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.

2017b_ren+17-cdc

Population regulation in microbial consortia using dual feedback control
Xinying Ren, Ania-Ariadna Baetica, Anandh Swaminathan, Richard M. Murray
Submitted, 2017 Conference on Decision and Control (CDC)


2017b_fm17-cdc

Hiding variables when decomposing specifications into GR(1) contracts
Ioannis Filippidis and Richard M. Murray
Submitted, 2017 Conference on Decision and Control (CDC)


2017b_dm17-cdc

Decomposing GR(1) Games with Singleton Liveness Guarantees for Efficient Synthesis
Sumanth Dathathri and Richard M. Murray
Submitted, 2017 Conference on Decision and Control (CDC)


2017a_shm17-seed

Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology
Anandh Swaminathan, Victoria Hsiao, Richard M Murray
Submitted, 2017 Synthetic Biology: Engineering, Evolution, and Design (SEED) Conference


2017a_phm17-seed

Engineering pulsatile communication in bacterial consortia
James Parkin, Victoria Hsiao, Richard M Murray
Submitted, 2017 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2017a_sm17-seed

Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli
Andrey Shur and Richard M Murray
Submitted, 2017 Synthetic Engineering: Engineering, Evolution and Design (SEED) Conference


2016k_gm16-cdc

Quantifying Resource Competition and its Effects in the TX-TL System
Andras Gyorgy and Richard M. Murray
2016 Conference on Decision and Control (CDC)


2016i_yeu+17-biorxiv

The Effect of Compositional Context on 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
Submitted, Cell Systems (bioRxiv preprint)


2016h_ari+17-hscc

Fast Automatic Verification of Large-Scale Systems with Lookup Tables
Nikos Arichega, Sumanth Dathathri, Shashank Vernekar, Sicun Gao, Shin’Ichi Shiraishi, Richard M. Murray
Submitted, 2017 ACM International Conference on Hybrid Systems: Computation and Control (HSCC)


2016g_dlm17-iccps

Enhancing tolerance to unexpected jumps in GR(1) games
Sumanth Dathathri, Scott C. Livingston and Richard M. Murray
2017 Int'l Conference on Cyberphysical Systems (ICCPS)


2016f_gom17-acc

Connected Cruise Control Design Using Probabilistic Model Checking
Jin I. Ge, Gabor Orosz and Richard M. Murray
Submitted, 2017 American Control Conference (ACC)


2016e_fil+16-msc

Control design for hybrid systems with TuLiP: The temporal logic planning toolbox
Ioannis Filippidis, Sumanth Dathathri, Scott C. Livingston, Necmiye Ozay, Richard M. Murray
2016 IEEE Conference on Control Applications (CCA)


2016d_hsi+16-msb

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


2016c_ccom16-ssci

Synthesis of Control Protocols for Switched Electrical Power Systems for Commercial Applications with Safety Specifications
Benson Christalin, Michele Colledanchise, Petter Ogren, Richard M. Murray
2016 IEEE Symposium on Computational Intelligence in Control and Automation


2016b_nwgm16-seed

Design Space Exploration of the Violacein Pathway in Escherichia coli Based Cell-Free System
Phuc H.B. Nguyen, Yong Wu, Shaobin Guo, Richard M Murray
Submitted, 2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2016b_hcm16-seed

Design and application of stationary phase combinatorial promoters
Victoria Hsiao, Aileen Cheng and Richard M. Murray
Submitted, 2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2016b_ahhm16-seed

The role of single occupancy effects on integrase dynamics in a cell-free system
Georgios Artavanis, Victoria Hsiao, Clarmyra A. Hayes, Richard M. Murray
2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference (17 May 2016)


2016b_swa+16-seed

Stochastic Gene Expression in Single Gene Oscillator Variants
Anandh Swaminathan, Marcella M. Gomez, David L. Shis,Matthew R. Bennett, and Richard M. Murray
2016 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2016a_ram+16-tac

Model Predictive Control for Signal Temporal Logic Specifications
Vasumathi Raman, Alexandre Donze ́, Mehdi Maasoumy, Richard M. Murray, Alberto Sangiovanni-Vincentelli and Sanjit A. Seshia
Submitted, IEEE T. Automatic Control (2 Jan 2016)


2015n_far+16-ecc

Model Predictive Control for an Uncertain Smart Thermal Grid
Samira S. Farahani, Zofia Lukszo, Tamas Keviczky, Bart De Schutter, Richard M. Murray
2016 European Control Conference (ECC)


2015m_dlrm16-ieeeaero

Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications
Sumanth Dathathri, Scott C. Livingston, Leonard J. Reder, and Richard M. Murray
IEEE Aerospace Conference, 2016


2015l_sfzm15-jrsi

An analytical approach to bistable biological circuit discrimination using real algebraic geometry
Dan Siegal-Gaskins, Elisa Franco, Tiffany Zhou, Richard M. Murray
J. R. Soc. Interface 2015 12 20150288; DOI: 10.1098/rsif.2015.0288.


2015k_dlm16-cdc

Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications
Sumanth Dathathri, Scott C. Livingston and Richard M. Murray
Submitted, 2016 Conference on Decision and Control (CDC)


2015j_hay+16-wqbio

Rapid in vitro engineering of 16 two-input logic gates
Clarmyra A. Hayes, Emmanuel L.C. de los Santos, Enoch Yeung, Sean R. Sanchez, Seung Y. Lee, and Richard M. Murray
Presented, 2016 Winter q-Bio


2015j_hhrm16-wqbio

Use of population-level cell-state switching for recording transient inducer pulses
Victoria Hsiao, Yutaka Hori, Paul W.K. Rothemund, Richard M. Murray
Presented, 2016 Winter q-Bio (5 Nov 2015)


2015j_mbsm16-wqbio

Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively
Xianglin Meng, Ania A. Baetica, Vipul Singhal, and Richard M. Murray
Presented, 2016 Winter q-Bio Conference


2015i_nie15-elife

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


2015h_fm16-acc

Symbolic construction of GR(1) contracts for systems with full information
Ioannis Filippidis and Richard M. Murray
2016 American Control Conference (ACC)


2015h_sm16-acc

Linear System Identifiability from Distributional and Time Series Data
Anandh Swaminathan and Richard M. Murray
2016 American Control Conference (ACC)


2015g_gmb15-siads

The effects of time-varying temperature on delays in genetic networks
Marcella M. Gomez, Richard M. Murray and Matthew R. Bennett
Submitted, SIAM J. Applied Dynamical Systems (SIADS)


2015f_mm15-aiaa

Application of Correct-by-Construction Principles for a Resilient Risk-Aware Architecture
Catharine L. McGhan and Richard M. Murray
AIAA Space 2015 Conference and Exposition


2015e_tak+15-methods

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


2015d_pm15-cdc

Control System Analysis on Symmetric Cones
Ivan Papusha and Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015d_hmm15-cdc

Synthesis of Distributed Longitudinal Control 1 Protocols for a Platoon of Autonomous Vehicles
Duo Han, Yilin Mo, Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015d_hm15-cdc

Engineering Principles of Synthetic Biochemical Oscillators with Negative Cyclic Feedback
Yutaka Hori and Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015d_bygm15-cdc

A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks
Ania A. Baetica, Ye Yuan, Jorge Goncalves and Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015d_ykgm15-cdc

Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks
Enoch Yeung, Jongmin Kim, Jorge Gonc ̧alves, and Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015d_sm15-cdc

Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty
Shaunak Sen and Richard M. Murray
Submitted, 2015 Conference on Decision and Control (CDC)


2015c_fmh15-synt

Synthesis from multi-paradigm specifications
Ioannis Filippidis, Richard M. Murray and Gerard J. Holzmann
Submitted, 2015 Workshop on Synthesis (SYNT)


2015b_sssm15-seed

Design of a Toolbox of RNA Thermometers
Rohit Satija, Shaunak Sen, Dan Siegal-Gaskins, Richard M. Murray
Presented at Synthetic Biology: Engineering, Evolution and Design (SEED), 10-13 June 2015


2015b_smmm15-seed

Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor
Emmanuel Lorenzo Cornejo de los Santos, Joseph T Meyerowitz, Stephen L Mayo, Richard M Murray
ACS Synthetic Biology, 5(4):287–295, 2016.


2015b_wu+15-seed

Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system
Yong Y Wu, Stephanie Culler, Julia Khandurina, Stephen Van Dien, Richard M Murray
Presented at Synthetic Biology: Engineering, Evolution and Design (SEED), 10-13 June 2015


2015a_mm15-ccc

Multi-dimensional state estimation in adversarial environment
Yilin Mo and Richard M. Murray
Submitted, 2015 Chinese Control Conference (CCC)


2015a_af15-ms

Rapid prototyping of biomolecular circuits through module characterization in cell-free expression systems
Anton Frisk
Masters Thesis, Lund University


2014n_frm15-adhs

Robust Model Predictive Control for Signal Temporal Logic Synthesis
Samira S. Farahani, Vasumathi Raman, and Richard M. Murray
2015 IFAC Conference on Analysis and Design of Hybrid Systems (ADHS)


2014m_ghm15-wqbio

Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo
Shaobin Guo, Yutaka Hori, and Richard M Murray
Submitted, 2015 Winter q-bio Conference (5 Nov 2014)


2014m_hhm15-wqbio

Characterization of minimum inducer separation time for a two-input integrase-based event detector
Victoria Hsiao, Yutaka Hori, and Richard M Murray
Presented, 2015 Winter q-bio Conference (5 Nov 2014)


2014l_mcg+15-ieeeaero

A Risk-Aware Architecture for Resilient Spacecraft Operations
Catharine L. R. McGhan, Richard M. Murray, Romain Serra, Michel D. Ingham, Masahiro Ono, Tara Estlin and Brian C. Williams
Submitted, 2015 IEEE Aerospace Conference


2014k_hm15-ecc

A State-space Realization Approach to Set Identification of Biochemical Kinetic Parameters
Yutaka Hori and Richard M. Murray
2015 European Control Conference (ECC)


2014j_rfwm15-hscc

Online Horizon Selection in Receding Horizon Temporal Logic Planning
Vasumathi Raman, Mattias Fält, Tichakorn Wongpiromsarn, Richard M. Murray
Submitted, 2015 International Conference on Hybrid Systems: Computation and Control (HSCC)


... further results