Further results on stabilization of periodic trajectories for a chemostat with two species,

Abstract We discuss an important class of problems involving the tracking of prescribed trajectories in the chemostat model. We provide new tracking results for chemostats with two species and one limiting substrate, based on Lyapunov function methods. In particular, we use a linear feedback control of the dilution rate and an appropriate time-varying substrate input concentration to produce a locally exponentially stable oscillatory behavior. This means that all trajectories for the nutrient and corresponding species concentrations in the closed loop chemostat that stay near the oscillatory reference trajectory are attracted to the reference trajectory exponentially fast. We also obtain a globally stable oscillatory reference trajectory for the species concentrations, using a nonlinear feedback control depending on the dilution rate and the substrate input concentration. This guarantees that all trajectories for the closed loop chemostat dynamics are attracted to the reference trajectory. Finally, we construct an explicit Lyapunov function for the corresponding global error dynamics. We demonstrate the efficacy of our method in a simulation

Productivity analysis and non-linear gain scheduling approach for multi-species bioprocesses with product inhibition

International audienceBioprocesses with product inhibition are known to allow species coexistence. In this work, we first study the productivity of the different possible equilibria, depending on the operating conditions, and show that single species offers the best performances. Then, we propose a control strategy to stabilize the dynamics about the desired equilibria, in presence of instability. Based on output feedback linearization, we propose a family of controllers and a gain-scheduling approach to adapt the controller. Finally, we illustrate our approach on numerical simulations, showing that the attraction basin of the closed-loop system is improved by considering the gain-scheduling approach

Global stabilisation of continuous bioreactors: tools for analysis and design of feeding laws

[EN] This work revisits the dynamic behaviour of stirred continuous reactors in which a single bioreaction with unknown kinetics occurs. Conditions on the feeding strategy to avoid washing out the biomass and falling in batch operation are obtained. These conditions derive in a closed positively invariant region including the desired operating point. It is stated that no closed orbits may exist in this region and, furthermore, that no fixed point exists but on one of its borders. Therefore, global stability is achieved by finding a feeding law that fulfils the aforementioned invariant conditions and gives a single equilibrium for a first-order dynamics. These results are useful to determine the stability properties of different control laws and, more importantly, to design new ones. The main advantages of the proposed approach are its simplicity and that, differing from previous results, input saturation does not affect stability results. The potentiality of the developed tools is illustrated by means of classical and novel feeding laws. (C) 2017 Elsevier Ltd. All rights reserved.Financed by I216-2016 (UNLP), PICT2014-2394 (ANPCyT) and PIP112-2015-01-00837 (CONICET), Argentina; and by DPI2014-55276-C5-1-R MINECO/AEI/FEDER, UE. The material in this paper was not presented at any conference.De Battista, H.; Jamilis, M.; Garelli, F.; Picó, J. (2018). Global stabilisation of continuous bioreactors: tools for analysis and design of feeding laws. Automatica. 89:340-348. https://doi.org/10.1016/j.automatica.2017.12.041S3403488

Output Feedback Linearization of Turbidostats After Time Scaling

"© 2019 IEEE. Personal use of this material is permitted. Permissíon from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertisíng or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works."[EN] Turbidostats are a class of bioreactors gaining interest due to the recent availability of microscale and small-scale devices for characterization and scalingup of the biotechnological systems relevant in the biotech and pharma industries. The goal is to keep cell density constant in continuous operation. Thus, the control law, i.e., the substrate feeding strategy, must guarantee global or semiglobal convergence to an equilibrium point. However, their control is difficult due to the uncertain, time varying, and nonlinear nature of the processes involved. In this brief, we propose an adaptive control law that globally stabilizes the desired biomass setpoint. Furthermore, in a certain region of the state space, the controller linearizes the dynamic behavior after some time scaling. By this way, the orbits of the closedloop system are imposed by the designer. The intrinsic integral action of the gain adaptation rejects the parameter uncertainties. Moreover, the controller implementation only assumes the biomass concentration to be measured. Both the simulated and experimental results show the performance of the controller.This work was supported in part by the National University of La Plata under Grant 11-I127, in part by ANPCyT under Grant PICT2014 2394, in part by CONICET under Grant PIP112 2015 0837, and in part by MINECO/AEI/FEDER, UE under Grant DPI2014-55276-C5-1-R and Grant DPI2017-82896-C2-1-R. The work of F. N. Santos-Navarro was supported by ai2-UPV.De Battista, H.; Picó-Marco, E.; Santos-Navarro, FN.; Picó, J. (2019). Output Feedback Linearization of Turbidostats After Time Scaling. IEEE Transactions on Control Systems Technology. 27(4):1668-1676. https://doi.org/10.1109/TCST.2018.2834882S1668167627

Output Feedback Linearization of Turbidostats After Time Scaling

Turbidostats are a class of bioreactors gaining interest due to the recent availability of microscale and small-scale devices for characterization and scalingup of the biotechnological systems relevant in the biotech and pharma industries. The goal is to keep cell density constant in continuous operation. Thus, the control law, i.e., the substrate feeding strategy, must guarantee global or semiglobal convergence to an equilibrium point. However, their control is difficult due to the uncertain, time varying, and nonlinear nature of the processes involved. In this brief, we propose an adaptive control law that globally stabilizes the desired biomass setpoint. Furthermore, in a certain region of the state space, the controller linearizes the dynamic behavior after some time scaling. By this way, the orbits of the closed-loop system are imposed by the designer. The intrinsic integral action of the gain adaptation rejects the parameter uncertainties. Moreover, the controller implementation only assumes the biomass concentration to be measured. Both the simulated and experimental results show the performance of the controller.Instituto de Investigaciones en Electrónica, Control y Procesamiento de Señale

Instrumentation and control of anaerobic digestion processes: a review and some research challenges

The final publication is available at Springer via http://dx.doi.org/10.1007/s11157-015-9382-6[EN] To enhance energy production from methane or resource recovery from digestate, anaerobic digestion processes require advanced instrumentation and control tools. Over the years, research on these topics has evolved and followed the main fields of application of anaerobic digestion processes: from municipal sewage sludge to liquid mainly industrial then municipal organic fraction of solid waste and agricultural residues. Time constants of the processes have also changed with respect to the treated waste from minutes or hours to weeks or months. Since fast closed loop control is needed for short time constant processes, human operator is now included in the loop when taking decisions to optimize anaerobic digestion plants dealing with complex solid waste over a long retention time. Control objectives have also moved from the regulation of key variables measured online to the prediction of overall process perfor- mance based on global off-line measurements to optimize the feeding of the processes. Additionally, the need for more accurate prediction of methane production and organic matter biodegradation has impacted the complexity of instrumentation and should include a more detailed characterization of the waste (e.g., biochemical fractions like proteins, lipids and carbohydrates)andtheirbioaccessibility andbiodegradability characteristics. However, even if in the literature several methodologies have been developed to determine biodegradability based on organic matter characterization, only a few papers deal with bioaccessibility assessment. In this review, we emphasize the high potential of some promising techniques, such as spectral analysis, and we discuss issues that could appear in the near future concerning control of AD processes.The authors acknowledge the financial support of INRA (the French National Institute for Agricultural Research), the French National Research Agency (ANR) for the "Phycover" project (project ANR-14-CE04-0011) and ADEME for Inter-laboratory assay financial support.Jimenez, J.; Latrille, E.; Harmand, J.; Robles Martínez, Á.; Ferrer Polo, J.; Gaida, D.; Wolf, C.... (2015). Instrumentation and control of anaerobic digestion processes: a review and some research challenges. Reviews in Environmental Science and Biotechnology. 14(4):615-648. doi:10.1007/s11157-015-9382-6S615648144Aceves-Lara CA, Latrille E, Steyer JP (2010) Optimal control of hydrogen production in a continuous anaerobic fermentation bioreactor. Int J Hydrogen Energ 35:10710–10718Aguado D, Montoya T, Ferrer J, Seco A (2006) Relating ions concentration variations to conductivity variations in a sequencing batch reactor operated for enhanced biological phosphorus removal. Environ Modell Softw 21:845–851Aguilar-Garnica E, Dochain D, Alcaraz-González V, González-Álvarez V (2009) A multivariable control scheme in a two-stage anaerobic digestion system described by partial differential equations. J Process Contr 19:1324–1332Ahring BK, Angelidaki I, Johansen K (1992) Anaerobic treatment of manure together with industrial waste. Water Sci Technol 25:311–318Ajeej A, Thanikal JV, Narayanan CM, Senthil Kumar R (2015) An overview of bio augmentation of methane by anaerobic co-digestion of municipal sludge along with microalgae and waste paper. Renew Sustain Energy Rev 50:270–276Alcaraz-González V, González-Álvarez V (2007) Selected topics in dynamics and control of chemical and biological processes. Springer, BerlinAlcaraz-González V, Harmand J, Rapaport A, Steyer JP, González-Álvarez V, Pelayo-Ortiz C (2005a) Robust interval-based regulation for anaerobic digestion processes. Water Sci Technol 52:449–456Alcaraz-González V, Salazar-Peña R, González-Alvarez V, Gouzé JL, Steyer JP (2005b) A tunable multivariable nonlinear robust observer for biological systems. C R Biol 328:317–325Alferes J, Irizar I (2010) Combination of extremum-seeking algorithms with effective hydraulic handling of equalization tanks to control anaerobic digesters. Water Sci Technol 61:2825–2834Alferes J, García-Heras JL, Roca E, García C, Irizar I (2008) Integration of equalisation tanks within control strategies for anaerobic reactors. Validation based on ADM1 simulations. Water Sci Technol 57:747–752Alimahmoodi M, Mulligan CN (2008) Anaerobic bioconversion of carbon dioxide to biogas in an upflow anaerobic sludge blanket reactor. J Air Waste Manage Assoc 58:95–103Alvarez JA, Otero L, Lema JM (2010) A methodology for optimising feed composition for anaerobic co-digestion of agro-industrial wastes. Bioresour Technol 101:1153–1158Alvarez-Ramirez J, Meraz M, Monroy O, Velasco A (2002) Feedback control design for an anaerobic digestion process. J Chem Technol Biotechnol 77:725–734Anderson GK, Yang G (1992) Determination of bicarbonate and total volatile acid concentration in anaerobic digesters using a simple titration. Water Environ Res 64:53–59Andrews JF, Graef SP (1971) Dynamic modelling and simulation of the AD process. Advances in chemistry series no. 105, Anaerobic Biological Treatment Processes. American Chemical Society, Washington, DC, p 126Andrews JF, Pearson EA (1965) Kinetics and characteristics of volatile acid production in anaerobic fermentation processes. Air Water Pollut 9:439–461Angelidaki I, Sanders W (2004) Assessment of the anaerobic biodegradability of macropllutants. Rev Environ Sci Biotechnol 3:117–129Antila J, Tuohiniemi M, Rissanen A, Kantojärvi U, Lahti M, Viherkanto K, Kaarre M, Malinen J (2014) MEMS- and MOEMS-based near-infrared spectrometers. Encycl Anal Chem 1–36. doi: 10.1002/9780470027318.a9376Antoniades CD, Christofides P (2001) Integrating nonlinear output feedback control and optimal actuator/sensor placement for transport-reaction processes. Chem Eng Sci 56:4517–4535APHA (2005) American Public Health Association/American Water Works Association/Water Environmental Federation, Standard methods for the Examination of Water and Wastewater, 21st edn. Washington, DC, USAAppels L, Baeyens J, Degrève J, Dewil R (2008) Principles and potential of the anaerobic digestion of waste-activated sludge. Prog Energ Combust 34:755–781Appels L, Lauwers J, Gins G, Degreve J, Van Impe J, Dewil R (2011) Parameter identification and modeling of the biochemical methane potential of waste activated sludge. Environ Sci Technol 45:4173–4178Aquino SF, Chernicharo CAL, Soares H, Takemoto SY, Vazoller RF (2008) Methodologies for determining the bioavailability and biodegradability of sludges. Environ Technol 29:855–862Astals S, Esteban-Gutiérrez M, Fernández-Arévalo T, Aymerich E, García-Heras JL, Mata-Alvarez J (2013a) Anaerobic digestion of seven different sewage sludges: a biodegradability and modelling study. Water Res 47:6033–6043Astals S, Nolla-Ardèvol V, Mata-Alvarez J (2013b) Thermophilic co-digestion of pig manure and crude glycerol: process performance and digestate stability. J Biotechnol 166:97–104Babary JP, Julien S, Nihtilä MT et al (1999) New boundary conditions and adaptive control of fixed-bed bioreactors. Chem Eng Process Process Intensif 38:35–44Barat R, Serralta J, Ruano MV, Jiménez E, Ribes J, Seco A, Ferrer J (2012) Biological nutrient removal model No 2 (BNRM2): a general model for wastewater treatment plants. Water Sci Technol 67:1481–1489Bastin G, Dochain D (1990) On-line estimation and adaptive control of bioreactors. Elsevier Science, AmsterdamBatstone DJ (2013) Modelling and control in anaerobic digestion: achievements and challenges. 13th IWA World Congress on Anaerobic Digestion (AD 13), pp 1–6Batstone DJ, Keller J, Angelidaki I et al (2002) Anaerobic digestion model No. 1. (ADM1). IWA Scientific and Technical Report No. 13. IWABatstone DJ, Tait S, Starrenburg D (2009) Estimation of hydrolysis parameters in full-scale anaerobic digesters. Biotechnol Bioeng 102:1513–1520Batstone DJ, Amerlinck Y, Ekama G et al (2012) Towards a generalized physicochemical framework. Water Sci Technol 66:1147–1161Baumann WT, Rugh WJ (1986) Feedback control of nonlinear systems by extended linearization. IEEE Trans Automat Contr AC-31:40–46Benyahia B, Campillo F, Cherki B, Harmand J (2012) Particle filtring for the chemostat. In: MED’12, Barcelone, SpainBernard O (2011) Hurdles and challenges for modelling and control of microalgae for CO2 mitigation and biofuel production. J Process Control 21:1378–1389Bernard O, Gouzé JL (2004) Closed loop observers bundle for uncertain biotechnological models. J Process Control 14:765–774Bernard O, Hadj-Sadok Z, Dochain D et al (2001a) Dynamical model development and parameter identification for an anaerobic wastewater treatment process. Biotechnol Bioeng 75:424–438Bernard O, Polit M, Hadj-Sadok Z, Pengov M, Dochain D, Estaben M, Labat P (2001b) Advanced monitoring and control of anaerobic wastewater treatment plants: software sensors and controllers for an anaerobic digester. Water Sci Technol 43:175–182Bernard O, Chachuat B, Hélias A, Rodriguez J (2005a) Can we assess the model complexity for a bioprocess? Theory and example of the anaerobic digestion process. Water Sci Technol 53:85–92Bernard O, Chachuat B, Hélias A, Le Dantec B, Sialve B, Steyer JP, Lavigne JF (2005b) An integrated system to remote monitor and control anaerobic wastewater treatment plants through the internet. Water Sci Technol 52:457–464Björnsson L, Hörnsten EG, Mattiasson B (2001a) Utilization of a palladium–metal oxide semiconductor (Pd-MOS) sensor for on-line monitoring of dissolved hydrogen in anaerobic digestion. Biotechnol Bioeng 73:35–43Björnsson L, Murto M, Jantsch TG, Mattiasson B (2001b) Evaluation of new methods for the monitoring of alkalinity, dissolved hydrogen and the microbial community in anaerobic digestion. Water Res 35:2833–2840Boe K (2006) Online monitoring and control of the biogas process. Technical University of DenmarkBoe K, Batstone D, Angelidaki I (2007) An innovative online VFA monitoring system for the anerobic process, based on headspace gas chromatography. Biotechnol Bioeng 96:712–721Boe K, Steyer JP, Angelidaki I (2008) Monitoring and control of the biogas process based on propionate concentration using online VFA measurement. Water Sci Technol 57:661–766Boe K, Batstone DJ, Steyer JP, Angelidaki I (2010) State indicators for monitoring the anaerobic digestion process. Water Res 44:5973–5980Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254Brinkmann K, Blaschke L, Polle A (2002) Comparison of different methods for lignin determination as a basis for calibration of near-infrared reflectance spectroscopy and implications of lignoproteins. J Chem Ecol 28:2483–2501Buendía IM, Fernández FJ, Villaseñor J, Rodríguez L (2008) Biodegradability of meat industry wastes under anaerobic and aerobic conditions. Water Res 42:3767–3774Buffiere P, Loisel D, Bernet N, Delgenes JP (2006) Towards new indicators for the prediction of solid waste anaerobic digestion properties. Water Sci Technol 53:233–241Cao Y, Pawlowski A (2012) Sewage sludge-to-energy approaches based on anaerobic digestion and pyrolysis: brief overview and energy efficiency assessment. Renew Sust Energ Rev 16:1657–1665Carballa M, Regueiro L, Lema JM (2015) Microbial management of anaerobic digestion: exploiting the microbiome-functionality nexus. Curr Opin Biotechnol 33:103–111Carlos-Hernandez S, Beteau JF, Sanchez EN (2007) Intelligent control strategy for an anaerobic fluidized bed reactor. In: Michel P (ed) Computer applications in biotechnology, vol 1. Cancun, Mexico, pp 73–78Carlos-Hernandez S, Sanchez EN, Bueno JA (2010) Neurofuzzy control strategy for an abattoir wastewater treatment process. In: Banga JR, Bogaerts P, Van Impe J, Dochain D, Smets I (eds) 11th International symposium on computer applications in biotechnology. Leuven, Belgium, pp 84–89Chandler JA, Jewell WJ, Gossett JM (1980) Predicting methane fermentation biodegradability. Biotechnol Bioeng Symp 10:93–107Chen YH (1990) Adaptive robust observers for non-linear uncertain systems. Int J Syst Sci 21:803–814Chen Y, Cheng JJ, Creamer KS (2008) Inhibition of anaerobic digestion process: a review. Bioresour Technol 99:4044–4064Chynoweth DP, Turick CE, Owens JM, Jerger DE, Peck MW (1993) Biochemical methane potential of biomass and waste feedstocks. Biomass Bioenerg 5:95–111Cirne DG, van der Zee FP, Fernandez-Polanco M, Fernandez-Polanco F (2008) Control of sulphide during anaerobic treatment of S-containing wastewaters by adding limited amounts of oxygen or nitrate. Rev Environ Sci Biotechnol 7:93–105Colombié S, Latrille E, Sablayrolles JM (2007) Online estimation of assimilable nitrogen by electrical conductivity measurement during alcoholic fermentation in enological conditions. J Biosci Bioeng 103:229–235Cord-Ruwisch R, Mercz TI, Hoh CY, Strong GE (1997) Dissolved hydrogen concentration as an on-line control parameter for the automated operation and optimization of anaerobic digesters. Biotechnol Bioeng 56:626–634Cossu R, Raga R (2008) Test methods for assessing the biological stability of biodegradable waste. Waste Manage 28:381–388Cresson R, Pommier S, Béline F et al (2014) Etude interlaboratoires pour l’harmonisation des protocoles de mesure du potentiel bio-méthanogène des matrices solides hétérogènes—Final report (in French) ADEMEDalmau J, Comas J, Rodríguez-Roda I, Pagilla K, Steyer JP (2010) Model development and simulation for predicting risk of foaming in anaerobic digestion systems. Bioresour Technol 101:4306–4314Davidsson A, Gruvberger C, Christensen TH, Hansen TL, Jansen J (2007) Methane yield in source-sorted organic fraction of municipal solid waste. Waste Manage 27:406–414De Baere L (2000) Anaerobic digestion of solid waste: state-of-the-art. Water Sci Technol 41:283–290De Baere L (2008) Partial stream digestion of residual municipal solid waste. Water Sci Technol 57:1073–1077De Gracia M, Grau P, Huete E et al (2009) New generic mathematical model for WWTP sludge digesters operating under aerobic and anaerobic conditions: model building and experimental verification. Water Res 43:4626–4642De Vrieze J, Verstraete W, Boon N (2013) Repeated pulse feeding induces functional stability in anaerobic digestion. Microb Biotechnol 6:414–424Delattre C, Dochain D, Winkin J (2004) Observability analysis of nonlinear tubular (bio)reactor models: a case study. J Process Control 14:661–669Di Pinto AC, Limoni N, Passino R, Rozzi A, Tomei MC (1990) Instrumentation, control and automation of water and wastewater treatment and transport systems. In: Proceedings of the 5th IAWPRC workshop, pp 51–58Díaz I, Pérez C, Alfaro N, Fdz-Polanco F (2015) A feasibility study on the bioconversion of CO2 and H2 to biomethane by gas sparging through polymeric membranes. Bioresour Technol 185:246–253Dochain D (2003) State and parameter estimation in chemical and biochemical processes: a tutorial. J Process Control 13:801–818Dochain D, Tali-Maamar N, Babary JP (1997) On modelling, monitoring and control of fixed bed bioreactors. Comput Chem Eng 21:1255–1266Dochain D, Perrier M, Guay M (2011) Extremum seeking control and its application to process and reaction systems: a survey. Math Comput Simulat 82:369–380Donoso-Bravo A, Garcia G, Pérez-Elvira S, Fernandez-Polanco F (2011) Initial rates technique as a procedure to predict the anaerobic digester operation. Biochem Eng J 53(3):275–280Doublet J, Boulanger A, Ponthieux A, Laroche C, Poitrenaud M, Cacho Rivero JA (2013) Predicting the biochemical methane potential of wide range of organic substrates by near infrared spectroscopy. Bioresour Technol 128:252–258Dreywood R (1946) Qualitative test for carbohydrate material. Industrial & Engineering Chemistry Analytical Edition. Am Chem Soc 18:499Dubois M, Gilles KA, Hamilton JK, Rebers PA, Smith F (1956) Colorimetric method for determination of sugars and related substances. Anal Chem 28:350–356Ekama GA, Sotemann SW, Wentzel MC (2007) Biodegradability of activated sludge organics under anaerobic conditions. Water Res 41:244–252Ellison WJ, Pedarros-Caubet F, Caubet R (2007) Automatic and rapid measurement of microbial suspension growth parameters: application to the evaluation of effector agents. J Rapid Meth Aut Mic 15:369–410Fang HHP (2012) Bioenergy production from waste and wastewater in China. In: Technical proceedings of the 2012 NSTI nanotechnology conference and expo, NSTI-nanotech 2012, pp 381–383Fannin KF, Chynoweth DP, Isaacson R (1987) Start-up, operation, stability, and control. Anaerob Dig Biomass 171–196Fdz-Polanco M, Díaz I, Pérez SI, Lopes AC, Fdz-Polanco F (2009a) Hydrogen sulphide removal in the anaerobic digestion of sludge by micro-aerobic processes: pilot plant experience. Water Sci Technol 60:3045–3050Fdz-Polanco M, Pérez-Elvira SI, Díaz I, García L, Torío R, Acevedo AF (2009b) Eliminación de H2S en digestión anaerobia de lodos por procesos microaerofílicos: experiencia en planta piloto. Tecnol del Agua 29:58–64Feitkenhauer H, von Sachs J, Meyer U (2002) On-line titration of volatile fatty acids for the process control of anaerobic digestion plants. Water Res 36:212–218Fernández YB, Soares A, Villa R, Vale P, Cartmell E (2014) Carbon capture and biogas enhancement by carbon dioxide enrichment of anaerobic digesters treating sewage sludge or food waste. Bioresour Technol 159:1–7Fountoulakis MS, Stamatelatou K, Lyberatos G (2008) The effect of pharmaceuticals on the kinetics of methanogenesis and acetogenesis. Bioresour Technol 99:7083–7090Francioso O, Rodriguez-Estrada MT, Montecchio D, Salomoni C, Caputo A, Palenzona D (2010) Chemical characterization of municipal wastewater sludges produced by two-phase anaerobic digestion for biogas production. J Hazard Mater 175:740–746Frigon JC, Roy C, Guiot SR (2012) Anaerobic co-digestion of dairy manure with mulched switchgrass for improvement of the methane yield. Bioprocess Biosyst Eng 35:341–349Frings CS, Dunn RT (1970) A colorimetric method for determination of total serum lipids based on the sulfo-phospho-vanillin reaction. Am J Clin Pathol 53:89–91Frølund B, Palmgren R, Keiding K, Nielsen PH (1996) Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Res 30:1749–1758Gaida D, Wolf C, Meyer C, Stuhlsatz A, Lippel J, Bäck T, Bongards M, McLoone S (2012) State estimation for anaerobic digesters using the ADM1. Water Sci Technol 66:1088–1095Ganesh R, Torrijos M, Sousbie P et al (2013) Anaerobic co-digestion of solid waste: effect of increasing organic loading rates and characterization of the solubilised organic matter. Bioresource Technol 130:559–569García-Diéguez C, Molina F, Roca E (2011) Multi-objective cascade controller for an anaerobic digester. Process Biochem 46:900–909García-Gen (2015) Modelling, optimisation and control of anaerobic co-digestion processes (2015), Ph.D. Thesis, Universidad de Santiago de Compostela, Departamento de Ingeniería QuímicaGarcía-Gen S, Sousbie P, Rangaraj G et al (2015) Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes. Waste Manag 35:96–104Gauthier JP, Kupka IAK (1994) Observability and observers for nonlinear systems. SIAM J Control Optim 32:975–994Gauthier JP, Hammouri H, Othman S (1992) A simple observer for nonlinear systems applications to bioreactors. Autom Control IEEE Trans 37:875–880Ge H, Jensen PD, Batstone DJ (2011) Increased temperature in the thermophilic stage in temperature phased anaerobic digestion (TPAD) improves degradability of waste activated sludge. J Hazard Mater 187:355–361Gendron S, Perrier M, Barrett J, Legault N (1993) Adaptive control of brightness: the model weighting approach. Annual meeting—technical section, Canadian Pulp and Paper Association, Preprints. Publ by Canadian Pulp & Paper AssocGhosh S, Conrad JR, Klass DL (1975) Anaerobic acidogenesis of waste activated sludge, WPCF 47Goffaux G, Van de Wouwer A (2005) Bioprocess state estimation: some classical and less classical approaches. Springer, BerlinGornall AG, Bardawill CJ, David MM (1949) Determination of serum proteins by means of the biuret reaction. J Biochem Chem 177:751–766Gouzé JL, Rapaport A, Hadj-Sadok MZ (2000) Interval observers for uncertain biological systems. Ecol Model 133:45–56Grau P, de Gracia M, Vanrolleghem PA, Ayesa E (2007) A new plant-wide modelling methodology for WWTPs. Water Res 41:4357–4372Gregersen KH (2003) Økonomien i biogasfællesanlæg, Udvikling og status medio (2002) Report no. 150. Institute of Food and Resource Economic, Rolighedsvej 25, DK 1958, Frederiksberg C, DenmarkGrepmeier M (2002) Experimentelle Untersuchungen an einer zweistufigen fuzzy-geregelten anaeroben Abwasserreinigungsanlage mit neuartigem Festbettmaterial. TU MunichGuay M, Dochain D, Perrier M (2004) Adaptive extremum seeking control of continuous stirred tank bioreactors with unknown growth kinetics. Automatica 40:881–888Gunaseelan VN (2007) Regression models of ultimate methane yields of fruits and vegetable solid wastes, sorghum and napiergrass on chemical composition. Bioresour Technol 98:1270–1277Gunaseelan VN (2009) Predicting ultimate methane yields of Jatropha curcus and Morus indica from their chemical composition. Bioresour Technol 100:3426–3429Guwy AJ, Hawkes FR, Wilcox SJ, Hawkes DL (1997) Neural network and on-off control of bicarbonate alkalinity in a fluidised-bed anaerobic digester. Water Res 31:2019–2025Guwy AJ, Dinsdale RM, Kim JR et al (2011) Fermentative biohydrogen production systems integration. Bioresour Technol 102:8534–8542Hao OJ (2003) Sulphate-reducing bacteria. In: Mara D, Horan N (eds) Handbook of water and wastewater microbiology. Academic Press Inc, London, pp 459–468Harremoës P, Capodaglio AG, H

Analysis and Control of Bacterial Populations in Synthetic Biology

Synthetic Biology is a new field of research that aims at engineering new functionalities in living beings. Analogously to electronic circuits, more advanced functionalities can be realised by putting together smaller functional modules that perform elementary tasks; however, the interaction of these basic pieces is somewhat complex and fragile. Therefore, to increase the robustness and reliability of the whole system, typical tools from Control Theory, such as feedback loops, can be employed. In the first part of this thesis we propose feedback control strategies to balance the gene expression of a bistable genetic circuit, known as genetic toggle switch, in an unstable region far away from its stable equilibria - a problem analogous to the stabilization of the inverted pendulum in mechanics. The effectiveness of the proposed control strategies is validated via realistic agent-based simulations of a bacterial population endowed with the genetic toggle switch. Later in the thesis we move towards the growth control of bacterial cells in bioreactors, introducing a novel open-source and versatile design of a turbidostat to host in vivo control experiments. In the last part, we want to control bioreactors to guarantee the coexistence of multiple species in the same environment. We analyse the dynamics of a simple one-chamber bioreactor, proposing control strategies to achieve the control goal. However, simple bioreactors have several drawback when the concentrations of multiple species are regulated at the same time; for these reason, we propose a novel layout for a bioreactor, with two growth chambers and a mixing one, to be used in multicellular in vivo control experiments

Advanced numerical treatment of chemotaxis driven PDEs in mathematical biology

From the first formulation of chemotaxis-driven partial differential equations (PDEs) by Keller and Segel in the 1970's up to the present, much effort has been expended in modelling complex chemotaxis re- lated processes. The shear complexity of such resulting PDEs crucially limits the postulation of analytical results. In this context the sup- port by numerical tools are of utmost interest and, thus, render the implementation of a numerically well elaborated solver an undoubt- edly important task. In this work I present different iteration strategies (linear/nonlinear, decoupled/monolithic) for chemotaxis-driven PDEs. The discretiza- tion follows the method of lines, where I employ finite elements to resolve the spatial discretization. I extensively study the numerical efficiency of the iteration strategies by applying them on particular chemotaxis models. Moreover, I demonstrate the need of numerical stabilization of chemotaxis-driven PDEs and apply a exible scalar algebraic ux correction. This methodology preserves the positivity of the fully discretized scheme under mild conditions and renders the numerical solution non-oscillatory at a low level of additional compu- tational costs. This work provides a first detailed study of accurate, efficient and exible finite element schemes for chemotaxis-driven PDEs and the implemented numerical framework provides a valuable basis for fu- ture applications of the solvers to more complex models

Towards the implementation of distributed systems in synthetic biology

The design and construction of engineered biological systems has made great strides over the last few decades and a growing part of this is the application of mathematical and computational techniques to problems in synthetic biology. The use of distributed systems, in which an overall function is divided across multiple populations of cells, has the potential to increase the complexity of the systems we can build and overcome metabolic limitations. However, constructing biological distributed systems comes with its own set of challenges. In this thesis I present new tools for the design and control of distributed systems in synthetic biology. The first part of this thesis focuses on biological computers. I develop novel design algorithms for distributed digital and analogue computers composed of spatial patterns of communicating bacterial colonies. I prove mathematically that we can program arbitrary digital functions and develop an algorithm for the automated design of optimal spatial circuits. Furthermore, I show that bacterial neural networks can be built using our system and develop efficient design tools to do so. I verify these results using computational simulations. This work shows that we can build distributed biological computers using communicating bacterial colonies and different design tools can be used to program digital and analogue functions. The second part of this thesis utilises a technique from artificial intelligence, reinforcement learning, in first the control and then the understanding of biological systems. First, I show the potential utility of reinforcement learning to control and optimise interacting communities of microbes that produce a biomolecule. Second, I apply reinforcement learning to the design of optimal characterisation experiments within synthetic biology. This work shows that methods utilising reinforcement learning show promise for complex distributed bioprocessing in industry and the design of optimal experiments throughout biology