Preprint archive

From MurrayWiki
Revision as of 16:12, 16 May 2016 by Murray (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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).

2019g_pm19-formats

Contracts of Reactivity
Tung Phan-Minh and Richard M. Murray
Submitted, Int'l Conf on Formal Modeling and Analysis of Timed Systems (FORMATS) 2019


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


2019f_PM19-iwbda

An automated model reduction tool to guide the design and analysis of synthetic biological circuits
Ayush Pandey, Richard M. Murray
2019 International Workshop on Biodesign Automation (IWBDA)


2019e_MMEL19-abb

A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression
John B. McManus, Richard M. Murray, Peter A. Emanuel, Matthew W. Lux
Submitted, Archives of Biochemistry and Biophysics, April 2019


2019d_pcm19-cdc

Towards Assume-Guarantee Profiles for Autonomous Vehicles
Tung Phan-Minh, Karena X. Cai, Richard M. Murray
Submitted, 2019 Conference on Decision and Control (CDC)


2019c_GHRM19-qbio

Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design
Leopold N. Green, Chelsea Y. Hu, Xinying Y. Ren, Richard M. Murray
qBio Conference 2019


2019c_MM19-qbio

Addressable, “Packet-Based” Intercellular Communication through Plasmid Conjugation
John P. Marken, Richard M. Murray
qBio 2019 Conference


2019c_HFM19-qbio

Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits
Andrew D. Halleran, Emanuel Flores-Bautista, Richard M. Murray
qBio 2019 Conference


2019b_WM19-seed

Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli
Rory L. Williams, Richard M. Murray
2019 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2019b_MPM19-seed

Control of density and composition in an engineered two-member bacterial community
Reed D. McCardell, Ayush Pandey, Richard M. Murray
Submitted, 2019 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2019b_HM19-seed

Design of a genetic layered feedback controller in synthetic biological circuitry
Chelsea Y. Hu, Richard M. Murray
2019 Synthetic Biology: Engineerinng, Evolution and Design (SEED) Conference


2019b_SM19-seed

Proof of concept continuous event logging in living cells
Andrey Shur, Richard M. Murray
2019 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2019a_SPHM19-biorxiv

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Anandh Swaminathan, William Poole, Victoria Hsiao, Richard M. Murray
bioRxiv


2018g_ols+18-cellsys

Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems
Noah Olsman, Ania-Ariadna Baetica, Fangzhou Xiao, Yoke Peng Leong, John Doyle, Richard Murray
Submitted, Cell Systems (Nov 2018)


2018g_blom18-cellsys

Design Guidelines For Sequestration Feedback Networks
Ania-Ariadna Baetica, Yoke Peng Leong, Noah Olsman, Richard M. Murray
Submitted, Cell Systems (Nov 2018)


2018f_rm19-ecc

Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia
Xinying Ren, Richard M Murray
Submitted, 2019 European Control Conference


2018f_mhm19-ecc

Model of Paradoxical Signaling Regulated T-Cell Population Control for Design of Synthetic Circuits
Michaelle N. Mayalu, Harman Mehta and Richard M. Murray
Submitted, 2019 European Control Conference (ECC)


2018e_comb19-aiaa

End-to-End Safe Reinforcement Learning through Barrier Functions for Safety-Critical Continuous Control Tasks
Richard Cheng, Gabor Orosz, Richard M. Murray, Joel W. Burdick
To appear, 2019 AAAI Conference on Artificial Intelligence


2018e_dgm19-aiaa

Inverse Abstraction of Neural Networks Using Symbolic Interpolation
Sumanth Dathathri, Sicun Gao, Richard M. Murray
To appear, 2019 AAAI Conference on Artificial Intelligence


2018d_gsma19-acc

Risk-aware motion planning for automated vehicle among human-driven cars
Jin I. Ge, Bastian Schurmann, Richard M. Murray, and Matthias Althoff
Submitted, 2019 American Control Conference (ACC)


2018d_chmc19-acc

Robust Estimation Framework with Semantic Measurements
Karena X. Cai, Alexei Harvard, Richard M. Murray, Soon-Jo Chung
Submitted, 2019 American Control Conference (ACC)


2018d_sm19-acc

Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability
Vipul Singhal and Richard M. Murray
Submitted, 2019 American Control Conference (ACC)


2018d_pha+19-acc

A modal interface contract theory for guarded input/output automata with an application in traffic system design
Tung Phan-Minh, Steve Guo, Bastian Schürmann, Matthias Althoff, and Richard M. Murray
Submitted, 2019 American Control Conference (ACC)


2018c_vai+18-anbio

On-chip membrane protein cell-free expression enables development of a direct binding assay: A curious case of potassium channel KcsA-Kv1.3
A. Vaisha, S. Guo, R. M.Murray, P. J..Grandsard and Q. Chen
Analytical Biochemistry, 556:70-77, 2018


2018b_gm18-cdc

Voluntary lane-change policy synthesis with reactive control improvisation
Jin I. Ge and Richard M. Murray
To appear, 2018 Conference on Decision and Control (CDC)


2018b_hamg18-cdc

Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts
Wolfgang Halter, Frank Allgower, Richard M. Murray and Andras Gyorgy
To appear, 2018 Conference on Decision and Control (CDC)


2018b_rm18-cdc

Role of interaction network topology in controlling microbial population in consortia
Xinying Ren, Richard M Murray
To appear, 2018 Conference on Decision and Control (CDC)


2018a_pm18-seed

Long-distance communication in synthetic bacterial consortia through active signal propagation
James M Parkin, Richard M Murray
2018 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2018a_hsm18-seed

Single day construction of multi-gene circuits with 3G assembly
Andrew D Halleran, Anandh Swaminathan, Richard M Murray
2018 Synthetic Biology: Engineering, Evolution and Design (SEED) Conference


2017m_hae+18-adhs

Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations
S. Haesaert, P. Nilsson, C. I. Vasile, R. Thakker, A. Agha-mohammadi, A. D. Ames and R. M. Murray
To appear in IFAC Conference on Analysis and Design of Hybrid Systems (ADHS), 2018


2017l_nil+18-rss

Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams
P. Nilsson, S. Haesaert, C. Vasile, R. Thakker, A. Agha-mohammadi. R. M. Murray and A. D. Ames
To appear in Robotics: Science and Systems (RSS), 2018.


2017k_MHGM18-wqbio

Control of bacterial population density with population feedback and molecular sequestration
Reed D McCardell, Shan Huang, Leopold N Green, Richard M Murray
2018 Winter q-bio


2017k_cm18-wqbio

Modeling Dynamic Transcriptional Circuits with CRISPRi
Samuel E Clamons, Richard M Murray
2018 Winter q-bio


2017k_dpm18-wqbio

Length and time scales of cell-cell signaling circuits in agar
Joy Doong, James Parkin, Richard M. Murray
2018 Winter q-bio


2017j_hsm17-ieeecsm

Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology
Victoria Hsiao, Anandh Swaminathan, and Richard M. Murray
IEEE Control Systems Magazine, 38(3):32-62 , June 2018


2017i_wu+17-biorxiv

System-level studies of a cell-free transcription-translation platform for metabolic engineering
Yong Y. Wu, Hirokazu Sato, Hongjun Huang, Stephanie J. Culler, Julia Khandurina, Harish Nagarajan, Tae Hoon Yang, Stephen Van Dien, Richard M. Murray
bioRxiv Technical Report


2017h_fm18-pieee

Layering assume-guarantee contracts for hierarchical system design
Ioannis Filippidis and Richard M. Murray
Proceedings of the IEEE, 2018


2017g_HM17-biorxiv

Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli
Andrew Halleran, Richard M. Murray
ACS Synthetic Biology, 7(2):752–755, 2017


2017f_mbsm17-rsi

Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks
X. Flora Meng, Ania-Ariadna Baetica, Vipul Singhal, Richard M. Murray
Royal Society Interface, 14(130), 2017


2017e_cmo17-iros

Synthesis of Correct-by-Construction Behavior Trees
Michele Colledanchise, Richard M. Murray, and Petter Ogren
Submitted, 2017 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)


2017e_yeu+17-cellsys

Biophysical Constraints Arising from Compositional Context in 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
Cell Systems, 5(1):11–24.e12, 2017


2017d_dfm17-isrr

Parallelizing Synthesis from Temporal Logic Specifications by Identifying Equicontrollable States
Sumanth Dathathri, Ioannis Filippidis and Richard M. Murray
Submitted, 2017 International Symposium on Robotics Research (ISRR)


2017c_dagm17-ijca

Learning-Based Abstractions for Nonlinear Constraint Solving
Sumanth Dathathri, Nikos Arechiga, Sicun Gao, and Richard M. Murray
2017 International Joint Conference on Artificial Intelligence (IJCAI)


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
2017 Conference on Decision and Control (CDC)


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


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
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


2016x_dlS+16-acssynbio

Engineering Transcriptional Regulator Effector Specificity Using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor
E. L. de los Santos, J. T. Meyerowitz, S. L. Mayo, R. M. Murray
ACS Synthetic Biology. 5(4):287-95, 2016


... further results