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.

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
To appear, 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)


2020i_LNM+20-ime

Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions
Liana N. Merk, Andrey S. Shur, Ayush Pandey, Richard M. Murray, Leopold N. Green
3rd International Microbiome Engineering Conference


2020i_YM+20-biorxiv

Synthetic mammalian signaling circuits for robust cell population control
Yitong Ma, Mark W. Budde, Michaëlle N. Mayalu, Junqin Zhu, Richard M. Murray, Michael B. Elowitz
Submitted, Cell Systems


2020d_WCM20-biorxiv

Analysis of Circuits for Dosage Control in Microbial Populations
Sophie J. Walton, Samuel E. Clamons, Richard M. Murray
Senior thesis


2020c_FK+20-icaps

Planning and Optimization for Multi-Robot Planetary Cave Exploration under Intermittent Connectivity Constraints
Filip Klaesson, Petter Nilsson, Tiago Stegun Vaquero, Scott Tepsuporn, Aaron D. Ames and Richard M. Murray
8th ICAPS Workshop on Planning and Robotics


2020c_PM21-wqbio

A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression
Ayush Pandey, Richard M. Murray
2020 Winter q-bio


... further results