F. Jacob and J. Monod, Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-0356, 1961.
DOI : 10.1016/S0022-2836(61)80072-7

A. Gann, Jacob and Monod: From Operons to EvoDevo, Current Biology, vol.20, issue.17, pp.718-723, 2010.
DOI : 10.1016/j.cub.2010.06.027

H. Kwak and J. Lis, Control of Transcriptional Elongation, Annual Review of Genetics, vol.47, issue.1, pp.483-508
DOI : 10.1146/annurev-genet-110711-155440

D. Dogini, V. Pascoal, S. Avansini, A. Vieira, and T. Pereira, Lopes-Cendes I: The new world of rnas, Genet Mol Biol, vol.2014, issue.371, pp.285-293

M. Hirsch, Convergent activation dynamics in continuous time networks, Neural Networks, vol.2, issue.5, pp.331-349, 1989.
DOI : 10.1016/0893-6080(89)90018-X

R. Thomas, D. Thieffry, and M. Kaufman, Dynamical behaviour of biological regulatory networks???I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state, Bulletin of Mathematical Biology, vol.29, issue.2, pp.247-276, 1995.
DOI : 10.1007/BF02460618

J. Gouzé, Positive and Negative Circuits in Dynamical Systems, Journal of Biological Systems, vol.06, issue.01, pp.611-626, 1998.
DOI : 10.1142/S0218339098000054

T. Gardner, C. Cantor, and J. Collins, Construction of a genetic toggle switch in Escherichia coli, Nature, vol.403, pp.339-342, 2000.

M. Elowitz and S. Leibler, A synthetic oscillatory network of transcriptional regulators, Nature, vol.403, issue.6767, pp.335-338, 2000.
DOI : 10.1038/35002125

V. Chellaboina, S. Bhat, M. Haddad, and D. Bernstein, Modeling and analysis of mass-action kinetics, IEEE Control Systems Magazine, vol.29, issue.4, pp.60-78, 2009.
DOI : 10.1109/MCS.2009.932926

I. Golding and E. Cox, Physical Nature of Bacterial Cytoplasm, Physical Review Letters, vol.96, issue.9, p.98102, 2006.
DOI : 10.1103/PhysRevLett.96.098102

S. Weber, A. Spakowitz, and J. Theriot, Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm, Physical Review Letters, vol.104, issue.23, pp.2381021752-0509125, 2010.
DOI : 10.1103/PhysRevLett.104.238102

B. English, V. Hauryliuk, A. Sanamrad, S. Tankov, N. Dekker et al., Single-molecule investigations of the stringent response machinery in living bacterial cells, Proceedings of the National Academy of Sciences, vol.108, issue.31, pp.365-373, 2011.
DOI : 10.1073/pnas.1102255108

A. Coquel, J. Jacob, M. Primet, A. Demarez, M. Dimiccoli et al., Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect, PLoS Computational Biology, vol.73, issue.1???2, p.1003038
DOI : 10.1371/journal.pcbi.1003038.s004
URL : https://hal.archives-ouvertes.fr/hal-00798053

B. Parry, I. Surovtsev, M. Cabeen, O. Hern, C. Dufresne et al., The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity, Cell, vol.156, issue.1-2, pp.183-194
DOI : 10.1016/j.cell.2013.11.028

T. Cremer and M. Cremer, Chromosome Territories, Cold Spring Harbor Perspectives in Biology, vol.2, issue.3, p.3889
DOI : 10.1101/cshperspect.a003889

T. Le, M. Imakaev, L. Mirny, and M. Laub, High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome, Science, vol.342, issue.6159, pp.731-734
DOI : 10.1126/science.1242059

F. Képès, Periodic Transcriptional Organization of the E.coli Genome, Journal of Molecular Biology, vol.340, issue.5, pp.957-964, 2004.
DOI : 10.1016/j.jmb.2004.05.039

P. Llopis, A. Jackson, O. Sliusarenko, I. Surovtsev, J. Heinritz et al., Spatial organization of the flow of genetic information in bacteria, Nature, vol.90, issue.7302, pp.46677-81, 2010.
DOI : 10.1038/nature09152

X. Weng and X. J. , Spatial organization of transcription in bacterial cells, Trends in Genetics, vol.30, issue.7, pp.287-297
DOI : 10.1016/j.tig.2014.04.008

V. Norris, G. Turnock, and D. Sigee, The Escherichia coli enzoskeleton, Molecular Microbiology, vol.19, issue.2, pp.197-204, 1996.
DOI : 10.1046/j.1365-2958.1996.373899.x

C. Vélot and P. Srere, Reversible Transdominant Inhibition of a Metabolic Pathway. IN VIVO EVIDENCE OF INTERACTION BETWEEN TWO SEQUENTIAL TRICARBOXYLIC ACID CYCLE ENZYMES IN YEAST, Journal of Biological Chemistry, vol.275, issue.17, pp.27512926-27512959, 2000.
DOI : 10.1074/jbc.275.17.12926

P. Amar, G. Legent, M. Thellier, C. Ripoll, G. Bernot et al., A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency, BMC Systems Biology, vol.2, issue.1, p.27, 2008.
DOI : 10.1186/1752-0509-2-27
URL : https://hal.archives-ouvertes.fr/hal-00643746

B. Caré and H. Soula, Impact of receptor clustering on ligand binding, BMC Systems Biology, vol.5, issue.1, p.48, 2011.
DOI : 10.1137/080733280

B. Caré and H. Soula, Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime, Physical Review E, vol.87, issue.1, p.12720
DOI : 10.1103/PhysRevE.87.012720

H. Soula, B. Caré, G. Beslon, and H. Berry, Anomalous versus Slowed-Down Brownian Diffusion in the Ligand-Binding Equilibrium, Biophysical Journal, vol.105, issue.9, pp.2064-2073
DOI : 10.1016/j.bpj.2013.07.023
URL : https://hal.archives-ouvertes.fr/hal-00720515

E. Roberts, A. Magis, J. Ortiz, W. Baumeister, and Z. Luthey-schulten, Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study, PLoS Computational Biology, vol.51, issue.3, p.1002010, 2011.
DOI : 10.1371/journal.pcbi.1002010.s003

J. Karr, J. Sanghvi, D. Macklin, M. Gutschow, J. Jacobs et al., A Whole-Cell Computational Model Predicts Phenotype from Genotype, Cell, vol.150, issue.2, pp.389-401
DOI : 10.1016/j.cell.2012.05.044

I. Thiele, R. Fleming, R. Que, A. Bordbar, D. Diep et al., Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage, PLoS ONE, vol.7, issue.9, p.45635
DOI : 10.1371/journal.pone.0045635.s008

E. Roberts, J. Stone, and Z. Luthey-schulten, Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation, Journal of Computational Chemistry, vol.24, issue.3, pp.245-255
DOI : 10.1002/jcc.23130

Y. Taniguchi, P. Choi, G. Li, H. Chen, M. Babu et al., Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells, Science, issue.5991, pp.329533-538, 2010.

L. So, A. Ghosh, C. Zong, L. Sepulveda, R. Segev et al., General properties of transcriptional time series in Escherichia coli, Nature Genetics, vol.27, issue.6, pp.554-560, 2011.
DOI : 10.1021/j100540a008

Y. Ishihama, T. Schmidt, J. Rappsilber, M. Mann, F. Hartl et al., Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, vol.9, issue.1, p.102, 2008.
DOI : 10.1186/1471-2164-9-102

J. Andersen, C. Sternberg, L. Poulsen, S. Bjorn, M. Givskov et al., New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria, Appl Environ Microbiol, vol.64, issue.6, pp.2240-2246, 1998.

S. Oehler, E. Eismann, H. Kramer, and B. Muller-hill, The three operators of the lac operon cooperate in repression, EMBO J, vol.9, issue.4, pp.973-979, 1990.

M. Guille and G. Kneale, Methods for the analysis of DNA-protein interactions, Molecular Biotechnology, vol.258, issue.1, pp.35-52, 1997.
DOI : 10.1007/BF02762338

J. Majka and C. Speck, Analysis of Protein???DNA Interactions Using Surface Plasmon Resonance, Adv Biochem Eng Biotechnol, vol.104, pp.13-36, 2007.
DOI : 10.1007/10_026

B. Volkmer and M. Heinemann, Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling, PLoS ONE, vol.7, issue.7, p.23126, 2011.
DOI : 10.1371/journal.pone.0023126.t001

R. Lutz and H. Bujard, Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements, Nucleic Acids Research, vol.25, issue.6, pp.1203-1210, 1997.
DOI : 10.1093/nar/25.6.1203

J. Van-zon, M. Morelli, S. Tanase-nicola, and P. Ten-wolde, Diffusion of Transcription Factors Can Drastically Enhance the Noise in Gene Expression, Biophysical Journal, vol.91, issue.12, pp.914350-4367, 2006.
DOI : 10.1529/biophysj.106.086157

D. Cottrell, P. Swain, and P. Tupper, Stochastic branching-diffusion models for gene expression, Proceedings of the National Academy of Sciences, vol.109, issue.25, pp.9699-9704
DOI : 10.1073/pnas.1201103109

P. De-gennes, Kinetics of diffusion???controlled processes in dense polymer systems. I. Nonentangled regimes, The Journal of Chemical Physics, vol.76, issue.6, pp.3316-3321, 1982.
DOI : 10.1063/1.443328

O. Benichou, C. Chevalier, J. Klafter, B. Meyer, and R. Voituriez, Geometry-controlled kinetics, Nature Chemistry, vol.2, issue.6, pp.472-477, 2010.
DOI : 10.1134/S1063774508010136

K. Lipkow, S. Andrews, and D. Bray, Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of Escherichia coli, Journal of Bacteriology, vol.187, issue.1, pp.45-53, 2005.
DOI : 10.1128/JB.187.1.45-53.2005

K. Takahashi, S. Tanase-nicola, and P. Ten-wolde, Spatio-temporal correlations can drastically change the response of a MAPK pathway, Proceedings of the National Academy of Sciences, vol.107, issue.6, pp.2473-2478, 2010.
DOI : 10.1073/pnas.0906885107

O. Maler, A. Halasz, O. Lebeltel, and O. Maler, Exploring the Dynamics of Mass Action Systems, Proceedings Second International Workshop on Hybrid Systems and Biology Italy: Electronic Proceedings in Theoretical Computer Science, pp.84-91, 2013.
DOI : 10.4204/EPTCS.125.6

O. Pulkkinen and R. Metzler, Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation, Physical Review Letters, vol.110, issue.19, 198101.
DOI : 10.1103/PhysRevLett.110.198101

C. Maeder, M. Hink, A. Kinkhabwala, R. Mayr, P. Bastiaens et al., Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling, Nature Cell Biology, vol.51, issue.11, pp.1319-1326, 2007.
DOI : 10.1038/ncb1652

M. Elowitz, M. Surette, P. Wolf, J. Stock, and S. Leibler, Protein mobility in the cytoplasm of Escherichia coli, J Bacteriol, vol.181, issue.1, pp.197-203, 1999.

L. Shapiro, H. Mcadams, and R. Losick, Why and How Bacteria Localize Proteins, Science, vol.326, issue.5957, pp.1225-1228, 2009.
DOI : 10.1126/science.1175685

E. Mauriello, D. Astling, O. Sliusarenko, and D. Zusman, Localization of a bacterial cytoplasmic receptor is dynamic and changes with cell-cell contacts, Proceedings of the National Academy of Sciences, vol.106, issue.12, pp.4852-4857, 2009.
DOI : 10.1073/pnas.0810583106

O. Sliusarenko, J. Heinritz, T. Emonet, and C. Jacobs-wagner, High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics, Molecular Microbiology, vol.77, issue.3, pp.612-627, 2011.
DOI : 10.1111/j.1365-2958.2011.07579.x

D. Landgraf, B. Okumus, P. Chien, T. Baker, and J. Paulsson, Segregation of molecules at cell division reveals native protein localization, Nature Methods, vol.9, issue.5, pp.480-485, 2012.
DOI : 10.1038/nmeth1171

J. Elf, G. Li, and X. Xie, Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell, Science, vol.316, issue.5828, pp.3161191-1194, 2007.
DOI : 10.1126/science.1141967

T. Kuhlman and E. Cox, Gene location and DNA density determine transcription factor distributions in Escherichia coli, Molecular Systems Biology, vol.9, p.610, 2012.
DOI : 10.1073/pnas.0911237107

C. Loverdo, O. Benichou, M. Moreau, and R. Voituriez, Enhanced reaction kinetics in biological cells, Nature Physics, vol.19, issue.2, pp.134-137, 2008.
DOI : 10.1038/nature06201

O. Benichou, C. Chevalier, B. Meyer, and R. Voituriez, Facilitated Diffusion of Proteins on Chromatin, Physical Review Letters, vol.106, issue.3, p.38102, 2011.
DOI : 10.1103/PhysRevLett.106.038102

T. Kuhlman and E. Cox, DNA-binding-protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion, p.22701

M. Morelli, R. Allen, and W. Prt, Effects of Macromolecular Crowding on Genetic Networks, Biophysical Journal, vol.101, issue.12, pp.2882-2891, 2011.
DOI : 10.1016/j.bpj.2011.10.053