The research reactor MARIA is channel type reactor situated in the National Center for Nuclear Research in Swierk and is an important supplier of the pharmaceutical radioisotopes for various uses. Apart from isotopes production, the research reactor it is used to investigate structural materials, which are operating in the irradiated environment and used in nuclear industry. With the conversion from the HEU (High Enriched Uranium) to LEU (Low Enriched Uranium), there was a need for coolant circuit design modifications and additional safety report preparation due to safety requirements of IAEA. The necessity of the modifications were caused by different geometry of LEU fuel comparing to the old design. The HEU fuel was designed as a six plates formed into the shape of cylinder, while the heat transfer area in active region for LEU design was decreased by one cylindrical pipe. Changes in primary circuit resulted in the requirement of the new model of the reactor thermalhydraulic system, for the purposes of the safety analysis report. The unique design of the reactor core demands the experience in modeling using thermalhydraulic code, but with the acknowledgement of some limitations of the code, which have to be omitted by the user. Due to the multiplicity of the channels type of LEU and HEU respectively, some channels are identical and can be merged into zones (peripheral and central), representing different power distributions. This decreases the time needed for the calculations of the scenarios and enables the flexibility to create various core configurations. The use of programming skills allowed to decrease the amount of actions taken by the code user while defining channels in the core. The automation is made by connections of the pre-modelled channels into zones and finally into core, by the use of dedicated program written in Python. Created model of research reactor will help to predict possible scenarios during operation and identified accident sequences. The presented results in the paper describe the progression of threatening scenarios: leakage of the coolant from the one of the channel circuits and loss of flow accident.