Journal Papers

A Load Driver Device for Engineering Modularity in Biological Networks
D. Mishra, P. M. Rivera-Ortiz, A. Lin, D. Del Vecchio(*), and R. Weiss(*), Nature Biotechnology, Accepted, September 2014.
(*)=co-corresponding authors

A Synthetic Tunable Amplifying Buffer Circuit in E. coli
K. Nilgiriwala, J. Jimenez, P. M. Rivera, and D. Del Vecchio, ACS Synthetic Biology Accepted October 2014.

Least Restrictive Supervisors for Intersection Collision Avoidance: A Scheduling Approach
A. Colombo and D. Del Vecchio, IEEE Trans. Aut. Control, Provisionally Accepted, June 2014.

Modular Composition of Gene Transcription Networks
A. Gyorgy and D. Del Vecchio, PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1003486, March 2014.

A Control Theoretic Framework for Modular Analysis and Design of Biomolecular Networks
D. Del Vecchio, IFAC Reviews in Control, Vol 37(2):333-345, December 2013.

Control for Safety Specifications of Systems with Imperfect Information on a Partial Order (draft)
R. Ghaemi and D. Del Vecchio, IEEE Trans. Automatic Control, Accepted, 2013.

Cooperative Collision Avoidance at Intersections: Algorithms and Experiments
M. Hafner, D. Cunningham, L. Caminiti, and D. Del Vecchio, IEEE Trans. Intelligent Transportation Systems, Accepted, 2013.

Retroactivity Controls the Temporal Dynamics of Gene Transcription
S. Jayanthi, K. Nilgiriwala, and D. Del Vecchio, ACS Synthetic Biology, Accepted, 2013.

Modularity in Signaling Systems - Perspective Paper
D. Del Vecchio, Physical Biology, Accepted, 2012.

A Contraction Theory Approach to Singularly Perturbed Systems
D. Del Vecchio and J-J. Slotine, IEEE Trans. Aut. Control, Accepted, 2012.

Tuning Genetic Clocks through DNA Binding Sites
S. Jayanthi and D. Del Vecchio, PLoS ONE, Accepted, 2012.

Computational Tools for the Safety Control of a Class of Piecewise Continuous Systems with Imperfect Information on a Partial Order
M. Hafner and D. Del Vecchio, SIAM J. on Control and Optimization, Accepted, 2011.

Load-induced Modulation of Signal Transduction Networks
P. Jiang, A. C. Ventura, S. D. Merajver, E. D. Sontag, A. J. Ninfa, and D. Del Vecchio, Science Signaling, Vol. 4, Issue 194, p. ra67, 2011.
(Read Editor's choice Enlightening the Load by L. Bryan Ray, Science, October 2011)

Semiautonomous Multivehicle Safety: A Hybrid Control Approach
R. Verma and D. Del Vecchio, IEEE Robotics and Automation Magazine, Vol. 18, Issue 3, page(s) 44 - 54, 2011.

Long Signaling Cascades Tend to Attenuate Retroactivity
H. R. Ossareh, A. C. Ventura, S. D. Merajver, and D. Del Vecchio, Biophysical Journal, vol. 100(7):1617-1626, 2011.

Safety Control of Hidden Mode Hybrid Systems
R. Verma and D. Del Vecchio, IEEE Trans. Aut. Control, Accepted, 2011.

Retroactivity Attenuation in Bio-molecular Systems Based on Timescale Separation
S. Jayanthi and D. Del Vecchio, IEEE Trans. Aut. Control, vol. 56(4), pages 748-761 , 2011.

Signaling properties of a covalent modification cycle are altered by a downstream target.
A. C. Ventura, P. Jiang, L. Van Wassenhove, D. Del Vecchio, S. D. Merajver, and A. J. Ninfa, Proc. Natl. Acad. Sci. USA, vol. 107(22), pages 10032-10037, 2010.

A Method for Determining the Robustness of Bio-molecular Oscillator Models.
R. Ghaemi, J. Sun, P. Iglesias, and D. Del Vecchio. BMC Systems Biology, 3:95, 2009.

Design and Characterization of a Three-terminal Transcriptional Device through Polymerase Per Second.
P. Varadarajan and D. Del Vecchio. IEEE Transactions on Nanobioscience, 8(3):281-9, 2009.

Engineering Principles in Bio-molecular Systems: From Retroactivity to Modularity.
D. Del Vecchio and E. D. Sontag. Special Issue of the European Journal of Control, vol. 15 (3-4), 2009.

Observer-based Control of Block-Triangular Discrete Time Hybrid Automata on a Partial Order
D. Del Vecchio. International Journal of Robust and Nonlinear Control--Special Issue, vol. 19(14), pages 1581-1602, 2009.

Cascade Estimators for Systems on a Partial Order
D. Del Vecchio. Systems & Control Letters, pages 842-850, 2008.

Modular Cell Biology: Retroactivity and Insulation
D. Del Vecchio, A. J. Ninfa, and E. D. Sontag. Nature/EMBO Molecular Systems Biology, 4:161, 2008.

Development of a Scaled Vehicle with Longitudinal Dynamics of a HMMWV for an ITS Testbed
R. Verma, D. Del Vecchio, and H. Fathy. IEEE/ASME Transactions on Mechatronics, vol. 13(1), pp. 46-57, 2008.

Discrete State Estimators for Systems on a Lattice
D. Del Vecchio, R. M. Murray, and E. Klavins. Automatica, vol. 42, pp. 271-285, 2006.

Boundary Control for an Industrial Under-actuated Tubular Chemical Reactor
D. Del Vecchio and N. Petit. Journal of Process Control, vol. 15, pp. 771-784, 2005.

Decomposition of Human Motion into Dynamics Based Primitives with Application to Drawing Tasks
D. Del Vecchio, R. M. Murray, and P. Perona. Automatica, vol. 39(12), pp. 2085-2098, 2003.

Adaptive Learning Control for Feedback Linearizable Systems
D. Del Vecchio, R. Marino, and P. Tomei. European Journal of Control, vol. 9, Nb. 5, 2003.

Adaptive Control of Feedback Linearizable Systems by Orthogonal Approximation Functions
D. Del Vecchio, R. Marino, and P. Tomei. International Journal of Adaptive Control and Signal Processing, vol. 16, pp. 635-652, 2002.

Books and Book Chapters

Biomolecular Feedback Systems
Princeton Publishing Press
D. Del Vecchio and R. M. Murray. Textbook, October 2014.

Synthetic Biology
D. Del Vecchio and R. M. Murray. In Encyclopedia of Systems and Control, Baillieul, John, Samad, Tariq (Eds.), Springer, March 2015. (Expository paper)

The Impact of Retroactivity on the Behavior of Bio- molecular Systems
D. Del Vecchio. In Design and Analysis of Bio-molecular Circuits, H. Koeppl, D. Densmore, M. di Bernardo, G. Setti (Eds), Springer-Verlag, 2011.

Synthetic Biology: A Systems Engineering Perspective
D. Del Vecchio and E. D. Sontag. In Control Theory and Systems Biology, P. A. Iglesias and B. P. Ingalls (Eds), pages 101-124, The MIT Press 2009.

Complexity management in the state estimation of multi-agent systems
D. Del Vecchio and R. M. Murray. In Cooperative Control of Distributed Multi-Agent Systems, J. Shamma (Ed), pages 377-407, John Wiley 2008.

Patents

Computationally Efficient Intersection Collision Avoidance (ICA) System with Guaranteed Safety Performance
L. Caminiti, E. Quisenberry, C. Peplin, D. Del Vecchio, and R. Verma. U.S. Patent 8639437, 2014.

Selected Papers in Conference Proceedings

Mitigation of resource competition in synthetic genetic circuits through feedback regulation
A. Amadeh and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, to appear 2014

Limitations and Trade-offs in Gene Expression due to Competition for Shared Cellular Resources
A. Gyorgy and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, to appear 2014

Integral Action with Time Scale Separation: A Mechanism for Modularity in Biological Systems
P. M. Rivera and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, to appear 2014

Design of safety distributed control under bounded communication delay
D. Bresh-Pietri and D. Del Vecchio. Proc. American Control Conference, 2014 (Invited Paper)

Supervisory control for intersection collision avoidance in the presence of uncontrolled vehicles
H. Ahn and D. Del Vecchio. Proc. American Control Conference, 2014

Tradeoffs between retroactivity and noise in connected transcriptional components
N. Herath and D. Del Vecchio. Proc. American Control Conference, 2014

Retroactivity Attenuation through Signal Transduction Cascades
P. M. Rivera and D. Del Vecchio. Proc. American Control Conference, 2014.

Supervisory Control for Collision Avoidance in Vehicular Networks with Imperfect Measurements (Invited Paper)
E. Dallal, A. Colombo, D. Del Vecchio, and S. Lafortune. Proc. IEEE Conference on Decision and Control, 2013.

How slaves affect a master module in gene transcription networks (Invited Paper)
A. Gyorgy and D. Del Vecchio. Proc. IEEE Conference on Decision and Control, 2013.

Robust multi-agent collision avoidance through scheduling
L. Bruni, A. Colombo, and D. Del Vecchio. Proc. IEEE Conference on Decision and Control, 2013.

A Control Theory Approach to Engineering Biomolecular Networks
D. Del Vecchio. Proc. IFAC Symposium on Nonlinear Control Systems (NOLCOS), 2013. (Semi-plenary lecture)
(Extended version submitted to IFAC Annual Reviews in Control: A Control Theoretic Framework for Modular Analysis and Design of Biomolecular Networks)

Optimal Design of Phosphorylation-Based Insulation Devices
P. M. Rivera and D. Del Vecchio. Proc. American Control Conference, 2013 .

Supervisory Control for Collision Avoidance in Vehicular Networks Using Discrete Event Abstractions
E. Dallal, A. Colombo, D. Del Vecchio and S. Lafortune. Proc. American Control Conference, 2013.

Retroactivity to the Input and Thevenin's Theorem for Complex Gene Transcription Networks(Invited Paper)
A. Gyorgy and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, 2012.

Stochastic Analysis of Retroactivity in Transcriptional Networks through Singular Perturbation
R. Ghaemi and D. Del Vecchio. Proc. American Control Conference, 2012.

Efficient algorithms for collision avoidance at intersections
A. Colombo and D. Del Vecchio. Hybrid Systems: Computation and Control, 2012.

Development and experimental validation of a semi-autonomous cooperative active safety system ( Invited Paper)
R. Verma and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, 2011.

Safety control of piece-wise continuous order preserving systems ( Invited Paper)
R. Ghaemi and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, 2011.

Supervisory control of differentially flat systems based on abstraction
A. Colombo and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, 2011.

Retroactivity Attenuation in Signaling Cascades ( Invited Paper)
H. R. Ossareh and D. Del Vecchio. Proc. IEEE Conf. on Decision and Control, 2011.

A Contraction Theory Approach to Singularly Perturbed Systems with Application to Retroactivity Attenuation
D. Del Vecchio and J-J. Slotine. Proc. IEEE Conf. on Decision and Control, 2011.

Control of Hidden Mode Hybrid Systems: Algorithm Termination ( Invited Paper)
R. Verma and D. Del Vecchio. Proc. of International IEEE Conference on Intelligent Transportation Systems 2011.

Automated Vehicle-to-Vehicle Collision Avoidance at Intersections
M. Hafner, D. Cunningham, L. Caminiti, and D. Del Vecchio. Proc. of World Congress on Intelligent Transport Systems , 2011.

Tuning an Activator-Repressor Clock Employing Retroactivity (Invited Paper)
S. Jayanthi, A. Rosenberg, and D. Del Vecchio. Proc. American Control Conference, 2011.

Control of Hybrid Automata with Hidden Modes: Translation to a Perfect State Information Problem .
R. Verma and D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, 2010.

Formal Design of a Provably Safe Robotic Roundabout System.
J. Duperret, M. Hafner, and D. Del Vecchio. Proc. of IEEE/RSJ International Conference on Intelligent Robots and Systems, 2010.

The Impact of Retroactivity on the Input/Output Characteristic of a Signaling Component (Invited Paper).
A. C. Ventura, P. Jiang, L. Van Wassenhove, A. J. Ninfa, S. D. Merajver, and D. Del Vecchio. Proc. of Dynamic Systems and Control Conference, 2010.

Design of an insulation device using phosphotransfer systems (Invited Paper).
S. Jayanthi and D. Del Vecchio. Proc. of IEEE International Symposium on Circuits and Systems (ISCAS), 2010.

Computation of Safety Control for Uncertain Piecewise Continuous Systems on a Partial Order.
M. Hafner and D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, 2009.

Continuous Control of Hybrid Automata with Imperfect Mode Information Assuming Separation between State Estimation and Control.
R. Verma and D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, 2009.

On the Compromise between Retroactivity Attenuation and Noise Amplification in Gene Regulatory Networks. (Invited Paper)
S. Jayanthi and D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, 2009.

Design of Insulating Devices for In Vitro Synthetic Circuits. (Invited Paper)
E. Franco, D. Del Vecchio and R. M. Murray. Proc. of IEEE Conference on Decision and Control, 2009.

Partial Order Techniques for Vehicle Collision Avoidance: Application to an Autonomous Roundabout Test-bed.
V. Desaraju, H. C. Ro, M. Yang, E. Tay, S. Roth, D. Del Vecchio. Proc. of International Conference on Robotics and Automation (ICRA), 2009.

A Separation Principle for a Class of Hybrid Automata on a Partial Order.
D. Del Vecchio, M. Malisoff, and R. Verma. Proc. of American Control Conference, 2009.

Engineering Principles in Bio-molecular Systems: From Retroactivity to Modularity.
D. Del Vecchio and E. D. Sontag. Proc. of European Control Conference (ECC), 2009 (To Appear). Selected for a Special Issue of the European Journal of Control

Retroactivity Attenuation in Transcriptional Networks: Design and Analysis of an Insulation Device
D. Del Vecchio and S. Jayanthi. Proc. of IEEE Conference on Decision and Control, December 2008, Cancun (Invited Paper).

Longitudinal Vehicle Dynamics Scaling and Implementation on a HIL Setup
R. Verma, D. Del Vecchio, and H. Fathy. Proc. of the Dynamic Systems and Control Conference, October 2008, Ann Arbor.

A Systems Theory with Retroactivity: Application to Transcriptional Modules
D. Del Vecchio, A. J. Ninfa, and E. D. Sontag. Proc. of American Control Conference, June 2008, Seattle.

A Partial Order Approach for Low Complexity Control of Block Triangular Hybrid Automata
D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, December 2007, New Orleans.

Observer-based Control for Block-triangular Hybrid Automata.
D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, December 2007, New Orleans,(Invited Paper).

Evaluating the Robustness of a Biochemical Network Model
R. Ghaemi and D. Del Vecchio. Proc. of IEEE Conference on Decision and Control, December 2007, New Orleans.

Design and Analysis of an Activator-Repressor Clock in E. coli
D. Del Vecchio. Proc. of American Control Conference, July 2007, New York.

Dynamics and Control of Synthetic Bio-molecular Networks
D. Del Vecchio and E.D. Sontag. Proc. of American Control Conference, July 2007, New York. (Tutorial Paper)

A Partial Order Approach to Discrete Dynamic Feedback in a Class of Hybrid Systems
D. Del Vecchio. Hybrid Systems: Computation and Control, April 2007, Pisa.

Discrete Dynamic Feedback for a Class of Hybrid Systems on a Lattice
D. Del Vecchio. IEEE CCA/CACSD/ISIC 2006, Munich. (Invited Paper)

Cascade Discrete-Continuous State Estimators for a Class of Monotone Systems
D. Del Vecchio and R.M. Murray. Proc. of IFAC 2005, Praha.

Existence of Cascade Discrete-Continuous State Estimators for Systems on a Partial Order
D. Del Vecchio and R.M. Murray. Hybrid Systems: Computation a nd Control, 2005 Zurich, Switzerland.

Repressilators and Promotilators: Loop Dynamics in Gene Regulatory Networks
H. El Samad, D. Del Vecchio, and M. Khammash. Proc. of American Control Conference, 2005. (Invited Paper)

Existence of Discrete State Estimators for Hybrid Systems on a Lattice
D. Del Vecchio and R.M. Murray. Proc. of IEEE Conference on Decision and Control, 2004 Atlantis, Bahamas. (Invited Paper)

Identification of Decision Rules in a Human Controlled System: Vehicles at a Traffic Intersection
C. L. Walton, D. Del Vecchio, and R. M. Murray. Proc. of International Conference of Robotics and Automation, 2004, New Orleans.

Vision as a Compensatory Mechanism for Disturbance Rejection in Upwind Flight
M. B. Reiser, J. S. Humbert, M. J. Dunlop, D. Del Vecchio, R. M. Murray, M. H. Dickinson. Proc. of American Control Conference, 2004, Boston.
Winner of best student paper competition

Discrete State Estimators for a Class of Hybrid Systems on a Lattice
D. Del Vecchio and R. M. Murray. Hybrid Systems: Computation and Control, 2004 Philadelphia, Pennsylvania.

Observation of Guarded Command Programs
D. Del Vecchio and E. Klavins. Proc of IEEE Conference on Decision and Control, 2003 Maui, Hawaii. (Invited Paper)

Classification of Human Motion into Dynamics Based Primitives with Application to Drawing Tasks
D. Del Vecchio, R. M. Murray, and P. Perona. Proc. of European Control Conference, 2003 Cambridge (UK).

Segmentation of Human Motion into Dynamics Based Primitives with Application to Drawing Tasks
D. Del Vecchio, R. M. Murray, and P. Perona. Proc of. American Control Conference, 2003 Denver, Colorado.

Primitives for Human Motion: A Dynamical Approach
D. Del Vecchio, R. M. Murray, and P. Perona. Proc. of IFAC, 2002 Barcelona, Spain.

An Adaptive Learning Control for Feedback Linearizable Systems.
D. Del Vecchio, R. Marino, and P. Tomei. Proc. of American Control Conference, Washington, VA 2001.

Adaptive Learning Control for Robot Manipulators.
D. Del Vecchio, R. Marino, and P. Tomei. Proc. of American Control Conference, Washington, VA 2001.

Abstracts

Combating context-dependence in biological circuits with a load driver.
D. Mishra, P. M. Rivera-Ortiz, D. Del Vecchio, and R. Weiss. International Conference on Systems Biology, Denmark, 2013.

Modular Composition of Gene Transcription Networks.
A. Gyorgy and D. Del Vecchio. International Conference on Systems Biology, Denmark, 2013.

Modularity in Complex Gene Transcrition Networks.
A. Gyorgy and D. Del Vecchio. International Conference on Systems Biology, Toronto, 2012.

Insulation Mechanisms of in vivo Biomolecular Circuits.
K. Nilgiriwala, P. M. Rivera, and D. Del Vecchio. International Conference on Systems Biology, Toronto, 2012.

Impact of Retroactivity on Transcriptional Components.
S. Jayanthi and D. Del Vecchio. The 5th Annual q-bio Conference on Cellular Information Processing, Santa Fe, 2012.

Engineering Insulation from Retroactivity of the Frequency Response of Covalent Modification Cycles.
D. Del Vecchio. IEEE Biomedical Circuits & Systems Conference, San Diego, 2011. (Invited)

Enforcing Safety of Cyber-Physical Systems Using Flatness and Abstraction.
A. Colombo and D. Del Vecchio. IEEE/ACM Second International Conference on Cyber-Physical Systems, Chicago, 2011.

A Control Theory Approach to Engineering Biomolecular Circuits.
D. Del Vecchio. 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society , Boston, 2011.

The Impact of Retroactivity on the Signal Processing of Transduction Networks.
P. Jiang, A. C. Ventura, S. Merajver, E. D. Sontag, A. J. Ninfa, and D. Del Vecchio. The 5th Annual q-bio Conference on Cellular Information Processing, Santa Fe, 2011. Poster

Retroactivity changes the input/output steady-state characteristic of a transcriptional component.
S. Jayanthi and D. Del Vecchio. SB5.0: The 5th International Meeting on Synthetic Biology, Stanford, 2011

A Dynamics Perspective on Modularity in Biomolecular Networks.
P. Jiang, A. C. Ventura, S. D. Merajver, A. J. Ninfa, and D. Del Vecchio. International Conference on Systems Biology, Edinburgh, 2010.

Long Signaling Cascades Attenuate Retroactivity.
H. R. Ossareh, A. C. Ventura, S. D. Merajver, and D. Del Vecchio. International Conference on Systems Biology, Edinburgh, 2010.

Control of Hybrid Automata with Imperfect Mode Information
D. Del Vecchio, Second Workshop on Numerical Software Verification , San Francisco 2009

From Retroactivity to Insulation: a Novel Engineering Principle Learned from Natural Bio-molecular Systems
D. Del Vecchio, Institute for Biological Engineering Conference , San Francisco 2009

Tutorial Session: Partial order techniques for the analysis and synthesis of hybrid and embedded systems
Organizer: D. Del Vecchio
Contributors: Jean-François Raskin (Computer Science Dept., Université Libre de Bruxelles), Georgios E. Fainekos and G Pappas (GRASP Lab, Upenn), Edward A. Lee (EECS, UC Berkeley), Derek Caveney and Lorenzo Caminiti (Toyota Technical Center, Ann Arbor)
Proc. of Conference on Decision and Control, New Orleans 2007.

Modules and Retroactivity: Theoretical Framework, Analysis, and Design.
D. Del Vecchio, A. J. Ninfa, and E. D. Sontag. International Conference on Systems Biology, Long Beach, 2007.
Poster Abstract

An Introduction to Control of Synthetic Bio-molecular Systems
D. Del Vecchio. Proc. of Conference on Decision and Control, New Orleans 2007.

Workshops

Analysis and Design of Cyber-Physical Transportation Systems: Challenges, Progress, and Future Directions
Organizer: D. Del Vecchio, American Control Conference, 2012.

News and Views on our work

Are we ready for driverless cars? by C. Gillis, Maclean's Canadian news magazine, November 2011

Enlightening the Load by L. Bryan Ray, Science, October 2011

'Smart cars' that are actually, well, smart by E. Finn MIT News Office, June 2011

Modularity Defined by H. Sauro, Nature/EMBO Molecular Systems Biology 2008

Submitted Conference Papers

Safety Control of a Class of Stochastic Order Preserving Systems with Application to Collision Avoidance near Stop Signs
M. Forghani, J. McNew, and D. Del Vecchio, Submitted to American Control Conference, 2015.

Stochastic Hybrid Models for Predicting the Behavior of Drivers Facing the Yellow-Light-Dilemma
D. Hoehener, P. A. Green, and D. Del Vecchio, Submitted to American Control Conference, 2015.

Model reduction for a class of singularly perturbed stochastic differential equations
N. Herath, A. Hamadeh, and D. Del Vecchio, Submitted to American Control Conference, 2015.

Effective interaction graphs arising from resource limitations in gene networks
Y. Qian and D. Del Vecchio, Submitted to American Control Conference, 2015.