Constraint-Based Modeling: Predicting Metabolic Capabilities from Stoichiometry
How mass balance alone predicts what cells can achieve without knowing reaction rates
Adaptation Speed-Accuracy Trade-offs in Biological Control Systems
Why every biological controller must choose between responding fast and regulating precisely—and how to navigate this inescapable constraint.
Spatial Organization in Synthetic Biology: Beyond Well-Mixed Assumptions
How scaffolds, condensates, and compartments unlock circuit behaviors impossible in homogeneous solutions
Incoherent Feed-Forward Loops: Nature's Pulse Generators and Filters
How three genes and four regulatory edges compute pulses, fold-changes, and accelerated responses through precisely timed competition.
Oscillator Design Principles: From Gene Networks to Synthetic Clocks
Deriving the mathematical requirements for sustained biochemical oscillations and comparing topological trade-offs in synthetic clock design
Noise Propagation in Genetic Cascades: A Systems Analysis
Understanding how stochastic gene expression cascades through regulatory networks reveals the architectural principles that separate noisy circuits from precise ones.
Bifurcation Analysis for Designing Cellular Decision Switches
Master the mathematical principles that transform uncertain genetic circuits into reliable biological switches with predictable thresholds and engineered memory.
Robustness Through Fragility: The Design Logic of Biological Systems
Why every engineered biological system must choose where to be vulnerable—and how to make that choice deliberately rather than discover it through failure.
Bow-Tie Architecture: Why Evolution Converges on This Network Topology
Discover why evolution repeatedly converges on bow-tie network architecture and how these principles transform biosynthetic pathway design.
Resource Competition: The Hidden Coupling in Synthetic Gene Networks
Understanding why your isolated circuits mysteriously influence each other reveals the economic constraints governing all synthetic biology design.
The Control-Theoretic Foundations of Metabolic Engineering
Mathematical control theory reveals why intuitive metabolic engineering fails and provides systematic frameworks for designing pathways that achieve predictable flux optimization.
The Theory of Ultrasensitive Response in Biochemical Networks
How cells convert gradual molecular signals into decisive switch-like responses through cooperative binding, enzyme saturation, and cascade multiplication.
The Mathematics of Robust Perfect Adaptation in Biological Networks
How integral feedback structures guarantee exact homeostasis regardless of biological parameter variations, enabling principled design of robust synthetic circuits.