Formal Modelling Of The Fate Of Pyruvate Under Aerobic And Anaerobic Conditions Using Petri-Net
Abstract
Human interest in studying biological systems is longstanding. Over the past three decades, advancements in cutting-edge genomics technologies have enabled scientists to generate vast amounts of complex biological data, including complete genomes. To better understand this complex data, including biological pathways, scientists use a range of modelling and simulation techniques. One such approach, Petri nets, has gained significant attention for modelling and simulating biological networks and pathways. Among the various Petri net models, hybrid functional Petri nets are particularly effective for modelling complex biological networks today.
In this study, we utilize Petri nets to model metabolic pathways, aiming to manage complex biological information and derive qualitative insights from the structural representation of pathways. Petri nets are introduced as a tool for computer-implementable pathway representation. They offer the potential to overcome current limitations and enable preliminary qualitative analysis through their various properties.
We apply Petri nets to model the different fates of pyruvate under aerobic and anaerobic conditions, which are crucial for cellular energy supply. During glycolysis, one molecule of glucose is converted into two molecules of pyruvate. Under aerobic conditions, pyruvate is converted into acetyl Co-A, while under anaerobic conditions, it is converted into lactate. Despite lower energy yield under anaerobic conditions compared to aerobic conditions, lactate can be a primary energy source for some cells and is useful in diagnosing disorders such as heart failure, shock, and cancer. When the body’s oxygen demand exceeds supply, cells automatically switch from aerobic to anaerobic conditions. We systematically model, simulate, and validate qualitative models of these pathways using the well-established Petri net analysis technique.
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