A. R. Akhmetzhanov, F. Grognard, and L. Mailleret, Optimal life-history strategies in seasonal consumer-resource dynamics, Evolution, vol.65, issue.11, pp.3113-3138, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00848376

W. R. Anesiadis, R. Cluett, and . Mahadevan, Dynamic metabolic engineering for increasing bioprocess productivity, Metab. Eng, vol.10, issue.5, pp.255-66, 2008.
DOI : 10.1016/j.ymben.2008.06.004

J. R. Banga, Optimization in computational systems biology, BMC Syst. Biol, vol.2, p.47, 2008.

J. R. Banga, E. Balsa-canto, C. G. Moles, and A. A. Alonso, Dynamic optimization of bioprocesses: Efficient and robust numerical strategies, J. Biotechnol, vol.117, issue.4, pp.407-426, 2005.

G. Bastin and D. Dochain, On-line Estimation and Adaptive Control of Bioreactors, 1990.

F. Bonnans, P. Martinon, D. Giorgi, V. Grélard, S. Maindrault et al., Bocop 2.0.5-user guide, 2017.

B. Bonnard and M. Chyba, Singular Trajectories and their Role in Control Theory, Mathématiques & Applications, vol.40, 2003.

D. Bosdriesz, B. Molenaar, F. J. Teusink, and . Bruggeman, How fast-growing bacteria robustly tune their ribosome concentration to approximate growthrate maximization, FEBS J, vol.282, issue.10, pp.2029-2073, 2015.

H. Bremer and P. P. Dennis, Modulation of chemical composition and other parameters of the cell at different exponential growth rates, Ecosal Plus: Cellular and Molecular Biology of E. coli, Salmonella, and the Enterobacteriaceae, 2013.

F. Ceroni, B. A. Blount, and T. Ellis, Sensing the right time to be productive, Cell Syst, vol.3, issue.2, pp.116-123, 2016.

L. Cesari, Optimization-Theory and Applications: Problems with Ordinary Differential Equations, vol.17, 1983.

M. Chaves and J. L. Gouzé, Exact control of genetic networks in a qualitative framework, Automatica, vol.47, issue.6, pp.1105-1117, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00507040

V. Chubukov, L. Gerosa, K. Kochanowski, U. Sauer, ;. Cinar et al., Mathematical Bioeconomics: The Optimal Management of Renewable Resources, Batch Fermentation: Modeling, Monitoring, and Control. Marcel Dekker, vol.12, pp.327-367, 1990.

H. Clarke, Y. S. Ledyaev, R. J. Stern, and P. R. Wolenski, Nonsmooth Analysis and Control Theory, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00863298

M. De-hijas-liste, E. Klipp, E. Balsa-canto, and J. R. Banga, Global dynamic optimization approach to predict activation in metabolic pathways, BMC Syst. Biol, vol.8, p.1, 2014.

H. Jong, S. Casagranda, N. Giordano, E. Cinquemani, D. Ropers et al., Mathematical modelling of microbes: metabolism, gene expression and growth, J. Roy. Soc. Interface, vol.14, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01666954

H. De-jong, J. Geiselmann, and D. Ropers, Resource reallocation in bacteria by reengineering the gene expression machinery, Trends Microbiol, vol.25, issue.6, pp.480-93, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01420729

H. El-samad, H. Kurata, J. C. Doyle, C. A. Gross, and M. Khammash, Surviving heat shock: Control strategies for robustness and performance, Proc. Natl. Acad. Sci. USA, vol.102, issue.8, pp.2736-2777, 2005.

J. Ewald, M. Bartl, T. Dandekar, and C. Kaleta, Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism, PLoS Comput. Biol, vol.13, issue.2, p.1005371, 2017.

A. Farewell and F. C. Neidhardt, Effect of temperature on in vivo protein synthetic capacity in Escherichia coli, J. Bacteriol, vol.180, issue.17, pp.4704-4714, 1998.

C. Fracassi, L. Postiglione, G. Fiore, and D. Di-bernardo, Automatic control of gene expression in mammalian cells, ACS Synth. Biol, vol.5, issue.4, pp.296-302, 2016.

R. Gabasov and F. M. Kirillova, Singular Optimal Control, 1982.

N. Giordano, F. Mairet, J. L. Gouzé, J. Geiselmann, and H. De-jong, Dynamical allocation of cellular resources as an optimal control problem: Novel insights into microbial growth strategies, PLoS Comput. Biol, vol.12, issue.3, p.1004802, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01332394

V. Grigorieva and E. N. Khailov, Optimal control of a nonlinear model of economic growth, Discrete Continuous Dyn. Syst. Ser. B, pp.456-66, 2007.

C. N. Hinshelwood, On the chemical kinetics of autosynthetic systems, J. Chem. Soc. (Res.), pp.745-55, 1952.

, Control Theory and Systems Biology, 2010.

J. Izard, C. G. Balderas, D. Ropers, S. Lacour, X. Song et al., A synthetic growth switch based on controlled expression of RNA polymerase, Mol. Syst. Biol, vol.11, issue.11, p.840, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01247993

H. Johnson and I. Lewin, The growth rate of E. coli in relation to temperature, quinine and coenzyme, J. Cell. Physiol, vol.28, issue.1, pp.47-75, 1946.

T. Kalisky, E. Dekel, and U. Alon, Cost-benefit theory and optimal design of gene regulation functions, Phys. Biol, vol.4, issue.4, pp.229-274, 2007.

A. S. Khalil and J. J. Collins, Synthetic biology: applications come of age, Nat. Rev. Genet, vol.11, issue.5, pp.367-80, 2010.

A. L. Koch, Why can't a cell grow infinitely fast?, Can. J. Microbiol, vol.34, issue.4, pp.421-427, 1988.

K. L. Larrabee, J. O. Phillips, G. J. Williams, and A. R. Larrabee, The relative rates of protein synthesis and degradation in a growing culture of Escherichia coli, J. Biol. Chem, vol.255, issue.9, pp.4125-4155, 1980.

S. Lenhart and J. T. Workman, Optimal Control Applied to Biological Models, 2007.

M. Lo, S. H. Chng, W. S. Teo, H. S. Cho, and M. W. Chang, A two-layer gene circuit for decoupling cell growth from metabolite production, Cell Syst, vol.3, issue.2, pp.133-176, 2016.

. Markley, Principles of Differential Equations, 2004.

A. Milias-argeitis, M. Rullan, S. K. Aoki, P. Buchmann, and M. Khammash, Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth, Nat. Commun, vol.7, p.12546, 2016.

R. Molenaar, D. Van-berlo, B. De-ridder, and . Teusink, Shifts in growth strategies reflect tradeoffs in cellular economics, Mol. Syst. Biol, vol.5, p.323, 2009.

R. D. Mosteller, R. V. Goldstein, and K. R. Nishimoto, Metabolism of individual proteins in exponentially growing Escherichia coli, J. Biol. Chem, vol.255, issue.6, pp.2524-2556, 1980.

G. V. Naumov, Construction of the switching curve for optimal control problems with chattering control, Izvestiya RAN: Teoriya i Sistemy Upravleniya, vol.3, pp.46-51, 2003.

E. J. Olson and J. J. Tabor, Optogenetic characterization methods overcome key challenges in synthetic and systems biology, Nat. Chem. Biol, vol.10, issue.7, pp.502-513, 2014.

D. A. Oyarzún and G. B. Stan, Synthetic gene circuits for metabolic control: design trade-offs and constraints, J. R. Soc. Interface, vol.10, issue.78, p.20120671, 2013.

M. Y. Pavlov and M. Ehrenberg, Optimal control of gene expression for fast proteome adaptation to environmental change, Proc. Natl. Acad. Sci. USA, vol.110, issue.51, pp.20527-20559, 2013.

F. J. Poelwijk, M. G. De-vos, and S. J. Tans, Tradeoffs and optimality in the evolution of gene regulation, Cell, vol.146, issue.3, pp.462-70, 2011.

S. Pontryagin, V. G. Boltyansky, R. V. Gamkrelidze, and E. F. Mishchenko, The Mathematical Theory of Optimal Processes, 1964.

M. Sauro, Control and regulation of pathways via negative feedback, J. R. Soc. Interface, vol.14, issue.127, p.20160848, 2017.

M. A. Savageau, Escherichia coli habitats, cell types, and molecular mechanisms of gene control, Am. Nat, vol.122, issue.6, pp.732-776, 1983.

M. Schaechter, J. L. Ingraham, and F. C. Neidhardt, , 2006.

H. Schattler and U. Ledzewicz, Geometric Optimal Control: Theory, Methods and Examples. Interdisciplinary Applied Mathematics, vol.38, 2012.

H. Schattler and U. Ledzewicz, Optimal Control for Mathematical Models of Cancer Therapies: An Application of Geometric Methods, Interdisciplinary Applied Mathematics, vol.42, 2015.

R. Schuetz, L. Kuepfer, and U. Sauer, Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli, Mol. Syst. Biol, vol.3, p.119, 2007.

T. Schuster, D. Pfeiffer, and . Fell, Is maximization of molar yield in metabolic networks favoured by evolution?, J. Theor. Biol, vol.252, issue.3, pp.497-504, 2008.

M. Scott, C. W. Gunderson, E. M. Mateescu, Z. Zhang, and T. Hwa, Interdependence of cell growth and gene expression: Origins and consequences, Science, vol.330, issue.6007, pp.1099-103, 2010.

M. Scott, S. Klumpp, E. M. Mateescu, and T. Hwa, Emergence of robust growth laws from optimal regulation of ribosome synthesis, Mol. Syst. Biol, vol.10, p.747, 2014.

E. D. Sontag, Molecular systems biology and control, Eur. J. Control, vol.11, issue.5, pp.396-435, 2005.

G. N. Stephanopoulos, A. A. Aristidou, and J. Nielsen, Metabolic Engineering: Principles and Methodologies, 1998.

V. Surovstev, J. J. Morgan, and P. A. , Whole-cell modeling framework in which biochemical dynamics impact aspects of cellular geometry, J. Theor. Biol, vol.244, issue.1, pp.154-66, 2007.

J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages et al., Long-term model predictive control of gene expression at the population and single-cell levels, Proc. Natl. Acad. Sci. USA, vol.109, pp.14271-14277, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01528440

H. A. Van-den-berg, Y. N. Kiselev, S. A. Kooijman, and M. V. Orlov, Optimal allocation between nutrient uptake and growth in a microbial trichome, J. Math. Biol, vol.37, issue.1, pp.28-48, 1998.

J. D. Van-elsas, A. V. Semenov, R. Costa, and J. T. Trevors, Survival of Escherichia coli in the environment: Fundamental and public health aspects, ISME J, vol.5, issue.2, pp.173-83, 2011.

D. Vecchio, A. J. Dy, and Y. Qian, Control theory meets synthetic biology, J. R. Soc. Interface, vol.13, issue.120, p.20160380, 2016.

N. Venayak, N. Anesiadis, W. R. Cluett, and R. Mahadevan, Engineering metabolism through dynamic control, Curr. Opin. Biotechnol, vol.34, pp.142-52, 2015.

C. Venkateswarlu, Advances in monitoring and state estimation of bioreactors, J. Sci. Indus. Res, vol.63, pp.491-499, 2005.

S. Waldherr, D. A. Oyarzún, and A. Bockmayr, Dynamic optimization of metabolic networks coupled with gene expression, J. Theor. Biol, vol.365, pp.469-85, 2015.

A. Y. Weiße, D. A. Oyarzún, V. Danos, and P. S. Swain, Mechanistic links between cellular trade-offs, gene expression, and growth, Proc. Natl. Acad. Sci. USA, vol.112, pp.1038-1085, 2015.

I. Yegorov, A. Bratus, and Y. Todorov, Synthesis of optimal control in a mathematical model of economic growth under R&D investments, Appl. Math. Sci, vol.9, issue.91, pp.4523-64, 2015.

I. Yegorov, F. Grognard, L. Mailleret, and F. Halkett, Optimal resource allocation for biotrophic plant pathogens, vol.50, pp.3154-3163, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01572090

I. Yegorov, F. Mairet, and J. L. Gouzé, Optimal resource allocation for bacterial growth with degradation. IFAC-PapersOnLine, vol.50, pp.9858-63, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01524917

I. Yegorov, F. Mairet, and J. L. Gouzé, Optimal feedback strategies for bacterial growth with degradation, recycling and effect of temperature, Optim. Control Appl. Methods, vol.39, issue.2, pp.1084-1109, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01655960

T. Yi, Y. Huang, M. I. Simon, and J. Doyle, Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Proc. Natl. Acad. Sci. USA, vol.97, issue.9, pp.4649-53, 2000.
DOI : 10.1073/pnas.97.9.4649

URL : http://www.pnas.org/content/97/9/4649.full.pdf

J. Yong and X. Y. Zhou, Stochastic Controls: Hamiltonian Systems and HJB Equations, 1999.

M. I. Zelikin and V. F. Borisov, Theory of Chattering Control with Applications to Astronautics, Robotics, Economics, and Engineering, 1994.

M. I. Zelikin and V. F. Borisov, Singular optimal regimes in problems of mathematical economics, J. Math. Sci, vol.130, issue.1, pp.4409-4570, 2005.