Guy-Bart STAN's research webpage

Who am I?

My name is Guy-Bart STAN. I was born in Liège, Belgium, in 1977. I received my electrical (electronics) engineering degree in June 2000 and my Ph.D. degree in March 2005, both from the University of Liège. I am currently working as a Lecturer in the Department of Bioengineering and the head of the Control Engineering Synthetic Biology group in the Centre for Synthetic Biology and Innovation of Imperial College London (U.K.). From August 2010 until September 2011, I was one of the organisers for the weekly Bioengineering Departmental Seminars.

From January 2006 until December 2009, I worked in the Control Group of the University of Cambridge (U.K.) as a Research Associate with support from EPSRC (EP/E02761X/1) for the period January 2007 - January 2010 and support from a European Commission FP6 Marie-Curie Intra-European Fellowship (EIF-FP6 025509 GASO) for the period January 2006 - January 2007. From January 2006 until December 2009, I was the weekly seminar organiser for the Cambridge University Control Group. Current and past seminars at the Cambridge University Control Group are accessible online via talks.cam. From June to December 2005, I worked as Senior DSP Engineer at Philips Applied Technologies. Until May 2005, I worked in the Nonlinear Systems and Control group at the Systems and Modeling research unit of the University of Liège with F.N.R.S. (Belgian National Fund for Scientific Research) support.

My webpage in the Department of Bioengineering of Imperial College London (U.K.).

My webpage in the Control Group of the University of Cambridge (U.K.).

I am a member of the The Institution of Engineering and Technology (The IET) and the The Institute of Electrical and Electronics Engineers (The IEEE).

Dr Guy-Bart Stan
Centre for Synthetic Biology and Innovation (CSynBI),
Department of Bioengineering at Imperial College,
703 Bessemer Building, Imperial College London,
South Kensington Campus, London SW7 2AZ, United Kingdom

E-mail:              g.stan "(at)" imperial.ac.uk
Office phone:    +44(0)207 59 46375
Mobile phone:  +44(0)7789 367 876

2013

• Building-in Biosafety for Synthetic Biology, O. Wright, G.-B. Stan, T. Ellis, Microbiology, Special Issue on Synthetic Biology, doi: 10.1099/mic.0.066308-0.
• Synthetic gene circuits for metabolic control: design trade-offs and constraints, D. Oyarzun, G.-B. Stan, J. R. Soc. Interface, Volume 10 (2013), n°78, doi: 10.1098/rsif.2012.0671.
• Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits : A Simulation Study, K. Papadimitriou, G.-B. Stan, M. Drakakis, PLoS ONE, Volume 8, n°2, February 2013, doi:10.1371/journal.pone.0053591.
• Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0, J. Quinn, J. Beal, S. Bhatia, P. Cai, J. Chen, K. Clancy, N. Hillson, M. Galdzicki, A. Maheshwari, U. P, M. Pocock, C. Rodriguez, G.-B. Stan, D. Endy, BBF RFC #93, 2013, doi: 1721.1/78249
• Decentralised Minimal-time Consensus, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Automatica, Volume 49, n°5 (2013), pp. 1227-1235, doi: 10.1016/j.automatica.2013.02.015
• Nonlinear Heat Transfer Processes in a Two-Phase Thermofluidic Oscillator, C. Markides, O. Adebayo, R. Solanki, G.-B. Stan, Applied Energy, Volume 104, (2013), pp. 958-977, doi:10.1016/j.apenergy.2012.11.056.
• Control of protein concentrations in heterogeneous cell populations, A. Vignoni, D. Oyarzun, J. Pico, G.-B. Stan, Proceedings of the 12th European Control Conference (ECC 2013), ETH Zurich, Switzerland, 17-19 July, 2013 (7 pages).
• Stochastic simulation of enzymatic reactions under transcriptional feedback regulation, J.-B. Lugagne, D. Oyarzun, G.-B. Stan, Proceedings of the 12th European Control Conference (ECC 2013), ETH Zurich, Switzerland, 17-19 July, 2013 (6 pages).

2012

• Engineering and ethical perspectives in synthetic biology, J. Anderson, N. Strelkowa, G.-B. Stan, T. Douglas, J. Savulescu, M. Barahona, and A. Papachristodoulou, EMBO reports, Volume 13 (2012), n°7, pp. 584-590, doi:10.1038/embor.2012.81.
• Global State Synchronization in Networks of Cyclic Feedback Systems, A. O. Hamadeh, G.-B. Stan, R. Sepulchre, and J. M. Gonçalves, IEEE Transacations on Automatic Control, Volume 57 (2012), n°2, pp. 478-483, doi:10.1109/TAC.2011.2164015.
• Arterial Reservoir-Excess Pressure and Ventricular Work, K. H. Parker, J. Alastruey, G.-B. Stan, Medical & Biological Engineering & Computing Journal, Volume 50 (2012), n°4, pp. 419-424, doi: 10.1007/s11517-012-0872-1, Supplementary material.
• Synthetic Biology Open Language (SBOL) Version 1.1.0, M. Galdzicki, M. L. Wilson, C. A. Rodriguez, M. R. Pocock, E. Oberortner, L. Adam, A. Adler, J. C. Anderson, J. Beal, C. Yizhi, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grunberg, T. S. Ham, J. N. Hillson, J. D. Johnson, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T. F. Smith, G.-B. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, BBF RFC 87, doi: 1721.1/73909
• Design constraints in an operon circuit for engineered control of metabolic networks, D. Oyarzun, G.-B. Stan, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012 (8 pages).
• Reconstruction of Arbitrary Biochemical Reaction Networks : A Compressive Sensing Approach, W. Pan, Y. Yuan, G.-B. Stan, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012 (8 pages).
• Dynamical Structure Function Identifiability Conditions Enabling Signal Structure Reconstruction, J. Adebayo, T. Southwick, V. Chetty, E. Yeung, Y. Yuan, J. Gonçalves, J. Grose, J. Prince, G.-B. Stan, S. Warnick, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012 (8 pages).
• Design tradeoffs in a synthetic gene control circuit for metabolic networks, D. Oyarzun, G.-B. Stan, Proceedings of the 2012 American Control Conference (ACC 2012), Montreal, Canada, 27-29 June, 2012.

2011

• The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose, N. Dalchau, S. J. Baek, H. M. Briggs, F. C. Robertson, A. N. Dodd, M. J. Gardner, M. A. Stancombe, M. J. Haydon, G.-B. Stan, J. M. Gonçalves, A. A. R. Webb, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Volume 108 (2011), n°12, pp. 5104-5109, doi: 10.1073/pnas.1015452108, Supplementary material.
• Essential information for synthetic DNA sequences, J. Peccoud, J. C. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. W. Lux, C. A. Rodriguez, G.-B. Stan, H. M. Sauro, Nature Biotechnology, Volume 22 (Jan 2011), n°1, p. 22, doi:10.1038/nbt.1753.
• Computational design approaches and tools for synthetic biology, J. MacDonald, C. Barnes, R. Kitney, P. Freemont, G.-B. Stan, Integrative Biology, Special Issue on Synthetic Biology, Volume 3 (2011), n°2, pp. 97-108, doi: 10.1039/c0ib00077a. Top ten most accessed Integrative Biology articles in February, March, May, June, July, and August 2011.
• Fast consensus via predictive pinning control, H.-T. Zhang, M. Z. Q. Chen, G.-B. Stan, IEEE Transaction on Circuits and Systems I, Volume 58 (2011), n°9, pp. 2247-2258, doi:10.1109/TCSI.2011.2123450.
• Robust dynamical network structure reconstruction, Y. Yuan, G.-B. Stan, S. Warnick, J. M. Gonçalves, Automatica, Special Issue on Systems Biology, Volume 47 (2011), n°6, pp. 1230-1235, doi:10.1016/j.automatica.2011.03.008.
• Synthetic Biology Open Language (SBOL) Version 1.0.0, M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, J. C. Anderson, J. Beal, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grunberg, T. S. Ham, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. F. Smith, G.-B. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, BBF RFC 84, doi: 1721.1/66172
• Network of passive oscillators, V. Kulkarni, M. Riedel, G.-B. Stan, Proceedings of the 49th Annual Allerton Conference on Communication, Control, and Computing, University of Illinois at Urbana-Champaign, Allerton Retreat Center, Monticello, Illinois, USA, 28-30 September, 2011.
• Decentralised Minimal-time Consensus, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Proceedings of the 50th IEEE Conference on Decision and Control (CDC 2011), Orlando, Florida, USA, 12-15 December, 2011.

2010

• Correct biological timing in Arabidopsis requires multiple light signaling pathways, N. Dalchau, K. E. Hubbard, C. T. Hotta, F. C. Robertson, H. M. Briggs, G.-B. Stan, J. M. Gonçalves, A. A. R. Webb, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Volume 107 (2010), n° 29, pp. 13171-13176, doi:10.1073/pnas.1001429107, Supplementary material.
• Constructive Synchronization of Networked Feedback Systems, A. O. Hamadeh, G.-B. Stan, J. Gonçalves, Proceedings of the 49th IEEE Conference on Decision and Control (CDC 2010), Atlanta, Georgia, USA, 15-17 December, 2010.
• Robust Dynamical Network Reconstruction, Y. Yuan, G.-B. Stan, S. Warnick, J. Gonçalves, Proceedings of the 49th IEEE Conference on Decision and Control (CDC 2010), Atlanta, Georgia, USA, 15-17 December, 2010.
• Minimal-time output final value of unknown DT-LTI systems with application to the decentralised network consensus problem, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2010), University Congress Center, Budapest, Hungary, 5-9 July, 2010.
• Robust dynamical network structure reconstruction with application to systems biology, Y. Yuan, G.-B. Stan, S. Warnick, J. Gonçalves, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2010), University Congress Center, Budapest, Hungary, 5-9 July, 2010.

2009

• Apoptosis characterizes immunological failure of HIV infected patients, M.-J. Mhawej, C. Brunet-François, R. Fonteneau, D. Ernst, V. Ferré, G.-B. Stan, F. Raffi, C. H. Moog, IFAC Control Engineering Practice, Volume 17 (2009), pp. 798-804, doi:10.1016/j.conengprac.2009.01.001
• Decentralized final value theorem for discrete-time LTI systems with application to minimal-time distributed consensus, Y. Yuan, G.-B. Stan, L. Shi, J. Gonçalves, Proceedings of the 48th IEEE Conference on Decision and Control (CDC 2009), Shangai, China, 16-18 December, 2009.
• Minimal dynamical structure realisations with application to network reconstruction from data, Y. Yuan, G.-B. Stan, Sean Warnick, J. Gonçalves, Proceedings of the 48th IEEE Conference on Decision and Control (CDC 2009), Shangai, China, 16-18 December, 2009.

2008

• Collective behavior coordination with predictive mechanisms, H.-T. Zhang, M. Z. Chen, G.-B. Stan, T. Zhou and J. M. Maciejowski, IEEE Circuits and Systems Magazine, Volume 8 (2008), n° 3, pp. 67-85 doi:10.1109/MCAS.2008.928446
• Ultrafast Consensus via Predictive Mechanisms, H.-T. Zhang, M. Z. Chen, T. Zhou, and G.-B. Stan, Europhysics Letters, Volume 83 (2008), n° 4, doi: 10.1209/0295-5075/83/40003
• Modelling the influence of activation-induced apoptosis of CD4+ and CD8+ T-cells on the immune system response of a HIV infected patient, G.-B. Stan, F. Belmudes, R. Fonteneau, F. Zeggwagh, M.-A. Lefebvre, C. Michelet, and D. Ernst, IET Systems Biology, Volume 2 (2008), n° 2, pp. 94-102, doi: 10.1049/iet-syb:20070029
• Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks, R. Howes, L. Eccleston, J. Gonçalves, G.-B. Stan, S. Warnick, Proceedings of the 47th IEEE Conference on Decision and Control (CDC 2008), Cancun, Mexico, 9-11 December, 2008.
• Robust Synchronization in Networks of Cyclic Feedback Systems, A. O. Hamadeh, G.-B. Stan, J. Gonçalves, Proceedings of the 47th IEEE Conference on Decision and Control (CDC 2008), Cancun, Mexico, 9-11 December, 2008.
• Global Asymptotic Stability of the Limit Cycle in Piecewise Linear versions of the Goodwin Oscillator, A. Salinas-Varela, G.-B. Stan, J. Gonçalves, Proceedings of the 17th IFAC World Congress (IFAC 2008), Seoul, Korea, 6-11 July, 2008.

2007

• Analysis of interconnected oscillators by dissipativity theory, G.-B. Stan, R. Sepulchre, IEEE Transactions on Automatic Control, Volume 52 (2007), n° 2, pp. 256-270, doi: 10.1109/TAC.2006.890471
• The cross-entropy method for power system combinatorial optimization problems, D. Ernst, M. Glavic, G.-B. Stan, S. Mannor, L. Wehenkel, Proceedings of the 7th IEEE Power Engineering Society (PowerTech 2007), Lausanne, Switzerland, 1-5 July, 2007.
• Output synchronization in networks of cyclic biochemical oscillators, G.-B. Stan, A. O. Hamadeh, J. Gonçalves, R. Sepulchre, Proceedings of the 26th American Control Conference (ACC 2007), Times Square, New York City, USA, July 11-13, 2007.

2006

• Clinical data based optimal STI strategies for HIV: a reinforcement learning approach, D. Ernst, G.-B. Stan, J. Gonçalves, L. Wehenkel, Proceedings of the 45th IEEE Conference on Decision and Control (CDC 2006), San Diego, CA, USA, December 13-15, 2006.
• Clinical data based optimal STI strategies for HIV: a reinforcement learning approach, D. Ernst, G.-B. Stan, J. Gonçalves, L. Wehenkel, Proceedings of the 15th annual machine learning conference of Belgium and The Netherlands (BENELEARN 2006), Ghent, Belgium, May 11-12, 2006.

2005

• Feedback Mechanisms for Global Oscillations in Lure Systems, R. Sepulchre, G.-B. Stan, Systems & Control Letters, Volume 54 (2005), n° 8 , pp. 809-818, doi:10.1016/j.sysconle.2004.12.004
• Global analysis and synthesis of oscillations: a dissipativity approach, G.-B. Stan, Ph.D. thesis, University of Liege, Belgium, March, 2005.

2004

• Global Analysis of Limit Cycles in Networks of Oscillators, G.-B. Stan, R. Sepulchre, Proceedings of the 6th IFAC International Symposium on Nonlinear Control Systems (NOLCOS 2004), Stuttgart, Germany, September 1-3, 2004, pp. 1433-1438.
• Dissipativity and Global Analysis of Limit Cycles in Networks of Oscillators, G.-B. Stan, R. Sepulchre, Proceedings of the 16th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2004), Leuven, Belgium, July 5-9, 2004.

2003

• Dissipativity characterization of a class of oscillators and networks of oscillators, G.-B. Stan, R. Sepulchre, Proceedings of the 42nd IEEE Conference on Decision and Control (CDC 2003), Maui, Hawaii, USA, December 9-12, 2003, pp. 4169-4173.

2002

• Comparison of Different Impulse Response Measurement Techniques, G.-B. Stan, J.-J. Embrechts, D. Archambeau, Journal of the Audio Engineering Society, Volume 50 (2002), n° 4, pp. 249-262.

2001

• Determination of the Scattering Coefficient of Random Rough Diffusing Surfaces for Room Acoustics Applications, J.-J. Embrechts, D. Archambeau, G.-B. Stan, Acta-Acoustica Acoustica, Volume 87 (2001), n° 4 pp. 482-494.

Internal Reports

• Comparison of Algorithms for Biological Network Reconstruction from Data, Openwetware webpage of Nuri Purswani as part of her MSc. project with me in 2010.
• Global Analysis of Limit Cycles in the Chua System, Internal report, Cambridge University, UK, April 2006, available upon request.
• Dissipativity and Global Analysis of Limit Cycles, Internal Report, Montefiore, Ulg, 2004, available upon request.

Abstract:

The main theme of this research concerns the global (as opposed to local) analysis of stable limit cycle oscillations in dynamical systems. The global analysis of oscillations in systems and networks of interconnected systems is a longstanding problem. Dynamical systems that exhibit robust nonlinear oscillations are called oscillators. Oscillators are ubiquitous in physical, biological, biochemical, and electromechanical systems. Detailed models of oscillators abound in the literature, most frequently in the form of a set of nonlinear differential equations whose solutions robustly converge to a limit cycle oscillation. Local stability analysis is possible by means of Floquet theory but global stability analysis is usually restricted to simple (second order) models. For these simple models, global analysis is performed by using specific low dimensional tools (phase plane methods, Poincaré-Bendixson theorem, etc.) which do not generalise easily to complex (high dimensional) models. As a consequence, global analysis of complex models is quite hard since there currently exists no general analysis method. This lack of general analysis methods typically forces complex models of oscillators to be studied only through numerical simulation methods. Although numerical simulations of these models may give a first insight into their behaviour, a more in-depth understanding is generally impeded by the complexity of the models and the challenge of rigorous global stability analysis. Moreover, even in the case of simple models, the low dimensional methods used for the analysis do not generalise to the analysis of a network of interconnected oscillators. These considerations show the need for developing general methods that allow the global analysis of oscillators, either isolated or in interconnection. This thesis constitutes the first step towards the development of such a unified oscillators theory. In this aim, this thesis considers an extension of the dissipativity theory introduced by Willems. Nowadays, dissipativity is considered as one of the most general nonlinear (global) stability analysis method for equilibrium points in dynamical systems and networks of interconnected dynamical systems. In this thesis, we show that dissipativity theory can be extended to allow (global) stability analysis of limit cycles in many Lure-type models of oscillators and networks of oscillators. These Lure-type models of oscillators have been named passive oscillators. As the main results of this research, we have showed the implications of this extended dissipativity theory for

• the global stability analysis of isolated passive oscillators
• the global stability analysis of networks of passive oscillators
• the global stability analysis of synchronised oscillations in networks of identical passive oscillators

Furthermore, based on these results, we also propose a limit cycle oscillations synthesis method based on the design of a nonlinear parametric proportional-integral controller aimed at the generation of limit cycle oscillations with large basin of attraction in stabilisable nonlinear systems.

Abstract:

In this research, we compare four of the most used impulse response measurement techniques : Maximum Length Sequence (MLS), Inverse Repeated Sequence (IRS), Time Stretched Pulses, and Logarithmic Sinesweep. These methods are generally used for the measurement of the impulse response of acoustical systems such as transducers, rooms, and binaural impulse responses. The choice of one of these methods depending on the measurement conditions is critical. Therefore an extensive comparison has been realised. This comparison has been done through the implementation and realisation of a complete, fast, reliable, and cheap measurement system. In particular, these different methods have been compared with respect to best achievable signal-to-noise ratio, ease of use, harmonic distortion rejection/measurement, and robustness to measurement conditions (temperature change, impulsive and white noise, etc.). It is shown that in the presence of non white noise, the MLS and IRS techniques are more appropriate. On the contrary, in quiet environments the Logarithmic Sinesweep method is the most accurate : it allows for a direct improvement of the signal-to-noise ratio of 30 dB over the other methods, which can be critical for audio virtual reality systems such as auralization systems. Indeed, capturing binaural room impulse responses for high-quality auralization purposes requires a signal-to-noise ratio of more than 90 dB which is unattainable with other measurement techniques due to inherent nonlinearities in the measurement system (especially the loudspeaker), but fairly easy to reach with logarithmic sinesweeps due to the possibility of completely rejecting (and measuring) harmonic distortions. As a consequence, the sinesweep method opens the way for the development of high-quality auralization and sound spatialisation systems which constitute the bases for advanced audio virtual reality systems.