Verification of Gyrokinetic codes: theoretical background and applications

In fusion plasmas the strong magnetic field allows the fast gyro-motion to be systematically removed from the description of the dynamics, resulting in a considerable model simplification and gain of computational time. Nowadays, the gyrokinetic (GK) codes play a major role in the understanding of the development and the saturation of turbulence and in the prediction of the subsequent transport. Naturally, these codes require thorough verification and validation. Here we present a new and generic theoretical framework and specific numerical applications to test the faithfulness of the implemented models to theory and to verify the domain of applicability of existing GK codes. For a sound verification process, the underlying theoretical GK model and the numerical scheme must be considered at the same time, which has rarely been done and therefore makes this approach pioneering. At the analytical level, the main novelty consists in using advanced mathematical tools such as variational formulation of dynamics for systematization of basic GK code's equations to access the limits of their applicability. The verification of numerical scheme is proposed via the benchmark effort. In this work, specific examples of code verification are presented for two GK codes: the multi-species electromagnetic ORB5 (PIC) and the radially global version of GENE (Eulerian). The proposed methodology can be applied to any existing GK code. We establish a hierarchy of reduced GK Vlasov-Maxwell equations implemented in the ORB5 and GENE codes using the Lagrangian variational formulation. At the computational level, detailed verifications of global electromagnetic test cases developed from the CYCLONE Base Case are considered, including a parametric $\beta$-scan covering the transition from ITG to KBM and the spectral properties at the nominal $\beta$ value.Comment: 16 pages, 2 Figures, APS DPP 2016 invited pape

First principles gyrokinetic analysis of electromagnetic plasma instabilities

A two-fold analysis of electromagnetic core tokamak instabilities in the framework of the gyrokinetic theory is presented. First principle theoretical foundations of the gyrokinetic theory are used to explain and justify the numerical results obtained with the global electromagnetic particle-in-cell code Orb5 whose model is derived from the Lagrangian formalism. The energy conservation law corresponding to the Orb5 model is derived from the Noether theorem and implemented in the code as a diagnostics for energy balance and conservation verification. An additional Noether theorem based diagnostics is implemented in order to analyse destabilising mechanisms for the electrostatic and the electromagnetic Ion Temperature Gradient (ITG) instabilities in the core region of the tokamak. The transition towards the Kinetic Ballooning Modes (KBM) at high electromagnetic $\beta$ is also investigated.Comment: 22 pages, 10 Figures, material form the ICPP conference 2018, invite

Linear and nonlinear excitation of TAE modes by external electromagnetic perturbations using ORB5

The excitation of toroidicity induced Alfv{\'e}n eigenmodes (TAEs) using prescribed external electromagnetic perturbations (hereafter ``antenna") acting on a confined toroidal plasma as well as its nonlinear couplings to other modes in the system is studied. The antenna is described by an electrostatic potential resembling the target TAE mode structure along with its corresponding parallel electromagnetic potential computed from Ohm's law. Numerically stable long-time linear simulations are achieved by integrating the antenna within the framework of a mixed representation and pullback scheme [A. Mishchenko, et al., Comput. Phys. Commun. \textbf{238} (2019) 194]. By decomposing the plasma electromagnetic potential into symplectic and Hamiltonian parts and using Ohm's law, the destabilizing contribution of the potential gradient parallel to the magnetic field is canceled in the equations of motion. Besides evaluating the frequencies as well as growth/damping rates of excited modes compared to referenced TAEs, we study the interaction of antenna-driven modes with fast particles and indicate their margins of instability. Furthermore, we show first nonlinear simulations in the presence of a TAE-like antenna exciting other TAE modes, as well as Global Alfv\'en Eigenmodes (GAE) having different toroidal wave numbers from that of the antenna

In vitro evaluation of the precision of working casts for implant-supported restoration with multiple abutments

OBJECTIVE: The purpose of this study was to compare the accuracy of two working cast fabrication techniques using strain-gauge analysis. METHODS: Two working cast fabrication methods were evaluated. Based on a master model, 20 working casts were fabricated by means of an indirect impression technique using polyether after splinting the square transfer copings with acrylic resin. Specimens were assigned to 2 groups (n=10): Group A (GA): type IV dental stone was poured around the abutment analogs in the conventional way; Group B (GB), the dental stone was poured in two stages. Spacers were used over the abutment analogs (rubber tubes) and type IV dental stone was poured around the abutment analogs in the conventional way. After the stone had hardened completely, the spacers were removed and more stone was inserted in the spaces created. Six strain-gauges (Excel Ltd.), positioned in a cast bar, which was dimensionally accurate (perfect fit) to the master model, recorded the microstrains generated by each specimen. Data were analyzed statistically by the variance analysis (ANOVA) and Tukey's test (α= 5%). RESULTS: The microstrain values (µepsilon) were (mean±SD): GA: 263.7±109.07µepsilon, and GB: 193.73±78.83µepsilon. CONCLUSION: There was no statistical difference between the two methods studied

Binge eating disorders and psychotherapy: is it possible to systematize a psychodynamic formulation case?

The Core Conflictual Relationship Theme (CCRT) method establishes psychotherapeutic guidelines for a patient's relational patterns. The CCRT was used in the analysis of narratives coming from psychodynamic psychotherapy sessions (taped and transcribed) from a patient suffering from Binge Eating Episodes. The CCRT method made it possible to systematize the connection between psychological conflicts and symptoms, not always an easy task for psychiatrists and psychologists in training.O método Tema Central de Conflito nos Relacionamentos - CCRT sistematiza as inferências feitas por psicoterapeutas dos padrões de relacionamento de pacientes submetidos à psicoterapia. O CCRT foi utilizado na análise das narrativas de uma paciente com Compulsão Alimentar Periódica, submetida a sessões de psicoterapia (gravadas e transcritas). Com o método CCRT foi possível sistematizar a relação entre os conflitos psíquicos e o aparecimento de sintomas, uma tarefa nem sempre fácil para psiquiatras e psicólogos em formação.Universidade Federal de São Paulo (UNIFESP)Universidade de São Paulo Instituto de PsicologiaUniversidade de São Paulo Faculdade de Filosofia, Ciência e Letras de Ribeirão PretoUniversidade de São Paulo Faculdade de Medicina Hospital das ClínicasUNIFESPSciEL

Characterization of novel calcium hydroxide- mediated highly porous chitosan- calcium scaffolds for potential application in dentin tissue engineering

The aim of this study was to develop a highly porous calcium- containing chitosan scaffold suitable for dentin regeneration. A calcium hydroxide (Ca[OH]2) suspension was used to modulate the degree of porosity and chemical composition of chitosan scaffolds. The chitosan solution concentration and freezing protocol were adjusted to optimize the porous architecture using the phase- separation technique. Scanning electron microscopy/energy- dispersive spectroscopy demonstrated the fabrication of a highly porous calcium- linked chitosan scaffold (CH- Ca), with a well- organized and interconnected porous network. Scaffolds were cross- linked on glutaraldehyde (GA) vapor. Following a 28- day incubation in water, cross- linked CH scaffold had no changes on humid mass, and CH- Ca featured a controlled degradability profile since the significant humid mass loss was observed only after 21 (26.0%) and 28- days (42.2%). Fourier- transform infrared spectroscopy indicated the establishment of Schiff base on cross- linked scaffolds, along with calcium complexation for CH- Ca. Cross- linked CH- Ca scaffold featured a sustained Ca2+ release up to 21- days in a humid environment. This porous and stable architecture allowed for human dental pulp cells (HDPCs) to spread throughout the scaffold, with cells exhibiting a widely stretched cytoplasm; whereas, the cells seeded onto CH scaffold were organized in clusters. HDPCs seeded onto CH- Ca featured significantly higher ALP activity, and gene expressions for ALP, Col1, DMP- 1, and DSPP in comparison to CH, leading to a significant 3.5 times increase in calcium- rich matrix deposition. In sum, our findings suggest that CH- Ca scaffolds are attractive candidates for creating a highly porous and bioactive substrate for dentin tissue engineering.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155906/1/jbmb34586.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155906/2/jbmb34586_am.pd