“…The modeling and simulations can examine not only the details of modular metabolic pathways of a mitochondrion, but can also be used to describe interactions of these pathways [ 117 , 118 ]. The major pathways ( Figure 5 ) include energy metabolism [ 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 ], ROS production [ 117 , 118 , 119 , 120 , 121 , 122 ], amino acid metabolism [ 123 ], calcium homeostasis [ 124 , 125 ], and biosynthesis of various molecules [ 126 ] ( Figure 5 ). Dysfunctions of these pathways are critical for the development of neurodegenerative diseases directly or indirectly via ROS-related pathways [ 19 , 127 ].…”