Welcome to SYSOS

Welcome to SySOS

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A group researching complex networked control systems, biological and technological

Our group develops tools and algorithms for the analysis and design of biological and technological systems and applies them in a range of areas, from Synthetic Biology to fluid mechanics. In particular, we have been developing theory to understand how nonlinear networked systems (System of Systems) operate how to design control laws for them, using computational tools based on the Sum of Squares decomposition and Semidefinite Programming. We have been applying this theory to understand and (re)design biological systems (Systems and Synthetic Biology) but also to analyse and design control laws for fluid flows, robust synchronization, multi-agent system consensus, smart power networks and congestion control for the Internet. Here is a short summary of the areas we work on - please follow the links below for more details.

• Nonlinear systems analysis, Sum of Squares optimization and Lyapunov techniques. In this spirit, we have developed methods for stability analysis of systems described by Ordinary, Delay and Partial Differential Equations, as well as switched/hybrid systems. Of current interest is how to scale these tools to handle much more complicated and richer system descriptions, of higher dimension.

• Systems and Synthetic Biology. We collaborate closely with groups in Engineering Science (Professor Wei Huang), Oxford Biochemistry (Professor Judith Armitage) and Plant Sciences (Professors Steve Kelly and Philip Poole) and other institutions for understanding biological pathways through mathematical modelling using experimental data and designing new experiments for model invalidation (Systems Biology), as well as proposing and implementing redesigns for existing biological systems for improved performance (Synthetic Biology).

• Software Development (SOSTOOLS). This can be found here.

• Large-scale Networked Systems analysis with communication and structural constraints. Examples in this field come from synchronization phenomena in oscillator networks, Network Congestion Control for the Internet and Power System analysis/Smart grid. We are also looking at multi-agent systems consensus under communication and structural constraints such as the effect of time delays and switching topologies.

• Fluid mechanics and Heat transfer, from a control perspective. We are taking a control engineering approach to understand questions in Hydrodynamic Stability and mechanisms for background noise energy amplification and subsequent reduction. We are also using a Sum of Squares approach for the stability analysis and control design of systems described by Partial Differential Equations.

• Complexity reduction of networked systems. We are investigating methods based on model decomposition and reduction to facilitate computational analysis and identification of large-scale and nonlinear systems. Systems of interest include biochemical reaction networks, power systems and consensus networks.

• Scaling Sum of Squares and Semidefinite Programming. We are using sparsity- and symmetry-exploiting algorithms for improving the scalability of semidefinite programming, including the development of software (such as CDCS) to implement relevant operator-splitting algorithms.

Current Members

• Professor Antonis Papachristodoulou - Academic

• Mr Patrick Green - DPhil candidate, July 2019-. Co-supervised with Professor Philip Poole.

• Mr Matthew Newton - DPhil Candidate, October 2019 -.

• Mr Emmanouil Alexis - DPhil Candidate, October 2019 -. Co-supervised with Professor Luca Cardelli.

• Mr Miroslav Gasparek - DPhil Candidate, October 2019 -. Co-supervised with Professor Harrison Steel.

• Mr Han Wang - DPhil Candidate, October 2020 -. Co-supervised with Professor Kostas Margellos.

• Mr Scott Stacey - Probationary Research Student, July 2021 -. Co-supervised with Professor Harrison Steel.

• Mr Bergthor Traustason - Probationary Research Student, July 2021 -. Co-supervised with Professor Philip Poole.

• Mr Liqun Zhao - Probationary Research Student, October 2021 -. Co-supervised with Dr Konstantinos Gatsis.

Current and Previous Externally Funded Projects

• EPSRC & BBSRC Centre for Doctoral Training in Synthetic Biology [1]

• EPSRC Fellowship for Growth in Synthetic Biology: Designing Feedback Control in Biology for Robustness and Scalability [2]

• Sum-of-Squares Approach to Global Stability and Control of Fluid Flows [3]

• Autonomous Behaviour and Learning in an Uncertain World [4]

• Control Engineering Inspired Design Tools for Synthetic Biology [5]

• Using Control Theory to Design Sustainable Policies for Greenhouse Gas Emissions in the Presence of Model Uncertainty [6]

• RoSBNet: Network in Synthetic Biology.

• European Space Agency project with GMV (Spain), NGC (Canada) and the University of Leicester, "Worst-Case and Safety Analysis Tools for Autonomous Rendezvous Systems".

• Control Theory Tools for Elucidating the Phosphotransfer Network in Rhodobacter sphaeroides: A Feasibility Study

• Oxford-Princeton Collaboration on Network Science with Professor Mung Chiang.

Collaborations

• Scaling Semidefinite Programming - Northeastern, USA
• Analysis of Partial Differential Equations Using Sum of Squares Programming - CentraleSupelec, France
• A Control Engineering Approach for Modelling High-Shear Flows - Johns Hopkins
• Multi-Agent-Systems and Delay Robustness in Cooperative Control - IST, Stuttgart
• Designing bio-feedback control circuits using small RNA - Northumbria

News

• Many congratulations to Dr Yang Zheng (see also updated website) who won the 2019 European PhD Award on Control for Complex and Heterogeneous Systems for his thesis "Chordal Sparsity in Control and Optimization of Large-scale Systems"!

• Workshop on Dynamics, Randomness, and Control in Molecular and Cellular Networks Center for Mathematical Sciences and Applications, Harvard University, 12-14 November 2019.
• International Workshop on Control Engineering and Synthetic Biology, Worcester College, Oxford, 9-11 September 2019.
• Chi.bio is released!

• Workshop on `New Vistas in computational systems and synthetic biology', May 2019, Vigo, Spain.
• Antonis Papachristodoulou is elevated to IEEE Fellow for his fundamental contributions to theory and applications of Sum of Squares Programming and networked control systems.

• Workshop on Vistas in Control at ETHZ, September 10-11, 2018.
• MBI Workshop on Control of Cellular and Molecular Systems, Mathematical Biosciences Institute, 2-6 October 2017.
• International Workshop on Control Engineering and Synthetic Biology. What next?, Prince Philip House, London, 17-18 July 2017.
• Thomas Prescott is awarded the 2015 European PhD Award for the Control of Complex and Heterogeneous networks for his thesis Large-Scale Layered Systems and Synthetic Biology: Model Reduction and Decomposition.

• Richard Mason and Antonis Papachristodoulou are awarded the O. Hugo Schuck Best Paper Award for their 2014 ACC paper on Chordal Sparsity, Decomposing SDPs and the Lyapunov Equation.

• Antonis Papachirstodoulou is awarded the 2015 European Control Award and will be giving a plenary at the 2015 European Control Conference.

• 5th IFAC Workshop on Distributed Estimation and Control in Networked Systems, Philadelphia, 10-11 September 2015.
• Antonis Papachristodoulou awarded an EPSRC Fellowship for Growth in Synthetic Biology.
• Richard Mason's paper Chordal Sparsity, Decomposing SDPs and the Lyapunov Equation has received the best student paper award at the 2014 American Control Conference. Download the PDF here.

• A workshop on Control Engineering and Synthetic Biology, Worcester College, Oxford, 10-12 September 2014.
• Towards Next Generation Synthetic Biology: 21-22 November 2013, Warwick, UK.
• Workshop on Algorithms for Dynamical Systems and Lyapunov Functions: 17 July -19 July 2013, Reykjavík, Iceland.
• Oberwolfach Workshop on Structured function systems and applications: 24 February - 3 March 2013, TU Dortmund, Germany.
• Optimization and Control for Smart Grids: 21-25 May 2012, Santa Fe, New Mexico, USA.
• Warwick Systems Biology DTC Annual Conference: 27-29 July 2011, Stratford Apon Avon, UK.
• Third RoSBNet Workshop: 20-22 July 2011, St Annes' College, University of Oxford.
• Exeter Synthetic Biology Sandpit: 3 June 2011, University of Exeter, UK.
• Dynamics, Control and Pricing in Power Systems: 18-20 May 2011, Lund University, Sweden.
• CDC2010: The 49th Conference on Decision and Control, Atlanta, Georgia, 15-17 December 2010. Special session on Decentralised Network Analysis, Control and Optimisation.
• Synthetic Components Network: SCN annual conference, 23-24 September, Oulton Hall, Leeds, U.K.
• Frontiers of Multidisciplinary Research: Mathematics, engineering, and biology, 21-24 September 2010, University of Exeter, U.K.
• Dynamics Days Europe 2010: Minisymposium on Cell Dynamics and Systems Biology, 6-10 September, 2010, University of Bristol, U.K.
• Application of Control Theory and Optimization in Biochemical Pathways: A Satellite Meeting of the 2010 ICM, 16-18 August, 2010, Hyderabad, India.
• Second RoSBNet Workshop: 12-14 July, 2010, St Annes' College, University of Oxford.
• MTNS 2010: Invited Session: Real Algebraic Geometry and Applications, 5-9 July, 2010, Budapest, Hungary.
• Banff Workshop: Randomization, Relaxation, and Complexity, 28 February - 5 March 2010, Banff International Research Station, Banff, Canada.
• Lund Center for Control of Complex Engineering Systems: Multi-agent coordination and estimation, Jan 18 - Feb 19: Workshop Feb 3-5, 2010.
• CDC 2009 Preconference Workshop: Full-day CDC 2009 Pre-conference Workshop on Biomolecular Circuit Analysis and Design, 15th December 2009.
• NE{S|T}COC: Symposium on Recent Trends in Networked Systems and Cooperative Control & Workshop on Network Induced Constraints in Control, 28-29 September, 2009, University of Stuttgart, Germany
• ARCC Workshop on Convex Algebraic Geometry, Optimization and Applications: 21-25 September, 2009, Palo Alto, California, USA.
• RoSBNet First Year Workshop: 14-16 September 2009, St. Annes' College, University of Oxford, U.K.
• RoSBNet Launch Meeting: A Network in Synthetic Biology, 6 July 2009, University of Oxford, U.K.
• IMA Thematic Year on Mathematics of Molecular and Cellular Biology
  • Organization of Biological Networks, 3-7 March, 2008
  • Design Principles in Biological Systems, 21-25 April, 2008
• IMA Thematic Year on Applications of Algebraic Geometry
  • Software for Algebraic Geometry, 23-27 October, 2006
  • Optimization and Control, 16-20 January, 2007
• Banff Workshop: Positive Polynomials and Optimization, 7-12 October, 2006, Banff International Research Station, Banff, Canada
• ARCC Workshop: Theory and Algorithms of Linear Matrix Inequalities, 1-5 August 2005, American Institute of Mathematics, Palo Alto, California.

Joining SySOS

• If you are an Oxford undergraduate interested in doing a summer internship, on any of the above research directions, get in touch.

• If you are finishing your undergraduate/masters degree and you want to apply for a DPhil (PhD) or MSc by Research in our group, then please contact us sooner than later to discuss possible projects. Note that there are several Centres of Doctoral Training that are relevant to our research, especially the Interdisciplinary Bioscience DTP as well as the EPSRC CDT in Autonomous Intelligent Machines and Systems. If you have a strong academic background, the chances of securing funding for your studies are higher the earlier you apply. Note that applications need to follow the Postgraduate Admissions guidelines.

• Any PDRA openings will be advertised on the departmental website. None are available now.

• There are several other routes for joining SySOS, mainly through fellowships. Please contact us to discuss.

Previous Members

• Ms Carolin Schulte - DPhil Candidate, July 2018- November 2021. Co-supervised with Professor Philip Poole.

• Mr Boon Lim - DPhil candidate, October 2018- November 2021. Co-supervised with Professor Wei Huang.

• Mr Licio Romao - DPhil Candidate, October 2017 - September 2021. Co-supervised with Professor Kostas Margellos.

• Ms Hayley Knights - Research Associate, Apr - Sep 2021

• Dr Harrison Steel - PDRA, June 2019- September 2020

• Dr Michael Schaub - Marie Skłodowska Curie Fellow, July 2017 - June 2020

• Dr Robert Habgood - PDRA, October 2019 - July 2020

• Dr Aivar Sootla - Post-Doctoral Research Associate, September 2016-June 2019.

• Mr James Scott-Brown (project page, personal site)- DPhil Candidate, October 2014-October 2018. Co-supervised with Dr Jonathan David (dstl).

• Mr Yang Zheng - DPhil Student, October 2015 - March 2019

• Dr Nicolas Delalez - Post-Doctoral Research Associate, January 2016 - January 2019.

• Dr Axel Nyström - DPhil Student, October 2013-2018. Co-supervised with Dr Andrew Angel.

• Dr Ciarán Kelly - Post-Doctoral Research Associate, December 2017-April 2018

• Dr Thomas Folliard - DPhil student, 2013-2017. Co-supervised with Professor Judith Armitage.

• Dr Andreas Harris - DPhil student, 2013-2017.

• Dr Dhruva Raman - DPhil student, 2013-2017. Co-supervised with Dr James Anderson

• Dr Mohamadreza Ahmadi - DPhil student, 2013-2016. Co-supervised with Dr Giorgio Valmorbida.

• Dr James Anderson DPhil student, 2008 - 2011, Post-Doctoral Research Associate 2011-2012, Junior Research Fellow, 2012-2016.

• Dr Thomas P. Prescott - DPhil student, 2011 - 2015, Post-Doctoral Research Associate, 2015-2016

• Dr Richard P. Mason - DPhil student, 2011-2016

• Dr Xuan Zhang - DPhil student, October 2011-2015

• Dr Giorgio Valmorbida - Post-Doctoral Research Associate, 2013-2015

• Dr Edward Hancock - Post-Doctoral Research Associate, 2013 - 2015

• Dr Bing Chu - Postdoctoral Research Assistant, June 2010-March 2012

• Dr Yo-Cheng (Mark) Chang DPhil, co-supervised with Professor Judith Armitage, Department of Biochemistry, January 2007-January 2011.

• Dr Bence Mélykúti, DPhil, co-supervised with Professor Alison Etheridge, Department of Statistics, January 2008-February 2011.

• Dr Abdullah Hamadeh, March 2009 - October 2009

• Miss Nassia Inglessis, September 2009 - October 2009

• Mr Christoph Maier, April 2009 - July 2009

• Dr Mark Roberts, October 2007 - December 2008

• Dr Elias August, October 2007 - December 2008

Useful Links

• Engineering Science Control Group

• Doctoral Training Centres