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Understanding non-linearly coupled physics between plasma transport and free-boundary equilibrium evolution is essential to operating future tokamak devices, such as ITER and DEMO, in the advanced tokamak operation regimes. To study the non-linearly coupled physics, we need a simulation tool which can self-consistently calculate all the main plasma physics, taking the operational constraints into account. As the main part of this thesis work, we have developed a full tokamak discharge simulator by combining a non-linear free-boundary plasma equilibrium evolution code, DINA-CH, and an advanced transport modelling code, CRONOS. This tokamak discharge simulator has been used to study the feasibility of ITER operation scenarios and several specific issues related to ITER operation. In parallel, DINA-CH has been used to study free-boundary physics questions, such as the magnetic triggering of edge localized modes (ELMs) and plasma dynamic response to disturbances. One of the very challenging tasks in ITER, the active control of kinetic plasma profiles, has also been studied. In the part devoted to free-boundary tokamak discharge simulations, we have studied dynamic responses of the free-boundary plasma equilibrium to either external voltage perturbations or internal plasma disturbances using DINA-CH. Firstly, the opposite plasma behaviour observed in the magnetic triggering of ELMs between TCV and ASDEX Upgrade has been investigated. Both plasmas experience similar local flux surface expansions near the upper G-coil set and passive stabilization loop (PSL) when the ELMs are triggered, due to the presence of the PSLs located inside the vacuum vessel of ASDEX Upgrade. Secondly, plasma dynamic responses to strong disturbances anticipated in ITER are examined to study the capability of the feedback control system in rejecting the disturbances. Specified uncontrolled ELMs were controllable with the feedback control systems. However, the specifications for fast H-L mode transitions were not fully achievable due to a vertical displacement event (VDE) caused by a strong inward plasma movement. In the part dedicated to full tokamak discharge simulations, firstly, we have introduced the combined DINA-CH/CRONOS tokamak discharge simulator. DINA-CH self-consistently calculates the non-linear evolution of the free-boundary plasma equilibrium with the plasma current diffusion, in response to both controlled poloidal field (PF) coil currents and inductively driven currents in the surrounding conducting system. CRONOS provides the evolution of the plasma profiles by self-consistently solving heat and particle transport with source profiles. Secondly, we have successfully simulated ITER operation scenario 2 as a demonstration of the capabilities of the combined simulator, as well as being a design study in itself. The fusion power ratio to the total auxiliary power Q was about 10 with the application of 53MW of auxiliary heating and current drive (H&CD) power. We have investigated several specific issues related to the tokamak operation, such as the vertical instability, PF coil current limits and poloidal flux consumption during the current ramp-up. Lower hybrid (LH) applied from the initial phase of the plasma current ramp-up increased the safety margins in operating the superconducting PF coils both by reducing resistive ohmic flux consumption and by providing non-inductively driven plasma current. Lastly, we have studied ITER hybrid mode operation, focusing on the operational capability of obtaining a stationary at safety factor (q/) profile at the start of at-top (SOF) phase and sustaining it as long as possible by combining various non-inductively driven current sources. Application of a near on-axis electron cyclotron current drive (ECCD) appears to be effective compared to the far off-axis lower hybrid current drive (LHCD), at least on short time scales. In the active plasma profile control part, we have developed a robust control technique that simplifies the active real-time control of several kinetic plasma profiles in ITER. The response of the plasma profiles to power changes of auxiliary H&CD systems is modelled. To allow real-time update of the plasma profile response model, the related physics are simplified with several assumptions. The electron temperature profile response is modelled by simplifying the electron heat transport equation. The q profile response is modelled by directly relating it to the changes of source current density profiles. The required actuator power changes are calculated using the singular value decomposition (SVD) technique, taking the saturation of the actuator powers into account. The potential of this control technique has been shown by applying it to simulations of the ITER hybrid mode operation.