# Antonis

### From SYSOS

# Biographical Sketch

In 2000 I obtained an MA/MEng degree in Electrical and Information Sciences from the University of Cambridge, U.K., as a member of Robinson College. In 2005 I completed a PhD in Control and Dynamical Systems at the California Institute of Technology, with a PhD Minor in Aeronautics. My thesis was on "Scalable Analysis of Nonlinear Systems Using Convex Optimization". After a short David Crighton Fellowship at the University of Cambridge and a postdoctoral fellowship at the California Institute of Technology, I joined the Department of Engineering Science at the University of Oxford in January 2006, where I am now an Associate Professor in Engineering Science (Control Engineering), a Tutorial Fellow at Worcester College, Oxford and the Director of the EPSRC & BBSRC Centre for Doctoral Training in Synthetic Biology. I serve regularly on Technical Programme Committees for conferences, and I am associate editor for *Automatica* and *IEEE Transactions on Automatic Control*.

# Research Interests

- Modern Control Theory, Robust Stability Analysis and Design.
- Nonlinear Dynamical Systems, Lyapunov stability.
- Convex optimization (Linear and Semidefinite Programming, LMIs). Sum of Squares programming.
- Systems and Synthetic Biology.
- Networked systems: Multi-agent systems, consensus, flocking, alignment. Synchronization of oscillator networks. Internet congestion Control. Population dynamic systems. Biochemical Reaction Networks.
- Aerospace systems and flow control.

# Selected Publications

## Systems & Synthetic Biology

- T. P. Prescott and A. Papachristodoulou. Synthetic Biology: A Control Engineering perspective. In Proceedings of the European Control Conference, 2014. PDF
- T. P. Prescott and A. Papachristodoulou. Layered decomposition for the model order reduction of timescale separated biochemical reaction networks. Journal of Theoretical Biology, 2014. [1]
- Y.-C. Chang, J. P. Armitage, A. Papachristodoulou, G. H. Wadhams. A single phosphatase can convert a robust step response into a graded, tuneable or adaptive response. Microbiology, 2013. [2]
- J. A. J. Arpino, E. J. Hancock, J. Anderson, M. Barahona, G.-B. Stan, A. Papachristodoulou and K. Polizzi. Tuning the Dials of Synthetic Biology. Microbiology, 2013. [3]
- J. Dolan, J. Anderson and A. Papachristodoulou. A loop shaping approach for designing biological circuits. In Proc. of the IEEE CDC 2012. [4]
- J. Anderson, N. Strelkowa, G.-B. Stan, T. Douglas, J. Savulescu, M. Barahona and A. Papachristodoulou. Engineering and ethical perspectives in synthetic biology. EMBO Reports, 13(7):584-590, 2012 [5] PDF
- T. P. Prescott and A. Papachristodoulou. Guaranteed error bounds for structured complexity reduction of biochemical networks. Journal of Theoretical Biology, 304:172-182, 2012. [6] PDF
- A. Hamadeh, E. August, M. A. J. Roberts, P. K. Maini, J. P. Armitage, B. P. Ingalls and A. Papachristodoulou. Feedback Control Architecture of the
*R. sphaeroides*Chemotaxis Network. In Proc of the IEEE CDC 2011. [7] PDF - A. Hamadeh, M. A. J. Roberts, E. August, P. E. McSharry, P. K. Maini, J. P. Armitage and A. Papachristodoulou. Feedback Control Architecture and the Bacterial Chemotaxis Network. PLoS Computational Biology, 7(5): e1001130, 2011. [8] PDF
- J. Anderson, Y.-C. Chang and A. Papachristodoulou. Model Decomposition and Reduction Tools for Large-Scale Networks in Systems Biology. Automatica 47(6):1165-1174, 2011. [9] PDF
- B. Mélykúti, E. August, A. Papachristodoulou and H. El-Samad. Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Systems Biology 2010, 4:38. [10] PDF
- M. A. J. Roberts, A. Papachristodoulou and J. P. Armitage. Adaptation and control circuits in bacterial chemotaxis. Biochemical Society Transactions, 38:1265–1269, 2010. [11]
- M. A. J. Roberts, E. August, A. Hamadeh, P. K. Maini, P. E. McSharry, J. P. Armitage and A. Papachristodoulou. A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in
*R. sphaeroides*. BMC Systems Biology 2009, 3:105. [12] PDF - J. Anderson and A. Papachristodoulou. On Validation and Invalidation of Biological Models. BMC Bioinformatics 2009, 10:132. [13] PDF
- E. August and A. Papachristodoulou. Efficient, sparse biological network determination. BMC Systems Biology 2009, 3:25. [14] PDF
- E. August and A. Papachristodoulou. A new computational tool for establishing model parameter identifiability. Journal of Computational Biology. June 2009, 16(6): 875-885. [15] PDF
- E. August, A. Papachristodoulou, B. Recht, M. A. J. Roberts and A. Jadbabaie. Determining Interconnections in Biochemical Networks Using Linear Programming. In Proc. of the IEEE CDC, 2008. [16] PDF
- A. Papachristodoulou and B. Recht. Determining Interconnections in Chemical Reaction Networks. In Proc. of the ACC, 2007. [17] PDF
- A. Papachristodoulou and H. El-Samad. Algorithms for Discriminating between Biochemical Reaction Network Models: Towards Systematic Experimental Design. In Proc. of the ACC, 2007. [18] PDF
- H. El-Samad, S. Prajna, A. Papachristodoulou, J. C. Doyle, and M. Khammash. Advanced Methods and Algorithms for Biological Networks Analysis. Proceedings of the IEEE, 94(4): 832 – 853, 2006. [19] PDF
- H. El-Samad, M. Fazel, X. Liu, A. Papachristodoulou, S. Prajna. Stochastic Reachability Analysis in Complex Biological Networks. In Proc. of the ACC, 2006. [20] PDF
- T.-M. Yi, M. Fazel, X. Liu, O. Otitoju, J. Gonçalves, A. Papachristodoulou, S. Prajna, J. C. Doyle. Application of Robust Model Validation Using SOSTOOLS to the Study of G-Protein Signaling in Yeast. In Proc. of Foundations of Systems Biology in Engineering, 2005. PDF
- H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash, and J.C. Doyle. Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS. In Proc. of the IEEE CDC, 2003. [21] PDF

## Sum of Squares Techniques

- Edward J. Hancock and Antonis Papachristodoulou. Generalised absolute stability and sum of squares. Automatica 49(4):960-967, 2013. [22]
- J. Anderson and A. Papachristodoulou. Robust nonlinear stability and performance analysis of an F/A-18 aircraft model using sum of squares programming. International Journal of Robust and Nonlinear Control, 2012. [23]
- M. Peet and A. Papachristodoulou. A Converse Sum of Squares Lyapunov Result with a Degree Bound. IEEE Transactions on Automatic Control 57(9):2281-2293, 2012. [24]
- J. Anderson and A. Papachristodoulou. A Decomposition Technique for Nonlinear Dynamical System Analysis. IEEE Transactions on Automatic Control 57(6):1516-1521, June 2012. [25]
- E. Hancock and A. Papachristodoulou. Structured Sum of Squares for Networked Systems Analysis. In Proc. of the IEEE CDC, 2011. [26]
- E. Hancock and A. Papachristodoulou. Generalized Absolute Stability and Sum of Squares. In Proc. of the ACC, 2011. [27]
- J. Anderson and A. Papachristodoulou. Dynamical System Decomposition for Efficient, Sparse Analysis. In Proc. of the IEEE CDC, 2010. [28]
- J. Anderson and A. Papachristodoulou. A Network Decomposition Approach for Efficient Sum-of-Squares Programming Based Analysis. In Proc. of the ACC, 2010. [29]
- M. Peet and A. Papachristodoulou. Inverses of Positive Linear Operators and State Feedback Design for Time-Delay Systems. In Proc. of the 8th IFAC Workshop on Time Delay Systems, 2009.
- A. Papachristodoulou and S. Prajna. Robust stability analysis of nonlinear hybrid systems. IEEE Transactions on Automatic Control. Volume 54, Issue 5, pp. 1037-1043 (2009) [30]
- A. Papachristodoulou, M. M. Peet and S. Lall. Analysis of polynomial systems with time delays via the sum of squares decomposition. IEEE Transactions on Automatic Control. Volume 54, Issue 5, 1061-1067 (2009) [31]
- M. M. Peet, A. Papachristodoulou and S. Lall. Positive forms and stability of linear time-delay systems. SIAM J. Control Optim. Volume 47, Issue 6, pp. 3237-3258 (2009) [32]
- M. M. Peet and A. Papachristodoulou. Using polynomial semi-separable kernels to construct infinite-dimensional Lyapunov functions. In Proc. of the IEEE CDC, 2008.
- A. Papachristodoulou, M. M. Peet and S.-I. Niculescu. Stability Analysis of Linear Systems with Time-Varying Delays: Delay Uncertainty and Quenching. In Proc. of the IEEE CDC, 2007.
- M. M. Peet and A. Papachristodoulou. Positivity of Kernel Functions for Systems with Communication Delay. In Proc. of the IEEE CDC, 2007.
- M. M. Peet, A. Papachristodoulou, and S. Lall. Positive Forms and Stability of Linear Time-Delay Systems. In Proc. of the IEEE CDC, 2006.
- A. Papachristodoulou and M. M. Peet. On the Analysis of Systems Described by Classes of Partial Differential Equations. In Proc. of the IEEE CDC, 2006.
- A. A. Salinas-Varela, A. Papachristodoulou and J. Gonçalves. On L2 Error Bounds between Systems. In Proc. of the International Symposium on Mathematical Theory of Networks and Systems, 2006.
- A. Papachristodoulou. Robust stabilization of nonlinear time delay systems using convex optimization. In Proc. of the IEEE CDC, 2005.
- A. Papachristodoulou, M. M. Peet and S. Lall. Constructing Lyapunov-Krasovskii Functionals for Linear Time Delay Systems. In Proc. of the American Control Conference, 2005.
- A. Papachristodoulou and S. Prajna. Analysis of non-polynomial systems using the sum of squares decomposition. In Positive Polynomials in Control, Springer-Verlag, 2005.
- S. Prajna, A. Papachristodoulou, and F. Wu. Nonlinear control synthesis by sum of squares optimization: A Lyapunov-based approach. In Proc. of the Asian Control Conference, 2004.
- A. Papachristodoulou. Analysis of nonlinear time delay systems using the sum of squares decomposition. In Proc. of the American Control Conference, 2004.
- S. Prajna and A. Papachristodoulou. Analysis of switched and hybrid systems – beyond piecewise quadratic methods. In Proc. of the American Control Conference, 2003.
- A. Papachristodoulou and S. Prajna. On the construction of Lyapunov functions using the sum of squares decomposition. In Proc. of the IEEE CDC, 2002.

## Large Scale Systems Analysis and Design

- R. P. Mason and A. Papachristodoulou. Dynamic edge adaptation in delayed oscillator networks. In Proc. of the IEEE CDC 2012. [33]
- G. S. Schmidt, A. Papachristodoulou, U. Münz and F. Allgöwer. Frequency synchronization and phase agreement in Kuramoto oscillator networks with delays. Automatica, 2012. [34]
- K. Kashima, K, A. Papachristodoulou and F. Allgöwer. Connection profile robustness in a heterogeneous network of piecewise affine FitzHugh-Nagumo models. In Proc. 2011 SICE. [35]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Delay Robustness in Non-Identical Multi-Agent Systems. IEEE Transactions on Automatic Control, 57(6): 1597 - 1603, 2012. [36]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Consensus in Multi-Agent Systems with Coupling Delays and Switching Topology. IEEE Transactions on Automatic Control, 56(12):2976-2982, 2012. [37]
- J. Anderson, A. Teixeira, H. Sandberg, A. Papachristodoulou. Dynamical System Decomposition Using Dissipation Inequalities. In Proc. of the IEEE CDC 2011. [38]
- B. Chu, S. Duncan, A. Papachristodoulou. A Structured Model Reduction Method for Large Scale Networks. In Proc. of the IEEE CDC 2011. [39]
- Y. Li, A. Papachristodoulou, M. Chiang and A. Robert Calderbank. Congestion Control and its Stability in Networks with Delay Sensitive Traffic. Computer Networks, 55(1):20–32, 2011. [40]
- U. Münz, A. Papachristodoulou, and F. Allgöwer. Robust Consensus Controller Design for Nonlinear Relative Degree Two Multi-Agent Systems with Communication Constraints. IEEE Transactions on Automatic Control, 56(1),145-151, 2011. [41]
- A. Papachristodoulou, Y.-C. Chang, E. August and J. Anderson. Structured model reduction for dynamical networked systems. In Proc. of the IEEE CDC 2010. [42]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Delay Robustness in Consensus Problems. Automatica, 46(8):1252-1265, 2010.[43]
- A. Papachristodoulou, A. Jadbabaie and U. Münz. Effects of Delay in Multi-Agent Consensus and Oscillator Synchronization. IEEE Transactions on Automatic Control, 55(6):1471-1477, 2010. [44]
- A. Papachristodoulou and A. Jadbabaie. Delay Robustness of Nonlinear Internet Congestion Control Schemes. IEEE Transactions on Automatic Control, 55(6):1421-1427, 2010. [45]
- U. Münz, A. Papachristodoulou, and F. Allgöwer. Robust Rendezvous of Heterogeneous Langrange Systems on Packet-Switched Networks. at - Automatisierungstechnik, Volume 58, Issue 4, April 2010, pages 184 - 191. [46]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Generalized Nyquist Consensus Condition for Large High-Order Linear Multi-Agent Systems with Communication Delays. In Proceedings of the IEEE Conference on Decision and Control, 2009. [47]
- J. Anderson and A. Papachristodoulou. A Decomposition/Synchronization Scheme for Formulating and Solving Optimization Problems. In Proceedings of the 1st IFAC workshop on distributed estimation and control in networked systems, 2009. [48]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Generalized Nyquist Consensus Condition for Linear Multi-Agent Systems with Heterogeneous Delays. In Proceedings of the 1st IFAC workshop on distributed estimation and control in networked systems, 2009. [49]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Output Consensus Controller Design for Nonlinear Relative Degree One Multi-Agent Systems with Delays. In Proceedings of the 8th IFAC Workshop on Time Delay Systems, 2009.
- U. Münz, A. Papachristodoulou and F. Allgöwer. Consensus Reaching in Multi-Agent Packet-Switched Networks with Nonlinear Coupling. International Journal of Control, Volume 82, Issue 5, May 2009, pages 953 - 969. [50]
- U. Münz, A. Papachristodoulou and F. Allgöwer. Delay-dependent rendezvous and flocking of large scale multi-agent systems with communication delays. In Proc. of the IEEE CDC, 2008.
- U. Münz, A. Papachristodoulou and F. Allgöwer. Nonlinear Multi-Agent System Consensus with Time-Varying Delays. In Proc. of the IFAC World Congress, 2008.
- A. Papachristodoulou and M. M. Peet. Global Stability Analysis of Primal Internet Congestion Control Schemes with Heterogeneous Delays. In Proc. of the IFAC World Congress, 2008.
- Y. Li, A. Papachristodoulou, M. Chiang and A. R. Calderbank. Stability of Congestion Control Schemes with Delay Sensitive Traffic. In Proc. of the American Control Conference, 2008.
- U. Münz, A. Papachristodoulou and F. Allgöwer. Multi-Agent System Consensus in Packet-Switched Networks. Proc. of the European Control Conference, 2007.
- A. Papachristodoulou, A. Jadbabaie. Synchronization in Oscillator Networks with Heterogeneous Delays, Switching Topologies and Nonlinear Dynamics. In Proc. of the IEEE CDC, 2006. [51]
- A. Papachristodoulou, A. Jadbabaie. Synchronization in Oscillator Networks: Switching Topologies and Non-homogeneous Delays. In Proc. of the IEEE CDC, 2005. [52]
- A. Papachristodoulou, L. Li and J. C. Doyle. Methodological Frameworks for Large-scale Network Analysis and Design. ACM SIGCOMM Comp. Comm. Reviews, 34(3): 7 – 20, 2004.
- A. Papachristodoulou. Global stability analysis of a TCP/AQM protocol for arbitrary networks with delay. In Proc. of the IEEE CDC, 2004.

## Software

- S. Prajna, A. Papachristodoulou, and P. A. Parrilo. SOSTOOLS – Sum of Squares Optimization Toolbox, User’s Guide. Available at http://www.eng.ox.ac.uk/control/sostools, 2002.
- S. Prajna, A. Papachristodoulou, and P. A. Parrilo. Introducing SOSTOOLS: A general purpose sum of squares programming solver. In Proc. of the IEEE CDC, 2002.
- S. Prajna, A. Papachristodoulou, P. Seiler, and P. A. Parrilo. SOSTOOLS and its Control Applications. In Positive Polynomials in Control, Springer-Verlag, 2005.

## Applications

- S.I. Chernyshenko, P. Goulart, D. Huang, A. Papachristodoulou. Polynomial sum of squares in fluid dynamics: A review with a look ahead. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 372(2020):20130350, 2014. [53]
- M. Anghel, F. Milano and A. Papachristodoulou. Algorithmic Construction of Lyapunov Functions for Power System Stability Analysis. IEEE Transactions on Circuits and Systems I: Regular Papers. [54]
- B. Chu, S. R. Duncan, A. Papachristodoulou, C. Hepburn. Analysis and control design of sustainable policies for greenhouse gas emissions. [55]
- S. R. Duncan, A. Papachristodoulou. Energy amplification in channel flow over riblets. In Proc. of the 2011 CACSD. [56]
- D. F. Gayme, B. J. McKeon, B. Bamieh, A. Papachristodoulou and J. C. Doyle. Amplification and nonlinear mechanisms in plane Couette flow. Phys. Fluids 23, 065108 (2011). [57]
- S. R. Duncan, C. Hepburn and A. Papachristodoulou. Optimal harvesting of fish stocks under a time-varying discount rate. Journal of Theoretical Biology, 269:1, 166-173, 2011. [58]
- D. Gayme, B. McKeon, A. Papachristodoulou, B. Bamieh and J. C. Doyle. A Streamwise Constant Model of Turbulence in Plane Couette Flow. Journal of Fluid Mechanics, 665:99-119, 2010. [59]
- C. Hepburn, S. R. Duncan and A. Papachristodoulou. Behavioural Economics, Hyperbolic Discounting and Environmental Policy. Environmental and Resource Economics, 2010. [60]
- N. Paulino, E. Di Sotto, S. Salehi, A. Kron, J.-F. Hamel, W. Wang, P. Menon, D. Bates, A. Papachristodoulou and C. Maier. VVAF - Worst case & safety analysis tools for autonomous rendezvous system. In Proc. of the AIAA Guidance, Navigation, and Control Conference, 2010.
- D. Gayme, B. J. McKeon, A. Papachristodoulou, and J.C. Doyle. 2D/3C Model of Large Scale Structures in Turbulence in Plane Couette Flow. Proceedings of the 6th International Symposium on Turbulence and Shear Flow Phenomena, Seoul, Korea, June 2009.
- A. Papachristodoulou and M. M. Peet. SOS for Nonlinear Delayed Models in Biology and Networking. In Topics in Time-Delay Systems: Analysis, Algorithms and Control, Springer-Verlag, 2008.
- S. Glavaski, D. Subramanian, K. Ariyur, R. Ghosh, N. Lamba and A. Papachristodoulou. A Nonlinear Hybrid Life Support System: Dynamic Modelling, Control Design, and Safety Verification. IEEE Transactions on Control Technology, 15(6): 1003 – 1017, 2007.
- A. Papachristodoulou, S. Prajna and S. Glavaski. Sum of Squares in Industry: An Algorithmic Analysis Approach. Tutorial Session at the American Control Conference, 2005.
- K. Krishnaswamy, G. Papageorgiou, S. Glavaski, and A. Papachristodoulou. Analysis of aircraft pitch axis stability augmentation system using sum of squares optimization. In Proc. of the American Control Conference, 2005.
- A. Papachristodoulou and C. Papageorgiou. Robust stability and performance analysis of a longitudinal aircraft model using sum of squares techniques. In Proc. of the Mediterranean Control Conference, 2005.
- S. Glavaski, A. Papachristodoulou and K. Ariyur. Computational challenges of controlled hybrid system safety verification. In Hybrid Systems: Computation and Control, Springer-Verlag, 2005.
- A. Papachristodoulou, J. C. Doyle, and S. H. Low. Analysis of nonlinear delay differential equation models of TCP/AQM protocols using sums of squares. In Proc. of the IEEE CDC, 2004.
- A. Papachristodoulou and F. E. C. Culick. Flight Mechanics of the Wright Aircraft 1903-1912. In AIAA 41st Aerospace Sciences Meeting and Exhibit, Paper number AIAA-2003-0097, 2003.

## Theses

- A. Papachristodoulou. Scalable Analysis of Nonlinear Systems Using Convex Optimization. PhD Thesis, California Institute of Technology, Pasadena CA, 2005.

# Teaching

- Academic Year 2006-2007
- Michaelmas 2006: C5A, Control and Optimization of Operations
- Hilary 2007: C4A, Networked Systems

- Academic Year 2007-2008
- Michaelmas 2007: C4A, Networked Systems
- Hilary 2008: C5B, Biosystem Modelling

- Academic Year 2008-2009
- Hilary 2009: C4A: Networked Systems, C5B: Biosystem Modelling.

- Academic Year 2009-2010
- Hilary 2010: C4A: Networked Systems, C5B: Biosystem Modelling.

- Academic Year 2010-2011
- Michealmas 2010: C4A: Networked Systems
- Hilary 2011: C5B: Biosystem Modelling, C5A: Control and Optimization of Operations

- Academic Year 2011-2012
- Michealmas 2011: C21: Networked Systems, C24: Dynamical Systems and C11: Control and Optimization of Operations.
- Hilary 2012: C10: Biosystem Modelling.

- Academic Year 2012-2013
- Michealmas 2012: C21: Networked Systems, C24: Dynamical Systems
- Hilary 2013: C11: Control and Optimization of Operations.

- Academic Year 2013-2014
- Michealmas 2013: C21: Networked Systems, C24: Dynamical Systems
- Hilary 2014: C11: Control and Optimization of Operations.

# Contact Info

- E-mail: antonis at eng point ox point ac point uk

- Department Address: Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K. Telephone: +44 1865 2 83036. Fax: +44 1865 283394

- College Address: Worcester College, Oxford, OX1 2HB, U.K. Telephone: +44 1865 2 78325