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AICS Cafe

AICS Cafe is a place where the researchers in AICS can frankly discuss about their researches beyond their own disciplinary wall in order to collaborate with each other. We plan to have it twice a month regularly. We welcome all people including the promotion office and administration division of K computer in AICS.

  • Purpose : In order to promote the research collaboration beyond each of existing research disciplines, this seminar provides the discussion field for exchanging information, understanding neighboring researchers, and collaboration between each other.
  • Place: Workshop room (6th floor) at AICS
  • Lang : presentation in Japanese or English, the slide in English
  • Etc.: Please give your presentations clearly to researchers in other fields. Please do not hesitate to ask a question to the speakers.

The 105th AICS Cafe
Date and Time: Wed. Feb. 1, 2017, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Exploring data assimilation for plants
Speaker: Hazuki Arakida (Data Assimilation Research Team)

Presentation Language: Japanese
Presentation Material: English

    Abstract: Detail

Vegetation models simulate functions of plants such as carbon and water exchanges between the atmosphere and land surface, and play an essential role in climate simulations. However, the vegetation models have large uncertainties. For example, it is very difficult to simulate accurately the dates when the leaves grow and fall. Data assimilation combines the simulation with actual observations, and can reduce those uncertainties.
We developed a data assimilation system with a vegetation model known as the SEIB-DGVM (Spatially Explicit Individual Base Dynamic Global Vegetation Model). As the first step, an experiment was performed at a single location in Eastern Siberia by assimilating satellite-observed leaf area data. The results showed that the growth and decay of the leaves, carbon cycles and the parameters of the tree and grass were successfully estimated. As the second step, the experiment was expanded to multiple locations in Eastern Siberia. The results were promising.

The 104th AICS Cafe
Date and Time: Wed. Jan. 18, 2017, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Integrated meshing-and-analysis approach for fast-and-robust unstructured finite-element earthquake simulations
Speaker: Kohei Fujita (Computational Disaster Mitigation and Reduction Research Unit)

Presentation Language: English
Presentation Material: English

    Abstract: Detail

Unstructured finite-element methods are widely used in earthquake simulations for accurate modeling of complex three-dimensional geometry and nonlinear material properties. However, its applicability to large-scale problems is often limited by the difficulty of generating high quality mesh and large analysis cost. To overcome these difficulties, we have been developing robust mesh generators and fast analysis methods in an integrated approach. In this talk, I will show Tera Degrees-of-Freedom scale unstructured finite-element earthquake simulations enabled by using the developed method on the full K computer.

The 103rd AICS Cafe
Date and Time: Wed. Jan. 11, 2017, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Turbulence in Atmospheric Simulations
Speaker: Seiya Nishizawa (Computational Climate Science Research Team)

Presentation Language: Japanese
Presentation Material: English

    Abstract: Detail

There exist various spatiotemporal scale phenomena in the atmospheric variability, and they interact with each other. Atmospheric turbulence is small scale variability, and plays an important role in the larger scale phenomena. Because of its small scale, it has been difficult to represent the turbulence directly in atmospheric simulations, so far. The effects of turbulence on large scale phenomena have been taken into account through parameterizations based on empirical rules in simulations. As the development of computers, it has become possible to represent the turbulence in the simulations. I will introduce the importance of the turbulence in the atmospheric variability, and our study on representation of the turbulence in the simulations.

The 102nd AICS Cafe
Date and Time: Wed. Nov. 16, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Assembling a library of 2D projection images from 3D biological shapes to resolve XFEL data
Speaker: Sandhya Tiwari (Computational Structural Biology Research Unit)

Presentation Language: English
Presentation Material: English

    Abstract: Detail

X-ray free electron laser (XFEL) scattering experiments has been described as the future of structural biology. The technique has several advantages, including its ability to probe a single particle sample without the need for crystallisation, and to produce diffraction data before the sample is destroyed by radiation. However, resolving structures from XFEL diffraction patterns can be challenging due to the phase problem. Considering the novelty of the technique, there is also limited data available to provide initial models that fit new diffraction patterns. Therefore, we consider a strategy to provide efficient interpretation of XFEL data by searching them against a database of hypothetical biological shapes to obtain an initial structural model. To build a database of biological shapes, we assemble various three-dimensional (3D) structures in existing structure databanks, such as the Electron Microscopy Data Bank (EMDB). We can then reduce the assembled dataset to a minimal yet distinct set of hypothetical biological shapes. In the first part of this assembly, we present the analysis of single particle cryo-electron microscopy (cryo-EM) structures. Here, we analyse the variation in the shapes that exists within the 3D cryo-EM maps, and within their simulated two-dimensional (2D) projection images. This analysis provides us with the extent to which 2D images of two distinct 3D shapes can be similar, giving us an idea of the expected degeneracy when we compare experimental data to a hypothetical biological shape. In general, we expect that with a sufficient number of 3D shapes will allow us to provide candidate models for new XFEL data effectively.

The 101st AICS Cafe
Date and Time: Wed. Nov. 9, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Large ensemble data assimilation with atmospheric models
Speaker: Keiichi Kondo (Data Assimilation Research Team)

Presentation Language: Japanese
Presentation Material: English

    Abstract: Detail

The weather forecast model is known to be sensitive to the initial conditions because of chaos. Therefore, it is important to estimate accurately the initial conditions for the weather forecast. Data assimilation is a statistical approach to estimate the most optimal state using both model simulation and observation data. The ensemble Kalman filter (EnKF) is one of advanced data assimilation methods. Covariance localization plays an essential role with a limited ensemble size. Localization limits the influence of observations and reduces the impact of sampling errors. In this study, we increase the ensemble size up to 10240, much larger than the typical choice of about 100, and remove the localization completely on EnKF. We will present the results of 10240-member data assimilation experiments and some problems about the large ensemble data assimilation.

The 100th AICS Cafe
Date and Time: Wed. Oct. 19, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Efficient conformational search of proteins using the REST method
Speaker: Motoshi Kamiya (Computational Biophysics Research Team)

Presentation Language: Japanese
Presentation Material: English

    Abstract: Detail

Efficiency of “conformational search” is one of the fundamental issues in the atomic level classical molecular dynamics simulations of biomolecules. It also plays crucial roles in estimations of free energy changes due to structural changes, such as binding of drugs to proteins. Therefore, methodologies aiming at the efficient conformational search have been developed. One of such method, recently developed replica exchange with solute tempering (REST) aims at reducing computational costs without loss of conformational search efficiency. This REST method is proved to be powerful in conformational searches of small proteins.
However, there is a problem in this REST method. Once a trajectory finds a stable structure, the trajectory is often trapped at that structure for a very long period. This structural trapping due to its definition of the energy could introduce significant reductions of the sampling efficiency. To overcome this problem, we modified the REST method. This new REST variant was applied to the folding of artificial TRPcage protein (TC5b). We found that the new method is free from the trapping problem and the computational costs are further reduced in comparison with the original REST method.

The 99th AICS Cafe
Date and Time: Wed. Oct. 5, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: AMUSE simulations of planetary systems and young stellar regions
Speaker: Steven Rieder (Particle Simulator Research Team)

Presentation Language: English
Presentation Material: English

    Abstract: Detail

The number of known planets outside our Solar system has in recent years grown from a handful to a few thousand. Some of these systems have quite exotic planets; such as the recently imaged HD131399 system, which contains three stars and a large planet; and the "Super Saturn"-like ring planet J1407b. In many other systems, the planets are now at locations where they could not have formed, requiring some type of migration to have taken place.
Since most stars form in clustered fashion, the stellar density in their birth environment is relatively high. This makes stellar encounters that could be responsible for such migration possible. In order to get a good estimate of how frequent such encounters really are, accurate modelling of young stellar regions is required. To this end, we create models of observed stellar regions using data from the MYStIX (Massive Young Stellar regions in Infra-red and X-ray) survey and simulate them with AMUSE, the Astrophysical Multipurpose Software Environment. These simulations include gravity, gas dynamics, stellar evolution and binary/multiple stellar systems.
In my talk, I will discuss these models, as well as several other aspects of my ongoing work to simulate these regions, the encounters therein and the possible resulting planetary systems.

The 98th AICS Cafe
Date and Time: Wed. Sep. 21, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Numerical modeling of fluid-structure interaction and its applications
Speaker: Rahul Bale(Complex Phenomena Unified Simulation Research Team)

Presentation Language: English
Presentation Material: English

    Abstract: Detail

Fluid mechanics is the study of fluid flow. It deals with the mathematical modeling of fluid motion to understand the behavior of flow in different scenarios. The motion of a fluid is modeled by the Navier-Stokes (NS) equations. The numerical approach to solving the equations governing fluid flow is known as Computation Fluid Dynamics (CFD). As NS equations model the flow of a fluid isolated from other medium (such as a solid), typically CFD has been used to solve problems involving simple geometry (modeled as boundary conditions) and idealized flow conditions. A realistic scenario of fluid flow almost always involves flow of a fluid around complex geometries, be it man-made (such as a vehicle, urban environment, etc) or natural (such as birds, fishes, etc). One of the techniques of numerically modeling interaction between fluid and solid/structure with complex geometries is the immersed boundary method.
Immersed boundary method can enable numerical simulation of complex systems in engineering and biology to enhance our understanding of these systems.
The challenges, advantages and limitations of immersed boundary methods in the context of HPC will be presented. And, applications of immersed boundary method in engineering and biology will be discussed.

The 97th AICS Cafe
Date and Time: Wed. Sep. 14, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Three-dimensional reconstruction program for coherent diffraction patterns obtained by XFEL
Speaker: Miki Nakano (Computational Structural Biology Research Unit)

Presentation Language: Japanese
Presentation Material: English

    Abstract: Detail

Three-dimensional (3D) structural analysis for single particles using X-ray free electron laser (XFEL) is a new structural biology technique that enables us to observe the molecules, which are hard to be crystallized such as biological molecules and living tissue in the state close to nature. In order to restore the 3D structure of the molecule from the diffraction patterns obtained by XFEL experiments, computational algorithms are necessary as one needs to estimate the incident beam angles to the molecule. We are developing a program package for XFEL analysis based on Xmipp, which is commonly used for image processing of single-particle 3D cryo-electron microscopy. We performed the test of our reconstruction program using diffraction images obtained by tomography experiment for tantalum pentoxide.

The 96th AICS Cafe
Date and Time: Wed. Sep. 7, 2016, 15:30-16:30
Place: Workshop room (6th floor) at AICS

Title: Cooling Technique in Gas Turbine Engine: Film Cooling
Speaker: Chao Wei-Siang (Complex Phenomena Unified Simulation Research Team, Student Trainee)

Presentation Language: English
Presentation Material: English

    Abstract: Detail

As a high efficiency and energy saving engine, gas turbine engines are widely used in modern aircraft and power plant.
After burning all the fuel mixture inside the combustion chamber, gas with high temperature and pressure will be exhausted from the combustion chamber to the turbine stage, the method which gas turbine engine use to generate power is using the hot gas to drive the turbine blades in the turbine stage inside the engine, as a consequence turbine blades have to withstand high temperature and stress which is harmful to the turbine structure.
In order to protect the turbine blades inside the engine, effective cooling techniques are applied on the turbine blades, among all those cooling techniques film cooling is considered as the most necessary cooling technique.