Direct RNA sequence analysis of the E2 gene of wild-type MHV-4 and of neutralization resistant, neuroattenuated variants has identified a polymorphic region with respect to deletions. These variants had large deletions of 142 to 159 amino acids mapping to a localized region in the amino-terminal domain of the peplomer glycoprotein. The nucleotide sequence of the E2 gene for wild-type strain MHV-4 was found to be very similar to that of MHV-JHM but had an insertion of 423 nucleotides resulting in the addition of a stretch of 141 unique amino acids in the amino-terminal domain of E2. We propose that deletions reflect a major source of heterogeneity in the E2 protein of MHV.

Following intracerebral inoculation of adult Balb/c Byj mice, the MHV-4 strain of mouse hepatitis virus (MHV) had an LD50 of less than 0.1 PFU, whereas its monoclonal antibody resistant variant V5A13.1 had an LD50 of 10(4.2) PFU. To determine the basis for this difference in neurovirulence we have studied the acute central nervous system (CNS) infection of these two viruses by in situ hybridization. Both viruses infected the same, specific neuroanatomical areas, predominantly neurons, and spread via the cerebrospinal fluid, along neuronal pathways and between adjacent cells. The neuronal nuclei infected and the spread of virus within the brain are described. The main difference between the parental and variant viruses was the rate at which the infection spread. MHV-4 spread rapidly, destroying large numbers of neurons and the animals died within 4 days of infection. The variant virus spread to the same areas of the brain but at a slower rate. This difference in the rate of virus spread was also apparent from the brain virus titers. The slower rate of spread of the variant virus appears to allow intervention by the immune response. Consistent with this, the variant virus spread slowly in athymic nu/nu mice, but in the absence of an intact immune response, infection and destruction of neurons eventually reached the same extent as that of the parental virus and the mice died within 6 days of infection. We conclude that the V5A13.1 variant of MHV-4 is neuroattenuated by its slower rate of spread in the CNS.

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons analogous to Chen and Parker [Phys. Plasmas 8, 441 (2001)]. Two representative long wavelength modes, shear Alfvén waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries.

A gyrokinetic ion/mass-less fluid electron hybrid model as implemented in the GEM code [Y. Chen and S. E. Parker, J. Comput. Phys. 220, 837 (2007)] is used to study the reverse shear Alfvén eigenmodes (RSAE) observed in DIII-D, discharge #142111. This is a well diagnosed case with measurement of the core-localized RSAE mode structures and the mode frequency, which can be used to compare with simulations. Simulations reproduce many features of the observation, including the mode frequency up-sweeping in time and the sweeping range. A new algorithmic feature is added to the GEM code for this study. Instead of the gyrokinetic Poisson equation itself, its time derivative, or the vorticity equation, is solved to obtain the electric potential. This permits a numerical scheme that ensures the E × B convection of the equilibrium density profiles of each species cancel each other in the absence of any finite-Larmor-radius effects. These nonlinear simulations generally result in an electron temperature fluctuation level that is comparable to measurements, and a mode frequency spectrum broader than the experimental spectrum. The spectral width from simulations can be reduced if less steep beam density profiles are used, but then the experimental fluctuation level can be reproduced only if a collision rate above the classical level is assumed. © 2013 American Institute of Physics.

A fast edge turbulence suppression event has been simulated in the electrostatic version of the gyrokinetic particle-in-cell code XGC1 in a realistic diverted tokamak edge geometry under neutral particle recycling. The results show that the sequence of turbulent Reynolds stress followed by neoclassical ion orbit-loss driven together conspire to form the sustaining radial electric field shear and to quench turbulent transport just inside the last closed magnetic flux surface. The main suppression action is located in a thin radial layer around ψ0.96-0.98, where ψN is the normalized poloidal flux, with the time scale ∼0.1 ms.

A fully implicit particle-in-cell method for handling the v∥-formalism of electromagnetic gyrokinetics has been implemented in XGC. By choosing the v∥-formalism, we avoid introducing the nonphysical skin terms in Ampère's law, which are responsible for the well-known “cancellation problem” in the p∥-formalism. The v∥-formalism, however, is known to suffer from a numerical instability when explicit time integration schemes are used due to the appearance of a time derivative in the particle equations of motion from the inductive component of the electric field. Here, using the conventional δf scheme, we demonstrate that our implicitly discretized algorithm can provide numerically stable simulation results with accurate dispersive properties. We verify the algorithm using a test case for shear Alfvén wave propagation in addition to a case demonstrating the ion temperature gradient-kinetic ballooning mode (ITG-KBM) transition. The ITG-KBM transition case is compared to results obtained from other δf gyrokinetic codes/schemes, whose verification has already been archived in the literature.

Joint experiment/theory/modelling research has led to increased confidence in predictions of the pedestal height in ITER. This work was performed as part of a US Department of Energy Joint Research Target in FY11 to identify physics processes that control the H-mode pedestal structure. The study included experiments on C-Mod, DIII-D and NSTX as well as interpretation of experimental data with theory-based modelling codes. This work provides increased confidence in the ability of models for peeling-ballooning stability, bootstrap current, pedestal width and pedestal height scaling to make correct predictions, with some areas needing further work also being identified. A model for pedestal pressure height has made good predictions in existing machines for a range in pressure of a factor of 20. This provides a solid basis for predicting the maximum pedestal pressure height in ITER, which is found to be an extrapolation of a factor of 3 beyond the existing data set. Models were studied for a number of processes that are proposed to play a role in the pedestal ne and Te profiles. These processes include neoclassical transport, paleoclassical transport, electron temperature gradient turbulence and neutral fuelling. All of these processes may be important, with the importance being dependent on the plasma regime. Studies with several electromagnetic gyrokinetic codes show that the gradients in and on top of the pedestal can drive a number of instabilities. © 2013 IAEA, Vienna.