Yohei Yamada

The Non-hydrostatic Icosahedral Atmospheric Model: description and development

This article reviews the development of a global non-hydrostatic model, focusing on the pioneering research of the Non-hydrostatic Icosahedral Atmospheric Model (NICAM). Very high resolution global atmospheric circulation simulations with horizontal mesh spacing of approximately O (km) were conducted using recently developed supercomputers. These types of simulations were conducted with a specifically designed atmospheric global model based on a quasi-uniform grid mesh structure and a non-hydrostatic equation system. This review describes the development of each dynamical and physical component of NICAM, the assimilation strategy and its related models, and provides a scientific overview of NICAM studies conducted to date.

Task-specific signal transmission from prefrontal cortex in visual selective attention

Our voluntary behaviors are thought to be controlled by top-down signals from the prefrontal cortex that modulate neural processing in the posterior cortices according to the behavioral goal. However, we have insufficient evidence for the causal effect of the top-down signals. We applied a single-pulse transcranial magnetic stimulation over the human prefrontal cortex and measured the strength of the top-down signals as an increase in the efficiency of neural impulse transmission. The impulse induced by the stimulation transmitted to different posterior visual areas depending on the domain of visual features to which subjects attended. We also found that the amount of impulse transmission was associated with the level of attentional preparation and the performance of visual selective-attention tasks, consistent with the causal role of prefrontal top-down signals.

Hurricanes and Climate: The U.S. CLIVAR Working Group on Hurricanes

AbstractWhile a quantitative climate theory of tropical cyclone formation remains elusive, considerable progress has been made recently in our ability to simulate tropical cyclone climatologies and to understand the relationship between climate and tropical cyclone formation. Climate models are now able to simulate a realistic rate of global tropical cyclone formation, although simulation of the Atlantic tropical cyclone climatology remains challenging unless horizontal resolutions finer than 50 km are employed. This article summarizes published research from the idealized experiments of the Hurricane Working Group of U.S. Climate and Ocean: Variability, Predictability and Change (CLIVAR). This work, combined with results from other model simulations, has strengthened relationships between tropical cyclone formation rates and climate variables such as midtropospheric vertical velocity, with decreased climatological vertical velocities leading to decreased tropical cyclone formation. Systematic differences...

Revolutionizing Climate Modeling with Project Athena: A Multi-Institutional, International Collaboration

The importance of using dedicated high-end computing resources to enable high spatial resolution in global climate models and advance knowledge of the climate system has been evaluated in an international collaboration called Project Athena. Inspired by the World Modeling Summit of 2008 and made possible by the availability of dedicated high-end computing resources provided by the National Science Foundation from October 2009 through March 2010, Project Athena demonstrated the sensitivity of climate simulations to spatial resolution and to the representation of subgrid-scale processes with horizontal resolutions up to 10 times higher than contemporary climate models. While many aspects of the mean climate were found to be reassuringly similar, beyond a suggested minimum resolution, the magnitudes and structure of regional effects can differ substantially. Project Athena served as a pilot project to demonstrate that an effective international collaboration can be formed to efficiently exploit dedicated sup...

Computational challenges in cell simulation: a software engineering approach

Molecular biologys advent in the 20th century has exponentially increased our knowledge about the inner workings of life. We have dozens of completed genomes and an array of high-throughput methods to characterize gene encodings and gene product operation. The question now is how we will assemble the various pieces. In other words, given sufficient information about a living cells molecular components, can we predict its behavior? We introduce the major classes of cellular processes relevant to modeling, discuss software engineerings role in cell simulation, and identify cell simulation requirements. Our E-Cell project aims to develop the theories, techniques, and software platforms necessary for whole-cell-scale modeling, simulation, and analysis. Since the projects launch in 1996, we have built a variety of cell models, and we are currently developing new models that vary with respect to species, target subsystem, and overall scale.

Madden–Julian Oscillation prediction skill of a new-generation global model demonstrated using a supercomputer

Global cloud/cloud system-resolving models are perceived to perform well in the prediction of the Madden–Julian Oscillation (MJO), a huge eastward -propagating atmospheric pulse that dominates intraseasonal variation of the tropics and affects the entire globe. However, owing to model complexity, detailed analysis is limited by computational power. Here we carry out a simulation series using a recently developed supercomputer, which enables the statistical evaluation of the MJO prediction skill of a costly new-generation model in a manner similar to operational forecast models. We estimate the current MJO predictability of the model as 27 days by conducting simulations including all winter MJO cases identified during 2003–2012. The simulated precipitation patterns associated with different MJO phases compare well with observations. An MJO case captured in a recent intensive observation is also well reproduced. Our results reveal that the global cloud-resolving approach is effective in understanding the MJO and in providing month-long tropical forecasts.

Overcoming memory T-cell responses for induction of delayed tolerance in nonhuman primates.

The presence of alloreactive memory T cells is a major barrier for induction of tolerance in primates. In theory, delaying conditioning for tolerance induction until after organ transplantation could further decrease the efficacy of the regimen, since preexisting alloreactive memory T cells might be stimulated by the transplanted organ. Here, we show that such “delayed tolerance” can be induced in nonhuman primates through the mixed chimerism approach, if specific modifications to overcome/avoid donor‐specific memory T‐cell responses are provided. These modifications include adequate depletion of CD8+ memory T cells and timing of donor bone marrow administration to minimize levels of proinflammatory cytokines. Using this modified approach, mixed chimerism was induced successfully in 11 of 13 recipients of previously placed renal allografts and long‐term survival without immunosuppression could be achieved in at least 6 of these 11 animals.

Immune recognition and rejection of allogeneic skin grafts

The transplantation of allogeneic skin grafts is associated with a potent inflammatory immune response leading to the destruction of donor cells and the rejection of the graft. Shortly after transplantation, skin dendritic cells (DCs) migrate out of the graft through lymphatic vessels and infiltrate the recipients draining lymph nodes where they present donor antigens via two mechanisms: the direct pathway, in which T cells recognize intact donor MHC antigens on donor DCs; and the indirect pathway, involving T-cell recognition of donor peptides bound to self-MHC molecules on recipient DCs. Some recent studies have suggested that T cells can become activated via recognition of donor MHC molecules transferred on recipient antigen-presenting cells (semidirect pathway). Activation of T cells via direct or indirect allorecognition is sufficient to trigger acute rejection of allogeneic skin grafts. In addition, allospecific antibodies contribute to the rejection process either by killing allogeneic targets in a complement-dependent fashion or by opsonizing donor cells and forming immune complexes. Finally, several studies demonstrate that NK cells, activated due to missing self-MHC class I molecules on allogeneic cells, are involved in allogeneic skin graft rejection via direct killing of donor cells and through the production of proinflammatory cytokines including IFN-γ and TNF-α.

Projection of changes in tropical cyclone activity and cloud height due to greenhouse warming: Global cloud‐system‐resolving approach

[1]xa0Tropical cyclone (TC) activity change due to global warming (GW) has been investigated using general circulation models. However, they involve uncertainty in treating the ensemble effects of deep convections. Here we sidestep such uncertainty by using a global cloud-system-resolving model (GCRM) and assess TC changes with a time-slice experiment for the present-day and future GW experiments spanning 5 months each. The results support the Intergovernmental Panel on Climate Change Fourth Assessment Report; reduction in global frequency but increase in more intense TCs. Consistent with recent studies, frequency is reduced over the North Atlantic due to intensified vertical wind shear. Over the Pacific, frequency is almost unchanged and the genesis location shifts eastward under the prescribed El-Nino like sea surface temperature change. With the GCRMs advantage of representing mesoscale properties, we find that the cloud height becomes taller for more intense TCs and that this relationship is strengthened with GW.

The Intra-Seasonal Oscillation and its control of tropical cyclones simulated by high-resolution global atmospheric models

Project Athena is an international collaboration testing the efficacy of high-resolution global climate models. We compare results from 7-km mesh experiments of the Nonhydrostatic Icosahedral Atmospheric Model (NICAM) and 10-km mesh experiments of the Integrated Forecast System (IFS), focusing on the Intra-Seasonal Oscillation (ISO) and its relationship with tropical cyclones (TC) among the boreal summer period (21 May–31 Aug) of 8xa0years (2001–2002, 2004–2009). In the first month of simulation, both models capture the intra-seasonal oscillatory behavior of the Indian monsoon similar to the observed boreal summer ISO in approximately half of the 8-year samples. The IFS simulates the NW–SE-oriented rainband and the westerly location better, while NICAM marginally reproduces mesoscale organized convective systems and better simulates the northward migration of the westerly peak and precipitation, particularly in 2006. The reproducibility of the evolution of MJO depends on the given year; IFS simulates the MJO signal well for 2002, while NICAM simulates it well for 2006. An empirical orthogonal function analysis shows that both models statistically reproduce MJO signals similar to observations, with slightly better phase speed reproduced by NICAM. Stronger TCs are simulated in NICAM than in IFS, and NICAM shows a wind-pressure relation for TCs closer to observations. TC cyclogenesis is active during MJO phases 3 and 4 in NICAM as in observations. The results show the potential of high-resolution global atmospheric models in reproducing some aspects of the relationship between MJO and TCs and the statistical behavior of TCs.