Past Seminars (Until May 2014 at JAIST)
"Simulation Science" Seminars hosted by RCSS, JAIST

2013/11/18 Fri. 8th Simulation Science Seminar (finished)
TITLE: Understanding the STM and AFM contrast in graphene, reducible oxides and biomolecules
SPEAKER: Ruben Perez (Professor, Theory of Condensed Matter Department, Universidad Autonoma de Madrid, http://www.uam.es/spmth/)
TIME: 15:00-16:30
We’ll review the computational tools and protocols developed in our group in order to study the mechanical and transport properties of materials, and its application to the understanding of the atomic-resolution images obtained with the scanning tunneling (STM) and the force microscope (AFM) by different experimental groups on technologically relevant materials.
Firstly, we’ll focus on tuning of the electronic properties of graphene through the creation of defect and edge states, looking, in particular, to the connection of graphene with metal surfaces. Combining high resolution STM experiments and DFT calculations, we have unambiguously unveiled the atomic structure of the boundary between a graphene zigzag edge and a Pt(111) step. The graphene edges minimize their strain by inducing a 3-fold edge-reconstruction on the metal side. We have shown the existence of an unoccupied electronic state exclusively localized in the C-edge atoms of a particular graphene sublattice, which could be used to develop new dual-channel devices.
Metal oxides play a key role in a wide range of technological applications. While in many cases the same FM-AFM image can be explained by different models, and even different underlying tip-sample interactions, we show here that the combination of force spectroscopy (FS) measurements and first-principles simulations can provide an unambiguous identification of the tip structure and the image contrast mechanism in rutile TiO2 (110) and anatase TiO2 (101) surfaces. In the case of STM, we have made a comprehensive study of the (2√2x√2)R45゜ missing row reconstruction of the Cu(100) surface, using different tips and systematically varying bias voltage and tip sample distance, to explore the rich variety of image contrasts observed in the experiments. Our results achieve a conclusive understanding of fundamental STM imaging mechanisms and provide guidelines for experimentalists to achieve chemically selective imaging by selecting imaging parameters.
Finally, we’ll present our recent work on the structure and functionality of biological systems in their native liquid environment. We’ll discuss the application of large-scale steered Molecular Dynamics simulations, based on classical potentials developed by the molecular biology community and the use of GPUs as processing units, provide insight into the protein-graphene biocompatibility, the flexibility map of human antibodies, and the hydration properties of self-assembled monolayers of single-stranded DNA and its possible use as a label-free DNA sensor.


2013/11/5 Tue. 7th Simulation Science Seminar (finished)
TITLE: A material design support system using computer simulation and data mining
SPEAKER: Ryoko HAYASHI　(Assist. Prof., Kanazawa Institute of Technology)
TIME： 15:30-17:00
SUMMARY: Recently, we can use high-performance desktop computers and cloud computing so that we can use numerous small-scale or middle-scale of computing power. Furthermore, various rich simulation programs for computational chemistry or computational physics are developed and anyone can run sophisticated material design simulations with simple procedures. However, since the result of a simulation is a mass of numerical data, auto data processing is necessary for understanding the result. Fortunately, data mining technologies are full-grown and anyone can utilize important data mining methods today. Therefore this work aims at material design system based on huge number of simulations and auto data processing technology. This talk will introduce relational information and will describe recent work.


6th Simulation Science Seminar 磁石と構造材料の第一原理シミュレーション (finished)
SUMMARY: 磁石と構造材料は我々の日常生活でひろく活用されている材料ですが、近年のエネルギー問題の高まりから、 より高性能な材料の開発が求められています。文科省が推進する「元素戦略プロジェクト」においても 磁石と構造材料は中心的な課題です。二つの材料は一見、接点がないように思われますが、 どちらも鉄などの遷移金属が重要な役割を果たしています。「京」に代表される超並列計算機と量子力学に基づく 第一原理計算を活用し、これらの材料に対する設計指針を確立する試みが進められています。 本セミナーではその研究の一端をご紹介致します。
DATE/TIME, TITLE, SPEAKER:

[2013/8/26 Mon.]
13:30-14:30	鋼中NaCl型析出物界面の構造とエネルギーの第一原理計算　Hideaki Sawada (Nippon Steel)
14:40-15:20	超並列大規模電子状態計算手法の開発と応用　Taisuke Ozaki (JAIST)
15:30-16:20	電子論に基づくFe-Si合金中のらせん転位と固溶Siの相互作用の評価に向けて 　Masato Wakeda (Osaka Univ.)
[2013/8/27 Tue.]
9:10-10:00	永久磁石の新材料探索 Takashi Miyake (AIST)
10:10-11:00	永久磁石材料の微細構造と電子状態 Yoshihiro Gohda (Univ. of Tokyo)
11:10-12:00	磁石材料についての2成分相対論的電子状態計算 Shoji Ishibashi (AIST)



2013/4/16 Tue. 5th Simulation Science Seminar (finished)
TITLE: Understanding the STM and AFM contrast in graphene, reducible oxides and biomolecules
SPEAKER: Atsushi M. Ito, Assistant Professor, National Institute for Fusion Science
TIME: 13:30-15:00
SUMMARY: Helium irradiation onto tungsten surfaces brings about the growth of fuzzy tungsten fibers in the diameter of several ten nano-meter. This material, which is called "tungsten nano-structure", was found by the research on a plasma facing tungsten material in the inside walls of nuclear fusion reactors. Because the incident energy of the helium ions is less than that to sputter the tungsten atoms from the surface, the growth of the fuzzy fibers can be regarded as self-organized growth. The formation process of the tungsten nano-structure is not classified into the deposition and processing/etching, which are two kinds of typical processes to create surface nano-structures. The formation mechanisms of tungsten nano-structure have been not well understood.
We have grappled with the formation mechanisms of the tungsten-nano structure by using density functional theory with the OpenMX developed in JAIST, molecular dynamics and some simulation models. In this presentation, we introduce the interesting tungsten nano-structure with our simulation researches.


2013/1/8 Tue. 3rd Simulation Science Seminar (finished)
TITLE: Electronic structure and orbital polarization of LaNiO3/LaAlO3: GGA, +U, and DMFT calculations
SPEAKER: Myung Joon Han,　Assistant Professor, Dept. of Physics, KAIST (Korea Advanced Institute of Science and Technology)
TIME: 14:00-15:30
SUMMARY: Nickelate superlattices have created considerable interests especially due to the possible emergence of high-temperature superconductivity caused by heterostructuring and onsite correlation. To understand LaNiO3/LaAlO3-type of superlattices, we performed the electronic structure calculations. The systematic study with GGA (generalized gradient approximation) and tight-bonding analysis clearly shows that the non-transition-metal counter ions (e.g., Al, Ga, In) can be used to control the orbital polarization even if these ions have nominally zero valence. Taking correlation effects into account within GGA+U and DMFT (dynamical mean-field theory), we show that this heterostructure is unlikely to produce one-band model physics and therefore high-temperature superconductivity may not be realized. It is also found that the charge transfer between transition metal and oxygen is crucial, demonstrating the fundamental inadequacy of modeling the physics of late transition-metal oxides with Hubbard-like models.


2012/11/28 Wed. 2nd Simulation Science Seminar (finished)
TITLE: Ab initio molecular dynamics simulations in real space
SPEAKER: Eiji Tsuchida,　Researcher, Nanosystem Research Institute, AIST
TIME: 14:00-15:30
SUMMARY: I will introduce a method for large scale electronic structure calculations based on the finite element method. In particular, the choice of coordinates, multigrid-based Poisson solver, and the method for ground state calculations will be discussed.
I will also present our results on the Born-Oppenheimer molecular dynamics simula- tions of several molecular liquids including the phosphoric acid and liquid ethanol.


2012/9/28 Fri. 1st Simulation Science Seminar (finished)
TITLE: スーパーコンピュータ「京」とは
SPEAKER: Motoyoshi Kurokawa, Research and development staff of RIKEN 計算科学研究機構 運用技術部門
TIME: 10:00-11:00
SUMMARY: スーパーコンピュータ「京」は世界で初めて10ペタFLOPS超のLINPACK性能を達成したスーパーコンピュータである。「京」はスーパーコンピュータとして世界的に最高水準の総合性能を有し、使いやすい利用環境をユーザに提供できるスーパーコンピュータであり、その応用利用において、画期的な成果が期待されている。本講演では、「京」開発の経緯を示し、「京」の概要および開発された要素技術、詳細なシステム構成および「京」の設置されている施設を紹介する。


TITLE: 「京」による超並列第一原理電子状態計算の進展
SPEAKER: Taisuke Ozaki, Associate Professor of 　准教授 JAIST シミュレーション科学研究センター
TIME: 11:00-11:30
SUMMARY: より現実に近い物質系をより精密にシミュレーションすることで、計算機による物質デザインが可能になりつつある。スーパーコンピュータ「京」は70万コア以上から構成される超並列計算機であり、シミュレーションによる物質科学の進展を大きく後押しするものである。しかし「京」に代表される超大規模並列計算機を有効に活用するには物質科学と情報科学の強固な連携が必要となる。本講演では、「京」による超並列第一原理電子状態計算の最近の進展を紹介し、物質科学シミュレーションの今後の展望を議論する。