4 papers
Thermodynamic Constraints Drive Hierarchical Preemption in Cellular Decision-Making: A Hybrid Petri Net Framework with Application to Bacillus subtilis Sporulation
Eugenio Simao
Cellular decision-making under stress involves rapid pathway selection despite energy scarcity. Here we demonstrate that thermodynamic constraints actively drive energy-efficient s…
Unifying Weak Independence and Signal Hierarchy Theory: Extended Biological Petri Net Formalism with Application to Vibrio fischeri Quorum Sensing
Eugenio Simao
Biological Petri Nets (Bio-PNs) require extensions beyond classical formalism to capture biochemical reality: multiple reactions simultaneously affect shared metabolites through co…
Hierarchical Preemption: A Novel Information-Theoretic Control Mechanism in Lambda Phage Decision-Making
Eugenio Simao
Biological systems organize into hierarchies to manage complexity, yet the mechanisms governing hierarchical control remain incompletely understood. Using information theory and th…
Weak Independence and Coupled Parallelism in Biological Petri Nets
Eugenio Simao
Motivation: Biological Petri Nets (Bio-PNs) model biochemical pathways where multiple reactions simultaneously affect shared metabolites through convergent production or regulatory…