretical Study on Superexchange Interaction in KCoF₃ and Cs_1-xNa_xMn^II(CN)₃ by Chemical Bonding Rule

Taku ONISHI

Released: January 06, 2015

p.319-320

Previously, we demonstrated that Cs_1-xNa_xMn^II(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.

Misleading Dichotomy Between Constitutional Isomers and Stereoisomers

Shinsaku FUJITA

Released: January 06, 2015

p.321-322

[in Japanese]

Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine

Hiroaki UMEDA, Toshihiro HANAWA, Mitsuo SHOJI, Taisuke BOKU, Yasuteru SHIGETA

Released: January 06, 2015

p.323-324

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.

Real-Space Electronic Structure Calculations Based on Symmetric Smoothed Particle Hydrodynamics

Yasunari ZEMPO, Souichiro SUGIMOTO

Released: January 06, 2015

p.325-327

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

Origin of Attraction and Directionality of Halogen Bond

Seiji TSUZUKI, Tadafumi UCHIMARU

Released: January 19, 2015

p.328-329

[in Japanese]

Observation of the air pollution on Mt. Norikura

Toru YAGI, Junko KAMBE, Eiko NAKAYAMA, Umpei NAGASHIMA, Tomoo AOYAMA

Released: January 19, 2015

p.330-331

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.

RNA-Sequence Analysis by Next-Generation Sequencer for the Early Diagnosis of Respiratory Disease

Yoshihito FUKANO, Yuki MIYAZAWA, Taiju MIKOSHI, Toshio INOUE, Shuuichirou MARUOKA, Kazumichi KURODA, Yasuhiro GON, Shu HASHIMOTO, Kenji YAMAGISHI

Released: January 19, 2015

p.332-334

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.

Development of RDMA-based Communication Middleware Library for Molecular Orbital Program

Hiroaki HONDA, Yuichi INADOMI, Yoshiyuki MORIE, Takeshi NANRI, Toshiya TAKAMI

Released: January 19, 2015

p.335-336

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.

Molecular Simulation of Photon Interaction with Linear Oligomers

Toru IWATAKE, Kazuo NARUSHIMA

Released: January 19, 2015

p.337-339

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.

1 - 22 / 22 Articles.

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Back Issues

Volume And Issue List
Journal of Computer Chemistry, Japan

Predecessor

Journal of Computer Chemistry, Japan Vol. 13(2014) No. 6
Special Issue: Selected Papers from the Annual Autumn Meeting 2014

Foreword

My Dream as the Chemist

Letters (Selected Paper)

The Tube Length Dependence of Electronic Structures in Armchair Carbon Nanotubes - From the Standpoint of Topological Characteristics -
(SCCJ Annual Meeting 2014 Autumn Poster Award Article)

A Solution of 3d-Ising Model with Boundary

Theoretical Study for Inner-Shell Double-Core-Hole States

Development of NGS data Analysis Program for RNA-Seq

Creation of a Web Page for Learning "Dangerous Drugs" by Jmol Molecular Visualization

Structure Development of a hA_2AAR Antagonist with StarDrop/Nova Function

Analysis of Interactions between Mutant Vitamin D Receptor and Its Ligands: Fragment Molecular Orbital Study

Structural Stability of Halogenated Protein: Fragment Molecular Orbital Study

Establishment of Next-Generation Sequencer Data Analysis Methods and Exploration of Novel Gene Candidates

Molecular Orbital Calculation Study of Rreaction in the Refractories Containing Fumed Silica

Effective Usage of the Maximum Entropy Method in Optical Spectrum Analysis of Real-Time TDDFT

Structural Analysis of Iron(III) Complexes Relevant to Carcinogenicity

A Theoretical Study on Superexchange Interaction in KCoF₃ and Cs_1-xNa_xMn^II(CN)₃ by Chemical Bonding Rule

Misleading Dichotomy Between Constitutional Isomers and Stereoisomers

Performance Benchmark of FMO Calculation with GPU-Accelerated Fock Matrix Preparation Routine

Real-Space Electronic Structure Calculations Based on Symmetric Smoothed Particle Hydrodynamics

Origin of Attraction and Directionality of Halogen Bond

Observation of the air pollution on Mt. Norikura

RNA-Sequence Analysis by Next-Generation Sequencer for the Early Diagnosis of Respiratory Disease

Development of RDMA-based Communication Middleware Library for Molecular Orbital Program

Molecular Simulation of Photon Interaction with Linear Oligomers

System Maintenance

Announcement From J-STAGE

Journal Tools

Share this Title

Volume And Issue List Journal of Computer Chemistry, Japan

Predecessor

Journal of Computer Chemistry, Japan Vol. 13(2014) No. 6 Special Issue: Selected Papers from the Annual Autumn Meeting 2014

Foreword

Letters (Selected Paper)

The Tube Length Dependence of Electronic Structures in Armchair Carbon Nanotubes - From the Standpoint of Topological Characteristics - (SCCJ Annual Meeting 2014 Autumn Poster Award Article)

System Maintenance

Announcement From J-STAGE

Journal Tools

Share this Title

Volume And Issue List
Journal of Computer Chemistry, Japan

Journal of Computer Chemistry, Japan Vol. 13(2014) No. 6
Special Issue: Selected Papers from the Annual Autumn Meeting 2014

The Tube Length Dependence of Electronic Structures in Armchair Carbon Nanotubes - From the Standpoint of Topological Characteristics -
(SCCJ Annual Meeting 2014 Autumn Poster Award Article)