Molten Salt Reactors is a class of advanced reactors that is typically characterised by the presence of a molten inorganic salt of a fissile material as fuel. At the moment, this class of reactors is considered one of the promising options in the long run of nuclear power. In the context of safety assessment of the MSFR, a task on analysis of selected transients was planned by the SAMOFAR project, to which this thesis should contribute. In addition, fluids with high melting temperature bring with them challenges regarding solidification of the fluid and possible flow blockage, to which a method was implemented during this thesis to evaluate the consequences. The open core cavity with curved shape adds another issue where the core is highly turbulent and requires the use of unstructured mesh codes for routine analysis, adding uncertainty and computational burden to the analytical workflow. Using ATARI, the tool developed during this thesis, we: 1. Analyse the MSFR together with partners in support of a safety assessment task. 2. Consider the impact and how to include solidification/melting in an analytical methodology. 3. Evaluate options to manage/reduce uncertainties and the burden of routine use of high-fidelity codes. After a careful derivation of the conservation laws and assembling the code main algorithms, ATARI undergoes verification in a limited scope using the Stefan problem, manufactured solutions and energy balances. The nuclear cavity benchmark was performed between SAMOFAR partners showing equivalency of the codes within the scope of the benchmark. Then the participating institutions perform analysis of the MSFR for the safety assessment task, which ATARI is unable to followup with the transient analysis. The reason for failure is identified as the requirement of appropriate acceleration schemes by OpenFOAM-based multiphysics solvers, and the lack of one in ATARI. In the lack of accurate data regarding the heat exchangers, the impact of solidification is evaluated in a few simplified cases of a pipe with square cross-section and heat exchanger. For different salt compositions and different boundary conditions, the heat exchanger is found to recover from blockage if pump maintains its momentum and some cross-flow is allowed. The recovery of cases with abrupt solidification is questionable due to the required pressure head. The use of flow baffles is investigated as an option to structure the flow inside the reactor and reduce uncertainties originating from turbulence modelling while allowing the use of structured mesh codes for analysis. The concept is tested in a chloride based MSR, which retains its breed and burn mode while showing a quasi-1D flow appropriate for modelling with legacy codes. We recommend that the nuclear cavity benchmark should be expanded to include a more demanding transient case, representative of MSFR transient analysis requirements. A case is made for homogenised and economical models as used in ATARI to enable the practical use of coupling methods that promote the simultaneous solution of equations. A niche for ATARI is found as a special-mission code for analysis of challenging cases with deforming structure and flow field that justifies the use of unstructured meshes and the added computational burden. Due to design uncertainties and their nature, it is recommended to consider solidification implicitly when analysing the MSFR fuel circuit.