Preprint archive

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).

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)

... further results