Toward a first-principles integrated simulation of tokamak edge plasmas

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary first-principles, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); and (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns

Effect of plasma shaping on performance in the National Spherical Torus Experiment

The National Spherical Torus Experiment (NSTX) has explored the effects of shaping on plasma performance as determined by many diverse topics including the stability of global magnetohydrodynamic (MHD) modes (e.g., ideal external kinks and resistive wall modes), edge localized modes (ELMs), bootstrap current drive, divertor flux expansion, and heat transport. Improved shaping capability has been crucial to achieving Βt ∼40%. Precise plasma shape control has been achieved on NSTX using real-time equilibrium reconstruction. NSTX has simultaneously achieved elongation κ∼2.8 and triangularity δ∼0.8. Ideal MHD theory predicts increased stability at high values of shaping factor S≡ q95 Ip (a Bt), which has been observed at large values of the S∼37 [MA (m·T)] on NSTX. The behavior of ELMs is observed to depend on plasma shape. A description of the ELM regimes attained as shape is varied will be presented. Increased shaping is predicted to increase the bootstrap fraction at fixed Ip. The achievement of strong shaping has enabled operation with 1 s pulses with Ip =1 MA, and for 1.6 s for Ip =700 kA. Analysis of the noninductive current fraction as well as empirical analysis of the achievable plasma pulse length as elongation is varied will be presented. Data are presented showing a reduction in peak divertor heat load due to increasing in flux expansion. © 2006 American Institute of Physics

Physics Design Requirements for the National Spherical Torus Experiment Liquid Lithium Divertor

Recent NSTX high power divertor experiments have shown significant and recurring benefits of solid lithium coatings on PFC's to the performance of divertor plasmas in both L- and H- mode confinement regimes heated by high-power neutral beams. The next step in this work is installation of a liquid lithium divertor (LLD) to achieve density control for inductionless current drive capability (e.g., about a 15-25% ne decrease from present highest non-inductionless fraction discharges which often evolve toward the density limit, ne/nGW~1), to enable ne scan capability (x2) in the H-mode, to test the ability to operate at significantly lower density for future ST-CTF reactor designs (e.g., ne/nGW = 0.25), and eventually to investigate high heat-flux power handling (10 MW/m2) with longpulse discharges (>1.5s). The first step (LLD-1) physics design encompasses the desired plasma requirements, the experimental capabilities and conditions, power handling, radial location, pumping capability, operating temperature, lithium filling, MHD forces, and diagnostics for control and characterization

Evolution and networks in ancient and widespread symbioses between Mucoromycotina and liverworts

Like the majority of land plants, liverworts regularly form intimate symbioses with arbuscular mycorrhizal fungi (Glomeromycotina). Recent phylogenetic and physiological studies report that they also form intimate symbioses with Mucoromycotina fungi and that some of these, like those involving Glomeromycotina, represent nutritional mutualisms. To compare these symbioses, we carried out a global analysis of Mucoromycotina fungi in liverworts and other plants using species delimitation, ancestral reconstruction, and network analyses. We found that Mucoromycotina are more common and diverse symbionts of liverworts than previously thought, globally distributed, ancestral, and often co-occur with Glomeromycotina within plants. However, our results also suggest that the associations formed by Mucoromycotina fungi are fundamentally different because, unlike Glomeromycotina, they may have evolved multiple times and their symbiotic networks are un-nested (i.e., not forming nested subsets of species). We infer that the global Mucoromycotina symbiosis is evolutionarily and ecologically distinctive

Functional analysis of liverworts in dual symbiosis with Glomeromycota and Mucoromycotina fungi under a simulated Palaeozoic CO2 decline.

Most land plants form mutualistic associations with arbuscular mycorrhizal fungi of the Glomeromycota, but recent studies have found that ancient plant lineages form mutualisms with Mucoromycotina fungi. Simultaneous associations with both fungal lineages have now been found in some plants, necessitating studies to understand the functional and evolutionary significance of these tripartite associations for the first time. We investigate the physiology and cytology of dual fungal symbioses in the early-diverging liverworts Allisonia and Neohodgsonia at modern and Palaeozoic-like elevated atmospheric CO2 concentrations under which they are thought to have evolved. We found enhanced carbon cost to liverworts with simultaneous Mucoromycotina and Glomeromycota associations, greater nutrient gain compared with those symbiotic with only one fungal group in previous experiments and contrasting responses to atmospheric CO2 among liverwort-fungal symbioses. In liverwort-Mucoromycotina symbioses, there is increased P-for-C and N-for-C exchange efficiency at 440 p.p.m. compared with 1500 p.p.m. CO2. In liverwort-Glomeromycota symbioses, P-for-C exchange is lower at ambient CO2 compared with elevated CO2. No characteristic cytologies of dual symbiosis were identified. We provide evidence of a distinct physiological niche for plant symbioses with Mucoromycotina fungi, giving novel insight into why dual symbioses with Mucoromycotina and Glomeromycota fungi persist to the present day.The ISME Journal advance online publication, 27 November 2015; doi:10.1038/ismej.2015.204