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List of results

• An analytical approach to bistable biological circuit discrimination using real algebraic geometry  + (Journal paper)
• A population-based temporal logic gate for timing and recording chemical events  + (Journal paper)
• Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks  + (Journal paper)
• Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks  + (Journal paper)
• Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli  + (Journal paper)
• Layering assume-guarantee contracts for hierarchical system design  + (Journal paper)
• Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology  + (Journal paper)
• On-chip membrane protein cell-free expression enables development of a direct binding assay: A curious case of potassium channel KcsA-Kv1.3  + (Journal paper)
• Engineering Transcriptional Regulator Effector Specificity Using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor  + (Journal paper)
• Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop  + (Journal paper)
• A MATLAB toolbox for modeling genetic circuits in cell-free systems  + (Journal paper)
• Guidelines for Designing the Antithetic Feedback Motif  + (Journal paper)
• Data-driven network models for genetic circuits from time-series data with incomplete measurements  + (Journal paper)
• Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models  + (Journal paper)
• Layered Feedback Control Overcomes Performance Trade-Off in Synthetic Biomolecular Networks  + (Journal paper)
• Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates  + (Journal paper)
• BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts  + (Journal paper)
• Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications  + (Journal paper)
• Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape  + (Journal paper)
• Rules of the Road: Safety and Liveness Guarantees for Autonomous Vehicles  + (Journal paper)
• Control education for societal-scale challenges: A community roadmap  + (Journal paper)
• Development of cell-free transcription-translation systems in three soil Pseudomonads  + (Journal paper)
• Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation  + (Journal paper)
• Addressable and adaptable intercellular communication via DNA messaging  + (Journal paper)
• Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli  + (Journal paper)
• A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology  + (Journal paper)
• Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence  + (Journal paper)
• Flow-Based Synthesis of Reactive Tests for Discrete Decision-Making Systems with Temporal Logic Specifications  + (Journal paper)
• The effects of time-varying temperature on delays in genetic networks  + (Journal submission)
• Bootstrapping bilinear models of simple vehicles  + (Journal submission)
• Convex Optimal Uncertainty Quantification  + (Journal submission)
• Specification and Synthesis of Reactive Protocols for Aircraft Electric Power Distribution  + (Journal submission)
• Synthesis of Control Protocols for Autonomous Systems  + (Journal submission)
• Cone Invariance and Rendezvous of Multiple Agents  + (Journal submission)
• State Estimation Over Packet Dropping Networks Using Multiple Description Coding  + (Journal submission)
• On a Stochastic Sensor Selection Algorithm with Applications in Sensor Scheduling and Sensor Coverage  + (Journal submission)
• Receding Horizon Control of a Vectored Thrust Flight Experiment  + (Journal submission)
• Model Reduction for Compressible Flows using POD and Galerkin Projection  + (Journal submission)
• Model Predictive Control for Signal Temporal Logic Specifications  + (Journal submission)
• The Effect of Compositional Context on Synthetic Gene Networks  + (Journal submission)
• A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression  + (Journal submission)
• Analysis of primitive genetic interactions for the design of a genetic signal differentiator  + (Journal submission)
• Synthetic mammalian signaling circuits for robust cell population control  + (Journal submission)
• Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline  + (Journal submission)
• Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design  + (Journal submission)
• A Method for Cost-Effective and Rapid Characterization of Genetic Parts  + (Journal submissions)
• Delay-dependent Stability of Genetic Regulatory Networks  + (MS thesis)
• Future Directions in Control in an Information-Rich World  + (Magazine article)
• Appealing to a Non-traditional Audience: A New Approach to Teaching Feedback  + (Magazine article)
• Distributed Computation for Cooperative Control  + (Magazine submission)
• Experiments in Planar Manipulation and Grasping  + (Masters Report)
• Rapid prototyping of biomolecular circuits through module characterization in cell-free expression systems  + (Masters Thesis)
• On Measures of Non-Integrability of Pfaffian Systems  + (Paper)
• Modeling and Control of Epitaxial Thin Film Growth  + (Ph.D. Dissertation)
• Distributed Gradient Systems and Dynamic Coordination  + (PhD Dissertation)
• Bio-Inspired Visuomotor Convergence in Navigation and Flight Control Systems  + (PhD Dissertation)
• Coarse analysis of multiscale systems: diffuser flows, charged particle motion, and connections to averaging theory  + (PhD Dissertation)
• State Estimation in Multi-Agent Decision and Control Systems  + (PhD Dissertation)
• Real-Time Optimal Trajectory Generation for Constrained Dynamical Systems  + (PhD Dissertation)
• Effects of Actuator Limits in Bifurcation Control with Applications to Active Control of Fluid Instabilities in Turbomachinery  + (PhD Dissertation)
• Robotic Manipulation with Flexible Link Fingers  + (PhD Dissertation)
• Robotic Control and Nonholonomic Motion Planning  + (PhD Dissertation)

• Real-time trajectory generation for constrained nonlinear dynamical systems using non-uniform rational B-spline basis functions  + (PhD dissertation)

• Synthetic logic circuits using RNA aptamer against T7 RNA polymerase  + (Preprint)
• Population diversification in a yeast metabolic program promotes anticipation of environmental shifts  + (Preprint)
• Bootstrapping bilinear models of robotic sensorimotor cascades  + (Preprint)
• TuLiP: A Software Toolbox for Receding Horizon Temporal Logic Planning  + (Preprint)
• Quantification and Minimization of Crosstalk Sensitivity in Networks  + (Preprint)
• Distributed Synthesis of Control Protocols for Smart Camera Networks  + (Preprint)
• Decentralized Multi-Agent Optimization via Dual Decomposition  + (Preprint)
• Stability and Performance of Non-Homogeneous Multi-Agent Systems on a Graph  + (Preprint)
• Dynamics and Stability of Low Reynolds Number Swimming Near a Wall  + (Preprint)
• Networks with the Smallest Average Distance and the Largest Average Clustering  + (Preprint)
• Resource optimisation in a wireless sensor network with guaranteed estimator performance  + (Preprint)
• Delay-Based Controller Design for Continuous-Time and Hybrid Applications  + (Preprint)
• Receding Horizon Temporal Logic Planning  + (Preprint)
• Tuning a synthetic in vitro oscillator using control-theoretic tools  + (Preprint)
• Synthesis of Embedded Control Systems with High Sampling Frequencies  + (Preprint)
• A bio-plausible design for visual pose stabilization  + (Preprint)
• Automatic Synthesis of Robust Embedded Control Software  + (Preprint)
• Autonomous Driving in Urban Environments: Approaches, Lessons and Challenges  + (Preprint)
• Receding Horizon Control for Temporal Logic Specifications  + (Preprint)
• Experimental Demonstration of the Dynamics and Stability of a Low Reynolds Number Swimmer Near a Plane Wall  + (Preprint)
• Limits on the network sensitivity function for multi-agent systems on a graph  + (Preprint)
• Simple Delay-Based Implementation of Continuous-Time Controllers  + (Preprint)
• Controlling biological networks by time-delayed signals  + (Preprint)
• A bootstrappable bio-plausible design for visual pose stabilization  + (Preprint)
• Flight dynamics and control of evasive maneuvers: the fruit fly's takeoff  + (Preprint)
• Quantized Consensus via Adaptive Stochastic Gossip Algorithm  + (Preprint)
• A bio-plausible design for visual attitude stabilization  + (Preprint)
• Receding Horizon Temporal Logic Planning for Dynamical Systems  + (Preprint)
• Geometric Control of Particle Manipulation in a Two-Dimensional Fluid  + (Preprint)
• Design of insulating devices for in vitro synthetic circuits  + (Preprint)
• Compositional stability analysis based on dual decomposition  + (Preprint)
• Automatic Conversion Software for the Safety Verification of Goal-Based Control Programs  + (Preprint)
• Probabilistic Safety Analysis of Sensor-Driven Hybrid Automata  + (Preprint)
• On Quantized Consensus by Means of Gossip Algorithm -- Part II: Convergence Time  + (Preprint)
• On Quantized Consensus by Means of Gossip Algorithm -- Part I: Convergence Proof  + (Preprint)
• Real-valued average consensus over noisy quantized channels  + (Preprint)
• Control Program Verification for a Sample Titan Aerobot Mission  + (Preprint)
• Optimal Sensor Hop Selection: Sensor Energy Minimization and Network Lifetime Maximization with Guaranteed System Performance  + (Preprint)
• Kalman Filtering Over A Packet-delaying Network: A Probabilistic Approach  + (Preprint)
• Kalman Filtering Over A Packet Dropping Network: A Probabilistic Perspective  + (Preprint)
• Design and performance of in vitro transcription rate regulatory circuit  + (Preprint)
• Probabilistic Performance of State Estimation Across a Lossy Network  + (Preprint)
• Formal Verification of an Autonomous Vehicle System  + (Preprint)
• Analysis of Dynamics in Escaping Flight Initiation in Drosophila  + (Preprint)
• Failure Probability of Verifiable Goal-based Control Programs due to State Estimation Uncertainty  + (Preprint)
• Model reduction of interconnected linear systems  + (Preprint)
• Distributed Mission and Contingency Management for the DARPA Urban Challenge  + (Preprint)
• Situational Reasoning for Road Driving in an Urban Environment  + (Preprint)
• A Framework for Low--Observable Tra jectory Generation in the Presence of Multiple Radars  + (Preprint)
• Control Over a Packet Dropping Network with Norm Bounded Uncertainties  + (Preprint)
• Sensing, Navigation and Reasoning Technologies for the DARPA Urban Challenge  + (Preprint)
• Estimation schemes for networked control systems using UDP-like communication  + (Preprint)
• Flight control in a flapping-wing fruit fly simulator  + (Preprint)
• Conversion and Verification Procedure for Goal-Based Control Programs  + (Preprint)
• Using Hierarchical Decomposition to Speed Up Average Consensus  + (Preprint)
• Estimation Over Wireless Sensor Networks: Tradeoff between Communication, Computation and Estimation Qualities  + (Preprint)
• Safety Verification of Fault Tolerant Goal-based Control Programs with Estimation Uncertainty  + (Preprint)
• Convergence Properties of Dynamic Agents Consensus Networks with Broken Links  + (Preprint)
• Nonlinear Lateral Control Strategy for Nonholonomic Vehicles  + (Preprint)
• Optimal LQG control across packet-dropping links  + (Preprint)
• Data Transmission over Networks for Estimation and Control  + (Preprint)
• Consensus Seeking Using Multi-Hop Relay Protocol  + (Preprint)
• Asynchronous Distributed Averaging on Communication Networks  + (Preprint)
• Recent research in cooperative control of multivehicle systems  + (Preprint)
• Consensus and Cooperation in Networked Multi-Agent Systems  + (Preprint)
• Effective Sensor Scheduling Schemes in a Sensor Network by Employing Feedback in the Communication Loop  + (Preprint)
• Managing information in networked and multi-agent control systems  + (Preprint)
• A Multi-Model Approach to Identification of Biosynthetic Pathways  + (Preprint)
• Control Over a Network: Using Actuation Buffers to Reduce Transmission Frequency  + (Preprint)
• Analysis of a Digital Clock for Molecular Computing  + (Preprint)
• System architectures and environment modeling for high-speed autonomous navigation  + (Preprint)
• Alice: An information-rich autonomous vehicle for high-speed desert navigation  + (Preprint)
• Linear models for control of cavity flow oscillations  + (Preprint)
• Consensus problems in networks of agents with switching topology and time-delays  + (Preprint)
• Decomposition of Human Motion into Dynamics Based Primitives with Application to Drawing Tasks  + (Preprint)
• Graph Laplacians and Stabilization of Vehicle Formations  + (Preprint)
• Differentially Flat Systems with Inequality Constraints: An Approach to Real-Time Feasible Trajectory Generation  + (Preprint)
• Nonholonomic Mechanical Systems with Symmetry  + (Preprint)
• Rapid Hover to Forward Flight Transitions for a Thrust Vectored Aircraft  + (Preprint)
• Decompositions for Control Systems on Manifolds with an Affine Connection  + (Preprint)
• Real Time Trajectory Generation for Differentially Flat Systems with Unstable Zero Dynamics  + (Preprint)
• Nonlinear Control of Mechanical Systems: A Lagrangian Perspective  + (Preprint)
• Geometric Phases, Control Theory, and Robotics  + (Preprint)
• Stabilization of Trajectories for Systems with Nonholonomic Constraints  + (Preprint)
• Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli  + (Preprint)
• Analysis of Circuits for Dosage Control in Microbial Populations  + (Preprint)
• Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking  + (Preprint)
• How to model DNA replication in stochastic models of synthetic genetic circuits (and why)  + (Preprint)
• Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA  + (Preprint)
• A chemical reaction network model of PURE  + (Preprint)
• Negative autoregulation matches production and demand in synthetic transcriptional networks  + (Preprint (bioRxiv))
• Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation  + (Preprint (conference poster))
• Bifurcation Control of Rotating Stall with Actuator Magnitude and Rate Limits  + (Preprint (parts I & II))
• Cone invariance and rendezvous of multiple agents  + (Published version)
• Dynamics and stability of a class of low Reynolds number swimmers near a wall  + (Published version)
• To Drop or Not to Drop: Design Principles for Kalman Filtering Over Wireless Fading Channels  + (Published version)
• Communication and sensing trade-offs in cooperative mobile networks  + (Published version)
• Variational Principles in Constrained Systems: Theory and Experiments  + (Technical Report)
• Flat systems, equivalence and trajectory generation  + (Technical Report)
• Optimal and Cooperative Control of Vehicle Formations  + (Technical Report)
• Protein degradation in a TX-TL cell-free expression system using ClpXP protease  + (Technical Report)
• Synthesis of Reactive Protocols for Vehicle-to-Vehicle Communication  + (Technical Report)
• Extremal Properties of Complex Networks  + (Technical Report)
• Limits on the Network Sensitivity Function for Multi-Agent Systems on a Graph  + (Technical Report)
• Distributed Receding Horizon Control with Applications to Multi-Vehicle Formation Stabilization  + (Technical Report)
• Tracking for Fully Actuated Mechanical Systems: A Geometric Framework  + (Technical Report)
• Nonholonomic Motion Planning: Steering Using Sinusoids  + (Technical report)
• A Case Study in Approximate Linearization: The Acrobot Example  + (Technical report)
• System-level studies of a cell-free transcription-translation platform for metabolic engineering  + (Technical report)
• Control Primitives for Robot Systems  + (Technical report (preprint))
• The Mechanics and Control of Robotic Locomotion with Applications to Aquatic Vehicles  + (Thesis)
• Autonomous Reorientation of a Manuever-Limited Spacecraft Under Simple Pointing Constraints  + (Thesis)