The Biophysics of CRISPR-Based Transcriptional Control
Quantitative models linking guide RNA design, effector biophysics, and resource limits to predictable transcriptional control
Quorum Sensing: Engineering Collective Behavior in Cell Populations
Quantitative frameworks for programming density-dependent collective behaviors in engineered microbial populations
Optogenetic Control Systems: Light-Based Biological Interfaces
Analyzing the bandwidth, spatial precision, and feedback limits governing light-controlled biological regulation
Population Heterogeneity as Engineering Tool
How engineered cell subpopulations performing specialized tasks outperform uniform populations through systematic division of labor
Evolutionary Stability of Engineered Genetic Circuits
Why your genetic circuits fail and how to design systems that evolution preserves rather than destroys
The Logic of Combinatorial Promoter Design
From truth tables to transcription: systematic engineering of promoters that compute Boolean logic from transcription factor inputs.
The Thermodynamics of Genetic Regulatory Networks
How partition functions and binding energies enable principled prediction of gene expression from DNA sequence
Why Biological Circuits Fail: The Hidden Logic of Retroactivity
How molecular sequestration between connected modules undermines synthetic biology's foundational promise of composable design
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.