Choledochal cysts (CCs) are an important risk factor for cholangiocarcinoma, though their etiology remains debated. Given the vital role of bile fluid in digestive processes within the biliary system, examining such mechanisms from the perspective of bile fluid dynamics may offer additional insights for clinical use. This study utilized magnetic resonance imaging (MRI)-based patient-specific scans for detailed reconstruction and further employed the computational fluid dynamic method to assess the physiological functions of each system, including refilling and emptying processes. The impact of bile rheological property was also examined. Key biomechanical parameters—pressure and wall shear stress (WSS)—were displayed on a two-dimensional plane via surface mapping for enhanced visualization and comparative analysis. Outcomes demonstrated a significant reduction in bile flow velocity in CCs patients due to common bile duct's anatomical features and bile's shear-thinning, non-Newtonian nature, with a notable increase in pressure drop observed. In healthy biliary systems, WSS variations were minimal; however, in CCs patients, extreme WSS differences were found, with the highest WSS in the segmental bile duct and the lowest in the dilatation area, presenting a magnitude difference of approximately 1000. CCs one showed WSS levels 100–250 times higher than healthy ones in the common bile duct. Bile rheological properties substantially affect pressure and WSS patterns, particularly WSS, where pathological bile caused a tenfold increase in WSS compared to healthy bile. The findings aimed to enhance the understanding of biliary fluid mechanics in CCs and offer insights into selected fluidic variables for future microfluidic chip experiments.

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