Stable, high-performance operation of a tokamak requires several plasma control problems to be handled simultaneously. Moreover, the complex physics which governs the tokamak plasma evolution must be studied and understood to make correct choices in controller design. In this thesis, the two subjects have been merged, using control solutions as experimental tool for physics studies, and using physics knowledge for developing new advanced control solutions. The TCV tokamak at CRPP-EPFL is ideally placed to explore issues at the interface between plasma physics and plasma control, by combining a state-of-the-art digital real-time control system with a flexible and powerful set of actuators, in particular the electron cyclotron heating and current drive system (ECRH/ECCD). This unique experimental platform has been used to develop and test new control strategies for three important and reactor-relevant tokamak plasma physics instabilities, including the sawtooth, the edge localized mode (ELM) and the neoclassical tearing mode (NTM). These control strategies offer new possibilities for fusion plasma control and at the same time facilitate studies of the physics of the instabilities with greater precision and detail in a controlled environment. The period of the sawtooth crash, a periodic MHD instability in the core of a tokamak plasma, can be varied by localized deposition of ECRH/ECCD near the q = 1 surface, where q is the safety factor. Exploiting this known physical phenomenon, a sawtooth pacing controller was developed which is able to precisely control the time of appearance of the next sawtooth crash. It was also shown that each individual sawtooth period can be controlled in real-time. A similar scheme is applied to H-mode plasmas with type-I ELMs, where it is shown that pacing regularizes the ELM period. The regular, reproducible and therefore predictable sawtooth crashes obtained by the sawtooth pacing controller have been used to study the relationship between sawteeth and NTMs. It is known that post-crash MHD activity can provide the "seed" island for an NTM, which then grows under its neoclassical bootstrap drive. Experiments are shown which demonstrate that the seeding of 3/2 NTMs by long sawtooth crashes can be avoided by preemptive, crash-synchronized EC power injection pulses at the q = 3/2 rational surface location. NTM stabilization experiments in which the ECRH deposition location is moved in real-time with steerable mirrors have shown effective stabilization of both 3/2 and 2/1 NTMs, and have precisely localized the deposition location that is most effective. Studies of current-profile driven destabilization of tearing modes in TCV plasmas with significant amounts of ECCD show a great sensitivity to details of the current profile, but failed to identify a stationary region in the parameter space in which NTMs are always destabilized. This suggests that transient effects intrinsically play a role. Next to instability control, the simultaneous control of magnetic and kinetic plasma profiles is another key requirement for advanced tokamak operation. While control of kinetic plasma profiles around an operating point can be handled using standard linear control techniques, the strongly nonlinear physics of the coupled profiles complicates the problem significantly. Even more, since internal magnetic quantities are difficult to measure with sufficient spatial and temporal resolution —even after years of diagnostic development— routine control of tokamak plasma profiles remains a daunting and extremely challenging task. In this thesis, a model-based approach is used in which physics understanding of plasma current and energy transport is embedded in the control solution. To this aim, a new lightweight transport code has been derived focusing on simplicity and speed of simulation, which is compatible with the demands for real-time control. This code has been named RAPTOR (RApid Plasma Transport simulatOR). In a first-of-its-kind application, the partial differential equation for current diffusion is solved in real-time during a plasma shot in the TCV control system using RAPTOR. This concept is known in control terms as a state observer, and it is applied experimentally to the tokamak current density profile problem for the first time. The real-time simulation gives a physics-model-based estimate of key plasma quantities, to be controlled or monitored in real-time by different control systems. Any available diagnostics can be naturally included into the real-time simulation providing additional constraints and removing measurement uncertainties. The real-time simulation approach holds the advantage that knowledge of the plasma profiles is no longer restricted to those points in space and time where they are measured by a diagnostic, but that an estimate for any quantity can be computed at any time. This includes estimates of otherwise unmeasurable quantities such as the loop voltage profile or the bootstrap current distribution. In a first closed-loop experiment, an estimate of the internal inductance resulting from the real-time simulation is feedback controlled, independently from the plasma central temperature, by an appropriate mix of co- and counter- ECCD. As a tokamak plasma evolves from one state to another during plasma ramp-up or ramp-down, the profile trajectories must stay within a prescribed operational envelope delimited by physics instabilities and engineering constraints. Determining the appropriate actuator command sequence to navigate this operational space has traditionally been a trial-and-error procedure based on experience of tokamak physics operators. A computational technique is developed based on the RAPTOR code which can calculate these trajectories based on the profile transport physics model, by solving an open-loop optimal control problem. The solution of this problem is greatly aided by the fact that the code returns the plasma state trajectory sensitivities to input trajectory parameters, a functionality which is unique to RAPTOR. This information can also be used to construct linearized models around the optimal trajectory, and to determine the active constraint, which can be used for time-varying closed-loop controller design. This physics-model-based approach has shown excellent results and holds great potential for application in other tokamaks worldwide as well as in future devices.