This page contains a brief summary of my group's current research activities, broken up into the two main areas. More information is available on the individual project pages below and also in the recent publications from my group.
Analysis and Design of Biomolecular Feedback Systems
Feedback systems are a central part of natural biological systems and an important tool for engineering biocircuits that behave in a predictable fashion. The figure at the right gives a brief overview of the approach we are taking to both synthetic and systems biology. There are three main elements to our research:
- Modeling and analysis - we are working to develop rigorous tools for analyzing the phenotype of complex biomolecular systems based on data-driven models. We are particularly interested in systems involving feedback, since causal reasoning often fails in these systems due to the interaction of multiple components and pathways. Work in this are includes system identification, theory for understanding the role of feedback, and methods for building and analyzing models built using high-throughput datasets.
- In vitro testbeds - we are making use of both transcriptional expression systems and protein expression systems to develop "biomolecular breadboards" that can be used to characterize the behavior of circuits in a systematic fashion as part of the design process. Our goal is to help enable rapid prototyping and debugging of biomolecular circuits that can operate either in vitro or in vivo.
- Biocircuit design - engineered biological circuits required a combination of system-level principles, circuit-level design and device technologies in order to allow systematic design of robust systems. We are working on developing new device technologies for fast feedback as well as methods for combining multiple feedback mechanisms to provide robust operation in a variety of contexts. Our goal is to participate in the development of systematic methods for biocircuit design that allow us to overcome current limitations in device complexity for synthetic biocircuits.
- Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies (Army Research Office)
- Actuation of Synthetic Cells Via Proto-Flagellar Motors (NSF)
- An Open Synthetic Biology Toolkit for Engineering Reliable Genetic Circuits in Microbes in Soil (Resnick Sustainability Institute)
- Engineering Replication-, Growth-, and Division-Deficient E. coli for Safe, Stable and Efficient Function (Rosen Center for Bioengineering)
- Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways (NSF)
- Fundamental Biological Factors Underlying Human Performance: From Molecular Diagnostics and Detection to Behavior and Systems Biology (Army Research Office)
- Engineering Durable Cell-Free Biological Capabilities for Advanced Sensing and Prototyping (Army Research Office)
- Enabling Technologies for Cell-Silicon Interfacing (Army Research Office)
- Field-Programmable, Recombinase-Based Biomolecular Circuits (Army Research Office)
- A MATLAB toolbox for modeling genetic circuits in cell-free systems (Vipul Singhal, Zoltan A Tuza, Zachary Z Sun, Richard M Murray, Synthetic Biology, 6(1):ysab007, 2021)
- Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology (Victoria Hsiao, Anandh Swaminathan, and Richard M. Murray, IEEE Control Systems Magazine, 38(3):32-62 , June 2018)
- Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli (Andrew Halleran, Richard M. Murray, ACS Synthetic Biology, 7(2):752–755, 2017)
- Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks (X. Flora Meng, Ania-Ariadna Baetica, Vipul Singhal, Richard M. Murray, Royal Society Interface, 14(130), 2017)
- Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks (Enoch Yeung, Aaron J. Dy, Kyle B. Martin, Andrew H. Ng, Domitilla Del Vecchio, James L. Beck, James J. Collins, Richard M. Murray, Cell Systems, 5(1):11–24.e12, 2017)
- A population-based temporal logic gate for timing and recording chemical events (Victoria Hsiao, Yutaka Hori, Paul W.K. Rothemund, Richard M. Murray, Molecular Systems Biology, 12: 869, 2016)
- Rapid cell-free forward engineering of novel genetic ring oscillators (Henrike Niederholtmeyer, Zachary Sun, Yutaka Hori, Enoch Yeung, Amanda Verpoorte, Richard M Murray and Sebastian J Maerkl, eLife 2015;10.7554/eLife.09771)
- Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions (Melissa K Takahashi, Clarmyra A. Hayes, James Chappell, Zachary Z. Sun, Richard M Murray, Vincent Noireaux, Julius B. Lucks, Methods, 15(85):60-72, 2015)
Design of Reactive Protocols for Networked Control Systems
We are investigating the specification, design and verification of distributed systems that combine communications, computation and control in dynamic, uncertain and adversarial environments. Our goal is to develop methods and tools for designing control policies, specifying the properties of the resulting distributed embedded system and the physical environment, and proving that the specifications are met. We have recently developed a promising set of results in receding horizon temporal logic planning that allow automatic synthesis of protocols for hybrid (discrete and continuous state) dynamical systems that are guaranteed to satisfy the desired properties even in the presence of environmental action. The desired properties are expressed in the language of temporal logic, and the resulting system consists of a discrete planner that plans, in the abstracted discrete domain, a set of transitions of the system to ensure the correct behaviors, and a continuous controller that continuously implements the plan. Application areas include autonomous driving, vehicle management systems, and distributed multi-agent systems.
- Safety-Critical Cyber-Physical Systems: From Validation & Verification to Test & Evaluation (NSF)
- Formal Methods for V&V and T&E of Autonomous Systems (AFOSR)
- Synthesis of Control Protocols for Autonomous Systems, Tichakorn Wongpiromsarn, Ufuk Topcu, Richard M Murray. Unmanned Systems, 2013.
- Synthesis of Reactive Switching Protocols from Temporal Logic Specifications, Jun Liu, Necmiye Ozay, Ufuk Topcu, Richard M Murray. IEEE Transactions on Automatic Control, 2013.
- Receding Horizon Temporal Logic Planning, Tichakorn Wongpiromsarn, Ufuk Topcu, Richard M Murray. IEEE Transactions on Automatic Control, 2012.