pFBA

pFBA stands for primal-dual interior-point method for flux balance analysis. It is a computational method used in systems biology to determine the optimal metabolic flux distribution in a biological system. Flux balance analysis (FBA) itself is a technique that models cellular metabolism as a network of biochemical reactions and uses optimization principles to predict the flow of metabolites through this network under specific conditions.

pFBA is an enhancement to standard FBA. Standard FBA typically aims to maximize or minimize a single objective function, such as biomass production. However, biological systems are often more complex and may exhibit multiple optimal states or exhibit trade-offs between different objectives. pFBA addresses this by incorporating an additional objective function, often related to minimizing the total metabolic flux or energy expenditure, while still satisfying the primary objective.

The "primal-dual interior-point" aspect refers to the specific type of mathematical algorithm used to solve the optimization problem. This class of algorithms is known for its efficiency and robustness in handling large-scale linear programming problems, which are characteristic of metabolic network models. By solving the constrained optimization problem, pFBA can identify metabolic states that are not only efficient in terms of a primary goal but also energetically feasible and less wasteful. This provides a more realistic representation of cellular metabolism. The results from pFBA can help researchers understand metabolic trade-offs, identify potential bottlenecks, and engineer metabolic pathways for biotechnological applications.