Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in lactococcus lactis

© 2016 John Wiley & Sons Ltd. The second messenger cyclic-di-adenosine monophosphate (c-di-AMP) plays important roles in growth, virulence, cell wall homeostasis, potassium transport and affects resistance to antibiotics, heat and osmotic stress. Most Firmicutes contain only one c-di-AMP synthesizing diadenylate cyclase (CdaA); however, little is known about signals and effectors controlling CdaA activity and c-di-AMP levels. In this study, a genetic screen was employed to identify components which affect the c-di-AMP level in Lactococcus. We characterized suppressor mutations that restored osmoresistance to spontaneous c-di-AMP phosphodiesterase gdpP mutants, which contain high c-di-AMP levels. Loss-of-function and gain-of-function mutations were identified in the cdaA and gdpP genes, respectively, which led to lower c-di-AMP levels. A mutation was also identified in the phosphoglucosamine mutase gene glmM, which is commonly located within the cdaA operon in bacteria. The glmM I154F mutation resulted in a lowering of the c-di-AMP level and a reduction in the key peptidoglycan precursor UDP-N-acetylglucosamine in L. lactis. C-di-AMP synthesis by CdaA was shown to be inhibited by GlmMI154F more than GlmM and GlmMI154F was found to bind more strongly to CdaA than GlmM. These findings identify GlmM as a c-di-AMP level modulating protein and provide a direct connection between c-di-AMP synthesis and peptidoglycan biosynthesis. c-di-AMP is an essential signalling molecule which affects peptidoglycan homeostasis and resistance against various stressors, however little is known regarding how the c-di-AMP level is regulated in the cell. Here we identify the peptidoglycan biosynthesis enzyme GlmM as a modulator of c-di-AMP synthesis through its regulation of diadenylate cyclase enzyme CdaA activity in Lactococcus lactis

A Partitioned Finite Element Method for the Structure-Preserving Discretization of Damped Infinite-Dimensional Port-Hamiltonian Systems with Boundary Control

Many boundary controlled and observed Partial Differential Equations can be represented as port-Hamiltonian systems with dissipation, involving a Stokes-Dirac geometrical structure together with constitutive relations. The Partitioned Finite Element Method, introduced in Cardoso-Ribeiro et al. (2018), is a structure preserving numerical method which defines an underlying Dirac structure, and constitutive relations in weak form, leading to finite-dimensional port-Hamiltonian Differential Algebraic systems (pHDAE). Different types of dissipation are examined: internal damping, boundary damping and also diffusion models

Plasma internal profile control using IDA-PBC:application to TCV

\u3cp\u3eIn this paper, new results of plasma ι-profile and β control on TCV, using total plasma current I \u3csub\u3e p \u3c/sub\u3e, and ECCD (Electron Cyclotron heating and Current Drive) heating source have been discussed. The control model is governed by the resistive diffusion equation coupled with the thermal transport equation, written in PCH (Port-Controlled Hamiltonian) formulation. The IDA-PBC (Interconnection and Damping Assignment - Passivity based Control) controller is developed and tested on simulation as well as on TCV real plant. Two test scenarios are considered: ι control only, and ι and β control. The spatial distributions of ECCD profiles are pre-defined and only input powers are used for control design. Thus, a stationary control is defined in order to consider all non-linearity and actuator constraint, and a linear feedback IDA-PBC will ensure the convergence speed and the robustness of the closed-loop system. The obtained results are encouraging towards using routinely such plasma advanced control algorithm in a near future.\u3c/p\u3

Tokamak-agnostic actuator management for multi-task integrated control with application to TCV and ITER

\u3cp\u3eThe plasma control system (PCS) of a long-pulse tokamak must be able to handle multiple control tasks simultaneously, and must be capable of robust event handling with a limited set of actuators. For ITER, this is particularly challenging given the large number of actuator-conflicting control requirements. To deal with these issues, this work develops a task-based approach, where a plasma supervisory controller and an actuator manager make high-level decisions on how to handle the considered control tasks, using generic actuator resources and controllers. This simplifies the interface for operators and physicists since the generic control tasks (instead of controllers) can be directly defined from the general physics goals. This approach also allows one to decompose the PCS into a tokamak-dependent layer and a tokamak-agnostic layer. The developed scheme is first implemented and tested on TCV for simultaneous β control, neoclassical tearing mode (NTM) control, central co-current drive, and H-mode control tasks. It is then applied to an ITER test scenario to prove its flexibility and applicability to systematically handle a large number of tasks and actuators.\u3c/p\u3

Real-time plasma state monitoring and supervisory control on TCV

In ITER and DEMO, various control objectives related to plasma control must be simultaneously achieved by the plasma control system (PCS), in both normal operation as well as off-normal conditions. The PCS must act on off-normal events and deviations from the target scenario, since certain sequences (chains) of events can precede disruptions. It is important that these decisions are made while maintaining a coherent prioritization between the real-time control tasks to ensure high-performance operation.\u3cbr/\u3e\u3cbr/\u3eIn this paper, a generic architecture for task-based integrated plasma control is proposed. The architecture is characterized by the separation of state estimation, event detection, decisions and task execution among different algorithms, with standardized signal interfaces. Central to the architecture are a plasma state monitor and supervisory controller. In the plasma state monitor, discrete events in the continuous-valued plasma state are modeled using finite state machines. This provides a high-level representation of the plasma state. The supervisory controller coordinates the execution of multiple plasma control tasks by assigning task priorities, based on the finite states of the plasma and the pulse schedule.\u3cbr/\u3e\u3cbr/\u3eThese algorithms were implemented on the TCV digital control system and integrated with actuator resource management and existing state estimation algorithms and controllers. The plasma state monitor on TCV can track a multitude of plasma events, related to plasma current, rotating and locked neoclassical tearing modes, and position displacements.\u3cbr/\u3e\u3cbr/\u3eIn TCV experiments on simultaneous control of plasma pressure, safety factor profile and NTMs using electron cyclotron heating (ECH) and current drive (ECCD), the supervisory controller assigns priorities to the relevant control tasks. The tasks are then executed by feedback controllers and actuator allocation management. This work forms a significant step forward in the ongoing integration of control capabilities in experiments on TCV, in support of tokamak reactor operation

Profile control simulations and experiments on TCV:A controller test environment and results using a model-based predictive controller

\u3cp\u3eThe successful performance of a model predictive profile controller is demonstrated in simulations and experiments on the TCV tokamak, employing a profile controller test environment. Stable high-performance tokamak operation in hybrid and advanced plasma scenarios requires control over the safety factor profile (q-profile) and kinetic plasma parameters such as the plasma beta. This demands to establish reliable profile control routines in presently operational tokamaks. We present a model predictive profile controller that controls the q-profile and plasma beta using power requests to two clusters of gyrotrons and the plasma current request. The performance of the controller is analyzed in both simulation and TCV L-mode discharges where successful tracking of the estimated inverse q-profile as well as plasma beta is demonstrated under uncertain plasma conditions and the presence of disturbances. The controller exploits the knowledge of the time-varying actuator limits in the actuator input calculation itself such that fast transitions between targets are achieved without overshoot. A software environment is employed to prepare and test this and three other profile controllers in parallel in simulations and experiments on TCV. This set of tools includes the rapid plasma transport simulator RAPTOR and various algorithms to reconstruct the plasma equilibrium and plasma profiles by merging the available measurements with model-based predictions. In this work the estimated q-profile is merely based on RAPTOR model predictions due to the absence of internal current density measurements in TCV. These results encourage to further exploit model predictive profile control in experiments on TCV and other (future) tokamaks.\u3c/p\u3

Dependence on plasma shape and plasma fueling for small edge-localized mode regimes in TCV and ASDEX Upgrade

\u3cp\u3eWithin the EUROfusion MST1 work package, a series of experiments has been conducted on AUG and TCV devices to disentangle the role of plasma fueling and plasma shape for the onset of small ELM regimes. On both devices, small ELM regimes with high confinement are achieved if and only if two conditions are fulfilled at the same time. Firstly, the plasma density at the separatrix must be large enough (n\u3csub\u3ee,sep\u3c/sub\u3e/n\u3csub\u3eG\u3c/sub\u3e ∼ 0.3), leading to a pressure profile flattening at the separatrix, which stabilizes type-I ELMs. Secondly, the magnetic configuration has to be close to a double null (DN), leading to a reduction of the magnetic shear in the extreme vicinity of the separatrix. As a consequence, its stabilizing effect on ballooning modes is weakened.\u3c/p\u3

Overview of progress in European medium sized tokamaks towards an integrated plasma-edge/wall solution

\u3cp\u3eIntegrating the plasma core performance with an edge and scrape-off layer (SOL) that leads to tolerable heat and particle loads on the wall is a major challenge. The new European medium size tokamak task force (EU-MST) coordinates research on ASDEX Upgrade (AUG), MAST and TCV. This multi-machine approach within EU-MST, covering a wide parameter range, is instrumental to progress in the field, as ITER and DEMO core/pedestal and SOL parameters are not achievable simultaneously in present day devices. A two prong approach is adopted. On the one hand, scenarios with tolerable transient heat and particle loads, including active edge localised mode (ELM) control are developed. On the other hand, divertor solutions including advanced magnetic configurations are studied. Considerable progress has been made on both approaches, in particular in the fields of: ELM control with resonant magnetic perturbations (RMP), small ELM regimes, detachment onset and control, as well as filamentary scrape-off-layer transport. For example full ELM suppression has now been achieved on AUG at low collisionality with n = 2 RMP maintaining good confinement . Advances have been made with respect to detachment onset and control. Studies in advanced divertor configurations (Snowflake, Super-X and X-point target divertor) shed new light on SOL physics. Cross field filamentary transport has been characterised in a wide parameter regime on AUG, MAST and TCV progressing the theoretical and experimental understanding crucial for predicting first wall loads in ITER and DEMO. Conditions in the SOL also play a crucial role for ELM stability and access to small ELM regimes.\u3c/p\u3

Validation of the ICRF antenna coupling code RAPLICASOL against TOPICA and experiments

In this paper we validate the finite element code RAPLICASOL, which models radiofrequency wave propagation in edge plasmas near ICRF antennas, against calculations with the TOPICA code. We compare the output of both codes for the ASDEX Upgrade 2-strap antenna, and for a 4-strap WEST-like antenna. Although RAPLICASOL requires considerably fewer computational resources than TOPICA, we find that the predicted quantities of experimental interest (including reflection coefficients, coupling resistances, S- and Z-matrix entries, optimal matching settings, and even radiofrequency electric fields) are in good agreement provided we are careful to use the same geometry in both codes