Preprint archive
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This page contains a list of all papers, reports and preprints available on this wiki. Preprints are listed in reverse chronological order (more or less). In addition to the information on this page, you can also find all of my papers and many preprints on Google Scholar.
This is a searchable database.
2024e_Gra+24-TRO
- Flow-Based Synthesis of Reactive Tests for Discrete Decision-Making Systems with Temporal Logic Specifications
- Josefine B. Graebener, Apurva S. Badithela, Denizalp Goktas, Wyatt Ubellacker, Eric V. Mazumdar, Aaron D. Ames, Richard M. Murray
- Submitted, IEEE Transactions on Robotics, 2024
2024d_JM24-ACSSynBio
- Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence
- Zoila Jurado, Richard M. Murray
- Submitted, ACS Synthetic Biology, 2024
2024c_Inc+24-CDC
- Specifying and Analyzing Networked and Layered Control Systems Operating on Multiple Clocks
- Inigo Incer, Noel Csomay-Shanklin, Aaron Ames, Richard M. Murray
- To appear, 2024 Conference on Decision and Control (CDC)
2024b_Hu+24-ACSSynBio
- A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology
- Chelsea Y Hu, John B McManus, Fatemeh Aghlmand, Elin M Larsson, Azita Emami, Richard M Murray
- Submitted, ACS Synthetic Biology, 2024
2024a_Zha+24-SEED
- Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency
- Y. Zhang, Y. Qiu, M. Deveikis, Z. A. Martinez, T.-F. Chou, P. Freemont, R. M. Murray
- SEED, 2024
2023k_MMT23-SEED
- TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering
- Zachary A Martinez, Richard M. Murray, Matt W. Thomson
- Submitted, 2024 SEED
2023j_LMN23-ACSSynBio
- Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation
- Elin M. Larsson, Richard M. Murray, Dianne K. Newman
- ACS Synthetic Biology, 2024
2023i_mm24-acc
- Efficient local validation of partially ordered models via Baysian directed sampling
- Kellan Moorse and Richard Murray
- Submitted, 2024 American Control Conference (ACC)
2023h_JPM23-bioRxiv
- A chemical reaction network model of PURE
- Zoila Jurado, Ayush Pandey, Richard M. Murray
- BioRxiv preprint, 2023
2023h_Inc+23=TCPS
- Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design
- Inigo Incer, Apurva Badithela, Josefine Graebener, Piergiuseppe Mallozzi, Ayush Pandey, Sheng-Jung Yu, Albert Benveniste, Benoit Caillaud, Richard M. Murray, Alberto Sangiovanni-Vincentelli, Sanjit A. Seshia
- Submitted, ACM Transactions on Cyber-Physical Systems (TCPS), Aug 2023
2023f_MLM23-ACSSynBio
- Development of cell-free transcription-translation systems in three soil Pseudomonads
- Joseph T. Meyerowitz, Elin M. Larsson, Richard M. Murray
- To appear, ACS Synthetic Biology, 2024
2023d_MM23-NatureComms
- Addressable and adaptable intercellular communication via DNA messaging
- John P. Marken and Richard M. Murray
- Nature Communications, 14:2358, 2023
2023c_KM23-SEED
- Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation
- Manisha Kapasiawala and Richard M. Murray
- SEED 2023
2023c_Ros+23:ARC
- Control education for societal-scale challenges: A community roadmap
- John Anthony Rossiter, Christos G. Cassandras, João Hespanha, Sebastian Dormido, Luis de la Torre, Gireeja Ranade, Antonio Visioli, John Hedengren, Richard M. Murray, Panos Antsaklis, Francoise Lamnabhi-Lagarrigue, Thomas Parisini
- Annual Reviews in Control, 55:1-17, 2023
2023c_Agh+23-ISSCC
- A 65nm CMOS Living-Cell Dynamic Fluorescence Sensor with 1.05fA Sensitivity at 600/700nm Wavelengths
- Fatemeh Aghimand, Chelsea Hu, Saransh Sharma, Krishna K. Pochana, Richard M. Murray, Azita Emami
- 2023 IEEE International Solid-State Circuits Conference (ISSCC)
2023c_SGRM23-ICRA
- A Model-Free Algorithm for Extremely Resilient Navigation
- Christian J. Stromberger, Josefine B. Graebener, James F. Ragan, and Richard M. Murray
- Submitted, 2024 International Conference on Robotics and Automation (ICRA)
2023b_bwm23-iros
- Evaluation Metrics of Object Detection for Quantitative System-Level Analysis of Autonomous Systems
- Apurva Badithela, Tichakorn Wongpiromsarn, and Richard M. Murray
- To appear, 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)
2023a_Inc+23-FMCAD
- Context-Aided Variable Elimination for Requirement Engineering
- Inigo Incer, Albert Benveniste, Richard M. Murray, Alberto Sangiovanni-Vincentelli, Sanjit A. Seshia
- Submitted, 2023 Formal Methods in Computer-Aided Design (FMCAD)
2023a_AAMA23-TAC
- Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications
- Prithvi Akella, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames
- Submitted, IEEE Transactions on Automatic Control, 2023
2023a_bgim23-nfm
- Reasoning over Test Specifications using Assume-Guarantee Contracts
- Apurva Badithela, Josefine B. Graebener, Inigo Incer, and Richard M. Murray
- Submitted, NASA Formal Methods (NFM), 2023
2022o_whp+22-ploscompbio
- BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts
- William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M. Murray
- PLoS Computational Biology, 18(4), e1009987, 2022
2022n_PRPM22-biorxiv
- Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline
- Ayush Pandey, Makena L. Rodriguez, William Poole, Richard M. Murray
- ACS Synthetic Biology, 12(2):511–523, 2023
2022m_BGM22-rss_workshop
- Minimally Constrained Testing for Autonomy with Temporal Logic Specifications
- Apurva Badithela, Josefine Graebener, Richard M. Murray
- RSS 2022 Workshop on Envisioning an Infrastructure for Multi-Robot and Collaborative Autonomy Testing and Evaluation
2022k_WM22-NatureComms
- Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli
- Rory L. Williams and Richard M. Murray
- Nature Communications, 13:6822, 2022
2022k_Pan+23-JOSS
- Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
- Anandh Swaminathan, William Poole, Victoria Hsiao, Ayush Pandey, and Richard M. Murray
- Journal of Open Source Software (JOSS), 2023
2022d_Bad+23-ICRA
- Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows
- Apurva Badithela, Josefine B. Graebener, Wyatt Ubellacker, Eric V. Mazumdar, Aaron D. Ames, Richard M. Murray
- Submitted, 2023 International Conference on Robotics and Automation (ICRA)
2022d_HM22-NatureComms
- Layered Feedback Control Overcomes Performance Trade-Off in Synthetic Biomolecular Networks
- Chelsea Hu, Richard M. Murray
- Nature Communications 13(1):1-13, 2022
2022c_BMW23-ICRA
- Evaluation Metrics for Object Detection for Autonomous Systems
- Apurva Badithela, Tichakorn Wongpiromsarn, Richard M. Murray
- Submitted, 2023 International Conference on Robotics and Automation (ICRA)
2022b_DM22-CDC
- Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions
- Ersin Das, Richard M. Murray
- To appear, 2022 Conference on Decision and Control (CDC)
2022b_PISM22-IWBDA
- From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology
- Ayush Pandey, Inigo Incer, Alberto Sangiovanni-Vincentelli, Richard M. Murray
- 2022 International Workshop on Biodesign Automation (IWBDA)
2022b_GBM22-NFM
- Towards Better Test Coverage: Merging Unit Tests for Autonomous Systems
- Josefine Graebener, Apurva Badithela, Richard M. Murray
- 2022 NASA Formal Methods Symposium (NFM)
2022a_PM22-IJRNC
- Robustness guarantees for structured model reduction of dynamical systems with applications to biomolecular models
- Ayush Pandey, Richard M. Murray
- International Journal on Robust and Nonlinear Control (IJRNC), 1-29, 2022
2021x__Col+21-microbio
- Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates
- João Heitor Colombelli Manfrão-Netto, Fredrik Lund, Nina Muratovska, Elin M. Larsson, Nádia Skorupa Parachin, Magnus Carlquist
- Microbial Biotechnology, 14( 6), 2448– 2462, 2021
2021n_Ahm+21-AAAI
- Risk-Averse Decision Making Under Uncertainty
- Mohamadreza Ahmadi, Ugo Rosolia, Michel D. Ingham, Richard M. Murray, Aaron D. Ames
- 2021 AAAI Conference on Artificial Intelligence (AAAI-21)
2021n_cm21-biorxiv
- How to model DNA replication in stochastic models of synthetic genetic circuits (and why)
- Samuel E. Clamons, Richard M. Murray
- bioRxiv 2021.09.26.461880
2021m_Yeu+21-JRSI
- Data-driven network models for genetic circuits from time-series data with incomplete measurements
- Enoch Yeung, Jim Kim, Ye Yuan, Jorge Gonçalves, Richard M. Murray
- Journal of the Royal Society Interface 18 (182), 20210413
2021m_BWM21-cdc
- Leveraging Classification Metrics for Quantitative System-Level Analysis with Temporal Logic Specifications
- Apurva Badithela, Tichakorn Wongpiromsarn, Richard M Murray
- To appear, 2021 Conference on Decision and Control
2021e_MA+21-aaai
- Constrained risk-averse Markov decision processes
- Mohamadreza Ahmadi, Ugo Rosolia, Michel D Ingham, Richard M Murray, Aaron D Ames
- 35th AAAI Conference on Artificial Intelligence (AAAI-21)
2021e_JBM+21-jove
- A Method for Cost-Effective and Rapid Characterization of Genetic Parts
- John B. McManus, Casey B. Bernhards, Caitlin E. Sharpes, David C. Garcia, Stephanie D. Cole, Richard M. Murray, Peter A. Emanuel, Matthew W. Lux
- To appear, Journal of Visualized Experiments (JoVE)
2021e_BM21-nfm
- Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems
- Apurva Badithela, Richard M. Murray
- Submitted, 2021 NASA Formal Methods (NFM)
2021c_ful+21-cdc
- The Python Control Systems Library (python-control)
- Sawyer Fuller, Ben Greiner, Jason Moore, Richard M. Murray, Renee van Paassen, Rory Yorke
- IEEE Conference on Decision and Control (CDC), 2021
2021c_AP21-CDC
- Robustness Guarantees for Structured Model Reduction of Dynamical Systems
- Ayush Pandey, Richard M. Murray
- IEEE Conference on Decision and Control (CDC), 2021
2021c_Gra+21:CDC
- Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture
- Josefine Graebener, Tung Phan-Minh, Jiaqi Yan, Qiming Zhao, Richard M. Murray
- Submitted, 2021 Conference on Decision and Control (CDC)
2021c_CMB21-cdc
- Limits of probabilistic safety guarantees when considering human uncertainty
- Richard Cheng, Richard M. Murray, Joel W. Burdick
- Submitted, 2021 Conference on Decision and Control (CDC)
2021c_RAMA21-cdc
- Time-Optimal Navigation in Uncertain Environments with High-Level Specifications
- Ugo Rosolia, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames
- To appear, 2021 Conference on Decision and Control (CDC)
2021c_CPCM21-tro
- Rules of the Road: Safety and Liveness Guarantees for Autonomous Vehicles
- Karena X. Cai, Tung Phan-Minh, Soon-Jo Chung, Richard M. Murray
- IEEE Transactions on Robotics, 39(3)
2021a_STSM21-oupsynbio
- 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
2020k_YC+20-corl
- Reactive motion planning with probabilistic safety guarantees
- Yuxiao Chen, Ugo Rosolia, Chuchu Fan, Aaron D. Ames, Richard M. Murray
- Submitted, Conference on Robotic Learning (CoRL)
2020i_may+21-ecc
- Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis
- Michaëlle N. Mayalu, Anish Sarma, Fangzhou Xiao, John C. Doyle and Richard M. Murray
- 2021 European Control Conference (ECC)
2020i_RCMF21-acc
- Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations
- Xinying Ren, Christian Cuba Samaniego, Richard M. Murray, Elisa Franco
- 2021 American Control Conference (ACC)
