Richard M. Murray

This paper introduces dynamical structure functions to model genetic circuits from time-series data with incomplete measurements, demonstrating their ability to explain failure modes in genetic circuits.

The paper demonstrates how bistable switches and quorum sensing can enable ultrasensitive feedback control in microbial populations while avoiding cellular burden.

This paper describes a cost-effective and rapid method for characterizing genetic parts using cell-free lysates and high-throughput techniques.

The paper introduces a MATLAB toolbox for simulating genetic circuits in E. coli-based cell-free systems, demonstrating its ability to predict circuit behavior using Bayesian parameter inference.

The paper analyzes genetic circuits for dosage control in microbial populations using the Lux quorum sensing system and demonstrates the effects of negative feedback and degradase activity on circuit robustness.

The paper develops a two-state model of gene expression that captures chemical reaction dynamics with better accuracy and robustness than traditional models.

The paper develops a dynamical population model and type-1 IFFL controller to simulate and improve wound healing dynamics.

The paper assesses temperature robustness in negative feedback and feedforward loops using experiments and models, finding temperature-dependent changes and parameter regimes that improve robustness.

This paper introduces a layered feedback control system using quorum sensing and internal signaling to maintain homeostasis in heterogeneous cell populations, showing improved robustness against cell heterogeneity.

The paper introduces a theoretical framework for analyzing genetic circuit dynamics, focusing on structural properties to predict bistability and oscillations in biological systems.

The paper introduces a Python package to automatically generate phenomenological models of synthetic biological circuits by reducing complex chemical reaction models.

The paper develops a mathematical framework to analyze paradoxical signaling in synthetic circuits for population control in E. coli, showing non-monotonic growth rate relationships and stability benefits.

This study constructs a xylose-inducible system in Bacillus megaterium to express amyloids CsgA and TasA, finding that only TasA is exported and provides a growth benefit and increased adhesion.

The paper models CRISPRa and CRISPRi systems in E. coli, finding CRISPRa is less affected by dCas9 competition and can support more gRNAs with high activation.

The paper develops a method to characterize engineered T7-based transcription factors using cell-free protein synthesis and validates it through kinetic modeling.

This study shows cooperative interactions enhance robustness of coexistence in spatially structured microbial consortia, while competition leads to spatial heterogeneity and fragile coexistence.

The paper designs and analyzes a layered feedback controller in synthetic biology, showing it combines the benefits of cis and trans feedback mechanisms.

The paper demonstrates a synthetic two-member bacterial community that reaches density and composition steady states controlled by inducer inputs, but shows instability after perturbation.

This study uses stochastic simulations to show that random plasmid partitioning accelerates mutant allele fixation under certain selection regimes.

The paper develops a system for packet-based intercellular communication in bacteria using plasmid conjugation with gRNA-based addressing and integrase-mediated message editing.

This paper provides design guidelines for stable and effective sequestration feedback networks in synthetic biology.

The paper analyzes sequestration feedback systems using control theory to identify performance limits and tradeoffs in biological feedback mechanisms.

The paper models microbial consortia using network topology to show how communication structure affects population control and proposes strategies for robust consortium engineering.

The paper uses Bayesian inference to assess context dependence of parameters in an E. coli growth control circuit across different experimental conditions.

This paper designs a synthetic cell-cell signaling circuit that enables long-distance communication through active AHL pulse propagation in bacterial consortia.

This paper designs a synthetic control circuit to regulate population size and strain ratio in microbial consortia using dual feedback control.

The paper designs a synthetic bacterial community with population density control using feedback loops and molecular sequestration, showing absorbance methods overestimate population density when ccdB is used.

The paper investigates how cell-cell communication circuits operate in a heterogeneous environment, finding that signal diffusion and colony placement affect communication range and speed.

The paper characterizes three quorum sensing systems in E. coli using cell-free and in vivo methods, finding significant genetic and signal crosstalk.