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).

This is a searchable database.

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
Submitted, ACS Synthetic Biology, 2022


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


2022d_Str+23-ICRA

A Model-Free Algorithm for Extremely Resilient Navigation
Christian J. Stromberger, Josefine B. Graebener, James F. Ragan, Richard M. Murray
Submitted, 2023 International Conference on Robotics and Automation (ICRA)


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
To appear, 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
Submitted, IEEE T. Robotics, July 2021


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


2020b_PMS20-ACSsynbio

Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop
Abhilash Patel, Richard M. Murray, Shaunak Sen
ACS Synthetic Biology, 9(7):1581-1590, 2020


2020a_AAMA20-cdc

Formal Test Synthesis for Safety-Critical Autonomous Systems based on Control Barrier Functions
Prithvi Akella, Mohamadreza Ahmadi, Richard M. Murray, Aaron D. Ames
To appear, 2020 Conference on Decision and Control (CDC)


2019x_WM19-biorxiv

Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli
Rory L. Williams, Richard M. Murray
bioRxiv 614529, 2019 (revised 2020)


2019m_LMM19-biorxiv

Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA
Elin M. Larsson, John B. McManus, Richard M. Murray
bioRxiv 858266


2019l_ahm+20-acc

Risk-Averse Planning Under Uncertainty
Mohamadreza Ahmadi, Masahiro Ono, Michel D. Ingham, Richard M. Murray, Aaron D. Ames
2020 American Control Conference (ACC)


2019l_dnam20-acc

Invariant Sets for Integrators and Quadrotor Obstacle Avoidance
Ludvig Doeser, Petter Nilsson, Aaron D. Ames, and Richard M. Murray
2020 American Control Conference (ACC)


2019k_knam20-iccps

Intermittent Connectivity for Exploration in Communication-Constrained Multi-Agent Systems
Filip Klaesson, Petter Nilsson, Aaron D. Ames, Richard M. Murray
2020 International Conference on Cyberphysical Systems (ICCPS)


2019i_BAM20-acc

Learning pose estimation for UAV autonomous navigation and landing using visual-inertial sensor data
Francesca Baldini, Animashree Anandkumar, Richard M. Murray
2020 American Control Conference (ACC)


2019i_rm20-wqbio

Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations
Xinying Ren, Richard M. Murray
2020 Winter q-bio


2019i_mxm20-wqbio

A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
John P. Marken, Fangzhou Xiao, Richard M. Murray
2020 Winter q-bio


2019i_mm20-wqbio

Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli
Michaëlle N. Mayalu, Richard M. Murray
2020 Winter q-bio


2019i_pm20-wqbio

Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits
Ayush Pandey, Richard M. Murray
2020 Winter q-bio


2019h_cdpm19-corl

Counter-example Guided Learning of Bounds on Environment Behavior
Yuxiao Chen, Sumanth Dathathri, Tung Phan-Minh, Richard M. Murray
2019 Conference on Robot Learning (CoRL)


2019g_CM19-biorxiv

Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking
Samuel Clamons, Richard M. Murray
bioRxiv preprint


2019g_ham19-oupsynbio

Analysis of primitive genetic interactions for the design of a genetic signal differentiator
Wolfgang Halter, Richard M. Murray, Frank Allgower
Submitted, OUP Synthetic Biology, May 2019


... further results