E. H. Aarts and P. J. Van-laarhoven, Statistical Cooling : A General Approach to Combinatorial Optimization Problems, Philips Journal of Research, vol.40, pp.193-226, 1985.

K. Abul, A. H. Abbas, S. Lichtman, and . Pillai, Basic Immunology : Functions and Disorders of the Immune System, pp.83-89, 2014.

D. Alemani, F. Pappalardo, M. Pennisi, S. Motta, and V. Brusic, Combining cellular automata and lattice Boltzmann method to model multiscale avascular tumor growth coupled with nutrient diffusion and immune competition, Journal of Immunological Methods, vol.376, issue.1-2, pp.55-68, 2012.
DOI : 10.1016/j.jim.2011.11.009

G. Altan-bonnet and R. Germain, Modeling T Cell Antigen Discrimination Based on Feedback Control of Digital ERK Responses, PLoS Biology, vol.420, issue.11, pp.356-86, 2005.
DOI : 10.1371/journal.pbio.0030356.sd005

M. H. Andersen, D. Schrama, P. T. Straten, and J. C. Becker, Cytotoxic T Cells, Journal of Investigative Dermatology, vol.126, issue.1, pp.32-41, 2006.
DOI : 10.1038/sj.jid.5700001

B. R. Angermann, F. Klauschen, A. D. Garcia, T. Prustel, F. Zhang et al., Computational modeling of cellular signaling processes embedded into dynamic spatial contexts, Nature Methods, vol.7, issue.3, pp.283-289, 2012.
DOI : 10.1016/j.jcp.2007.05.025

R. Antia, C. T. Bergstrom, S. S. Pilyugin, S. M. Kaech, and R. Ahmed, Models of CD8+ Responses: 1. What is the Antigen-independent Proliferation Program, Journal of Theoretical Biology, vol.221, issue.4, pp.585-598, 2003.
DOI : 10.1006/jtbi.2003.3208

R. Antia, V. Vitaly, R. Ganusov, and . Ahmed, The role of models in understanding CD8+ T-cell memory, Nature Reviews Immunology, vol.4, issue.2, pp.101-111, 2005.
DOI : 10.1038/nri1355

V. Appay and S. , Lessons from the study of T-cell differentiation in persistent human virus infection, Seminars in Immunology, vol.16, issue.3, pp.205-212, 1920.
DOI : 10.1016/j.smim.2004.02.007

J. Arsenio, B. Kakaradov, P. J. Metz, S. H. Kim, G. W. Yeo et al., Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses, Nature Immunology, vol.9, issue.4, pp.365-372, 2014.
DOI : 10.1038/nprot.2009.9

M. Bajenoff, J. Egen, L. Y. Koo, J. P. Laugier, F. Brau et al., Stromal Cell Networks Regulate Lymphocyte Entry, Migration, and Territoriality in Lymph Nodes, Immunity, vol.25, issue.6, pp.989-1001, 2006.
DOI : 10.1016/j.immuni.2006.10.011
URL : https://hal.archives-ouvertes.fr/hal-00316442

V. Baldazzi, F. Castiglione, and M. Bernaschi, An enhanced agent based model of the immune system response, Cellular Immunology, vol.244, issue.2, pp.77-79, 2006.
DOI : 10.1016/j.cellimm.2006.12.006

V. Baldazzi, P. Paci, M. Bernaschi, and F. Castiglione, Modeling lymphocyte homing and encounters in lymph nodes, BMC Bioinformatics, vol.10, issue.1, p.57, 2009.
DOI : 10.1186/1471-2105-10-387
URL : https://hal.archives-ouvertes.fr/hal-00784447

A. L. Bauer, T. L. Jackson, and Y. Jiang, A Cell-Based Model Exhibiting Branching and Anastomosis during Tumor-Induced Angiogenesis, Biophysical Journal, vol.92, issue.9, pp.3105-3126, 2007.
DOI : 10.1529/biophysj.106.101501
URL : http://doi.org/10.1529/biophysj.106.101501

J. B. Beltman, A. F. Maree, and R. J. De-boer, Spatial modelling of brief and long interactions between T cells and dendritic cells, Immunology and Cell Biology, vol.166, issue.4, pp.306-320, 2007.
DOI : 10.1016/j.immuni.2004.08.006

S. Bernard, How to Build a Multiscale Model in Biology, Acta Biotheoretica, vol.58, issue.4, pp.291-303, 2013.
DOI : 10.1007/s00285-008-0211-1
URL : https://hal.archives-ouvertes.fr/hal-00867564

M. Bernaschi and F. Castiglione, Design and implementation of an immune system simulator, Computers in Biology and Medicine, vol.31, issue.5, pp.303-331, 2001.
DOI : 10.1016/S0010-4825(01)00011-7

]. M. Bernaschi, S. Succi, and F. Castiglione, Large-scale cellular automata simulations of the immune system response, Physical Review E, vol.164, issue.2, pp.611851-1854, 2000.
DOI : 10.1006/jtbi.1993.1139

C. Bidot, F. Gruy, C. Haudin, F. Hentati, B. Guy et al., Mathematical Modeling of T-Cell Activation Kinetic, Journal of Computational Biology, vol.15, issue.1, pp.105-128, 2008.
DOI : 10.1089/cmb.2007.0125
URL : https://hal.archives-ouvertes.fr/emse-00449722

G. Bogle and P. R. Dunbar, Agent-based simulation of T-cell activation and proliferation within a lymph node, Immunology and Cell Biology, vol.2, issue.2, pp.172-181, 2010.
DOI : 10.4049/jimmunol.181.6.3887

P. Bouillet, L. A. O-'reilly, and . Cd95, CD95, BIM and T cell homeostasis, Nature Reviews Immunology, vol.37, issue.7, pp.514-519, 2009.
DOI : 10.4049/jimmunol.173.5.2976

P. Bousso, T-cell activation by dendritic cells in the lymph node: lessons from the movies, Nature Reviews Immunology, vol.203, issue.9, pp.675-84, 2008.
DOI : 10.4049/jimmunol.178.12.7747

P. Bousso and E. Robey, Dynamics of CD8+ T cell priming by dendritic cells in intact lymph nodes, Nature Immunology, vol.4, issue.6, pp.579-85, 2003.
DOI : 10.1038/ni928

D. Brenner, P. H. Krammer, and R. Arnold, Concepts of activated T cell death, Critical Reviews in Oncology/Hematology, vol.66, issue.1, pp.52-64, 2008.
DOI : 10.1016/j.critrevonc.2008.01.002

V. R. Buchholz, M. Flossdorf, I. Hensel, L. Kretschmer, B. Weissbrich et al., Disparate Individual Fates Compose Robust CD8+ T Cell Immunity, Science, vol.318, issue.1, pp.630-635, 1921.
DOI : 10.1046/j.1365-8711.2000.03655.x

V. R. Buchholz, M. Flossdorf, I. Hensel, L. Kretschmer, B. Weissbrich et al., Disparate Individual Fates Compose Robust CD8+ T Cell Immunity, Science, vol.318, issue.1, pp.630-635, 2013.
DOI : 10.1046/j.1365-8711.2000.03655.x

A. Cappuccio, P. Tieri, and F. Castiglione, Multiscale modelling in immunology: a review, Briefings in Bioinformatics, vol.17, issue.3, p.86, 2015.
DOI : 10.1093/bib/bbv012

A. Cappuccio, P. Tieri, and F. Castiglione, Multiscale modelling in immunology: a review, Briefings in Bioinformatics, vol.17, issue.3, pp.408-418, 2016.
DOI : 10.1093/bib/bbv012

F. Castiglione, Agent based modeling, Scholarpedia, vol.1, issue.10, pp.1562-1605, 2006.
DOI : 10.4249/scholarpedia.1562

J. T. Chang, E. J. Wherry, and A. W. Goldrath, Molecular regulation of effector and memory T cell differentiation, Nature Immunology, vol.12, issue.12, pp.1104-1115, 2014.
DOI : 10.1038/nm1326
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386685

A. Chertock and A. Kurganov, On a practical implementation of particle methods, Applied Numerical Mathematics, vol.56, issue.10-11, pp.1418-1431, 0111.
DOI : 10.1016/j.apnum.2006.03.024

C. Chevalier and D. Ginsbourger, Fast Computation of the Multi-Points Expected Improvement with Applications in Batch Selection, Learning and Intelligent Optimization, pp.59-69, 2013.
DOI : 10.1007/978-3-642-44973-4_7
URL : https://hal.archives-ouvertes.fr/hal-00732512

A. Chhabra, Mitochondria-centric activation induced cell death of cytolytic T lymphocytes and its implications for cancer immunotherapy, Vaccine, vol.28, issue.29, pp.4566-4572, 2010.
DOI : 10.1016/j.vaccine.2010.04.074

A. Cohen and B. Perthame, Optimal Approximations of Transport Equations by Particle and Pseudoparticle Methods, SIAM Journal on Mathematical Analysis, vol.32, issue.3, pp.616-636, 0111.
DOI : 10.1137/S0036141099350353

I. Couckuyt, A. Forrester, D. Gorissen, F. De-turck, and T. Dhaene, Blind Kriging : Implementation and performance analysis Advances in Engineering Software, pp.1-13, 2012.
DOI : 10.1016/j.advengsoft.2012.03.002
URL : https://biblio.ugent.be/publication/2983177/file/2983185.pdf

I. Couckuyt, T. Dhaene, and P. Demeester, oodace toolbox : A flexible objectoriented kriging implementation, Journal of Machine Learning Research, vol.15, issue.159, pp.3183-3186, 2014.

F. Crauste, E. Terry, I. Le-mercier, J. Mafille, S. Djebali et al., Predicting pathogen-specific CD8 T cell immune responses from a modeling approach, Journal of Theoretical Biology, vol.374, issue.118, pp.66-82, 2015.
DOI : 10.1016/j.jtbi.2015.03.033
URL : https://hal.archives-ouvertes.fr/hal-01242319

F. Crauste, J. Mafille, L. Boucinha, S. Djebali, O. Gandrillon et al., Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny, Cell Systems, vol.4, issue.3, pp.93-154, 0193.
DOI : 10.1016/j.cels.2017.01.014
URL : https://hal.archives-ouvertes.fr/hal-01409637

A. C. Noel and . Cressie, Statistics for Spatial Data : Cressie/Statistics Wiley Series in Probability and Statistics, p.153, 1993.

F. Cruz-guilloty, M. E. Pipkin, I. M. Djuretic, D. Levanon, J. Lotem et al., Runx3 and T-box proteins cooperate to establish the transcriptional program of effector CTLs, The Journal of Experimental Medicine, vol.206, issue.1, pp.51-59, 2009.
DOI : 10.1093/nar/gkl006

W. Cui and S. M. Kaech, Generation of effector CD8+ T cells and their conversion to memory T cells, Immunological Reviews, vol.36, issue.1, pp.151-66, 2010.
DOI : 10.4049/jimmunol.172.11.6533

W. Cui, N. S. Joshi, A. Jiang, and S. M. Kaech, Effects of Signal 3 during CD8 T cell priming: Bystander production of IL-12 enhances effector T cell expansion but promotes terminal differentiation, Vaccine, vol.27, issue.15, pp.2177-2187, 2009.
DOI : 10.1016/j.vaccine.2009.01.088

G. Damblin, B. Couplet, and . Iooss, Numerical studies of space-filling designs: optimization of Latin Hypercube Samples and subprojection properties, Journal of Simulation, vol.82, issue.2, pp.276-289, 2013.
DOI : 10.1016/j.cpc.2012.07.002
URL : https://hal.archives-ouvertes.fr/hal-00848240

L. Courtney, F. R. Davis, and . Adler, Mathematical models of memory CD8+ T-cell repertoire dynamics in response to viral infections, Bulletin of Mathematical Biology, vol.75, issue.3, pp.491-522, 2013.

R. J. De-boer, M. Oprea, R. Antia, K. Murali-krishna, R. Ahmed et al., Recruitment Times, Proliferation, and Apoptosis Rates during the CD8+ T-Cell Response to Lymphocytic Choriomeningitis Virus, Journal of Virology, vol.75, issue.22, pp.10663-10669, 2001.
DOI : 10.1128/JVI.75.22.10663-10669.2001

D. Dupuy, C. Helbert, and J. Franco, DiceDesign and DiceEval : Two R Packages for Design and Analysis of Computer Experiments, Journal of Statistical Software, issue.11, pp.65-2015

K. E. Ewings, C. M. Wiggins, and S. J. Cook, Bim and the Pro-Survival Bcl-2 Proteins: Opposites Attract, ERK Repels, Cell Cycle, vol.6, issue.18, pp.2236-2240, 2007.
DOI : 10.4161/cc.6.18.4728

K. Fang, C. Ma, and P. Winker, Centered $L_2$-discrepancy of random sampling and Latin hypercube design, and construction of uniform designs, Mathematics of Computation, vol.71, issue.237, pp.275-297, 2000.
DOI : 10.1090/S0025-5718-00-01281-3

O. Feinerman, G. Jentsch, E. Karen, J. W. Tkach, . Coward et al., Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response, Molecular Systems Biology, vol.175, issue.78, pp.57-60, 2010.
DOI : 10.1038/ng1958

A. Friedman, C. Kao, and C. Shih, Asymptotic phases in a cell differentiation model, Journal of Differential Equations, vol.247, issue.3, pp.736-769, 2009.
DOI : 10.1016/j.jde.2009.03.033

A. Friedman, C. Kao, and C. Shih, Asymptotic limit in a cell differentiation model with consideration of transcription, Journal of Differential Equations, vol.252, issue.10, pp.5679-5711, 2012.
DOI : 10.1016/j.jde.2012.02.006

V. Ganusov, T Cell Differentiation, The Journal of Immunology, vol.179, issue.8, pp.5006-5013, 2007.
DOI : 10.4049/jimmunol.179.8.5006

X. Gao, C. Arpin, J. Marvel, S. Prokopiou, O. Gandrillon et al., IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study, BMC Systems Biology, vol.3, issue.26, pp.77-88, 2016.
DOI : 10.1038/ncomms2260
URL : https://hal.archives-ouvertes.fr/inserm-01354185

C. Gerlach, J. C. Rohr, L. Perie, N. Van-rooij, J. W. Van-heijst et al., Heterogeneous Differentiation Patterns of Individual CD8+ T Cells, Science, vol.167, issue.12, pp.635-639, 2013.
DOI : 10.4049/jimmunol.167.12.6983

D. Ginsbourger, Multiples métamodèles pour l'approximation et l'optimisation de fonctions numériques multivariables, p.169, 2009.

D. Ginsbourger, R. L. Riche, and L. Carraro, Kriging Is Well-Suited to Parallelize Optimization, Lim Meng Hiot
DOI : 10.1007/978-3-642-10701-6_6
URL : https://hal.archives-ouvertes.fr/emse-00436126

J. Glazier and F. Graner, Simulation of the differential adhesion driven rearrangement of biological cells, Physical Review E, vol.237, issue.3, pp.2128-2154, 1993.
DOI : 10.1126/science.3037697

C. Gong, J. T. Mattila, M. Miller, J. L. Flynn, J. J. Linderman et al., Predicting lymph node output efficiency using systems biology, Journal of Theoretical Biology, vol.335, pp.169-84, 2013.
DOI : 10.1016/j.jtbi.2013.06.016
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783027

A. D. Guerrero, R. L. Welschhans, M. Chen, and J. Wang, Cleavage of Anti-Apoptotic Bcl-2 Family Members after TCR Stimulation Contributes to the Decision between T Cell Activation and Apoptosis, The Journal of Immunology, vol.190, issue.1, pp.168-173, 2013.
DOI : 10.4049/jimmunol.1201610

N. D. Hayes, Roots of the Transcendental Equation Associated with a Certain Difference-Differential Equation, Journal of the London Mathematical Society, vol.1, issue.3, pp.1-25226, 1950.
DOI : 10.1112/jlms/s1-25.3.226

F. J. Hickernell, A generalized discrepancy and quadrature error bound Mathematics of Computation of the, pp.299-322, 1998.

A. David, Y. Hildeman, T. C. Zhu, J. Mitchell, P. Kappler et al., Molecular mechanisms of activated T cell death in vivo, Current Opinion in Immunology, vol.14, issue.24, pp.354-359, 2002.

T. Höfer, O. Krichevsky, and G. , Competition for IL-2 between Regulatory and Effector T Cells to Chisel Immune Responses, Frontiers in Immunology, vol.3, issue.78, pp.68-72, 2012.

K. K. Hoyer, H. Dooms, L. Barron, and A. K. Abbas, Interleukin-2 in the development and control of inflammatory disease, Immunological Reviews, vol.226, issue.1, pp.19-28, 2008.
DOI : 10.1111/j.1600-065X.2008.00697.x

D. Huh and J. Paulsson, Non-genetic heterogeneity from stochastic partitioning at cell division, Nature Genetics, vol.448, issue.2, pp.95-100, 2011.
DOI : 10.1073/PNAS.110057697
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208402

M. Clifford, C. Hurvich, and . Tsai, Regression and time series model selection in small samples, Biometrika, vol.76, issue.2, pp.297-337, 1989.

E. S. Hwang, J. H. Hong, and L. H. Glimcher, IL-2 production in developing Th1 cells is regulated by heterodimerization of RelA and T-bet and requires T-bet serine residue 508, The Journal of Experimental Medicine, vol.77, issue.9, pp.1289-1300, 2005.
DOI : 10.1126/science.275.5308.1930

A. Intlekofer, E. Wherry, and S. Reiner, Not-so-great expectations: re-assessing the essence of T-cell memory, Immunological Reviews, vol.173, issue.1, pp.203-213, 2006.
DOI : 10.1073/pnas.0501585102

R. Jin, W. Chen, and A. Sudjianto, An efficient algorithm for constructing optimal design of computer experiments, Journal of Statistical Planning and Inference, vol.134, issue.1, pp.268-287, 2005.
DOI : 10.1016/j.jspi.2004.02.014

D. R. Jones, M. Schonlau, and W. J. Welch, Efficient global optimization of expensive black-box functions, Journal of Global Optimization, vol.13, issue.4, pp.455-492, 1998.
DOI : 10.1023/A:1008306431147

S. Kaech and W. Cui, Transcriptional control of effector and memory CD8+ T cell differentiation, Nature Reviews Immunology, vol.16, issue.11, pp.749-761, 2012.
DOI : 10.1038/nm.2232
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137483

M. Susan, R. Kaech, and . Ahmed, Memory CD8+ T cell differentiation : Initial antigen encounter triggers a developmental program in naive cells, pp.415-422, 1920.

A. Kanhere, A. Hertweck, U. Bhatia, M. R. Gökmen, E. Perucha et al., T-bet and GATA3 orchestrate Th1 and Th2 differentiation through BIBLIOGRAPHIE lineage-specific targeting of distal regulatory elements, Nat Comm, vol.3, pp.2012-61, 1268.
DOI : 10.1038/ncomms2260
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535338

J. Kelly, R. Spolski, K. Imada, J. Bollenbacher, S. Lee et al., A Role for Stat5 in CD8+ T Cell Homeostasis, The Journal of Immunology, vol.170, issue.1, pp.210-217, 2003.
DOI : 10.4049/jimmunol.170.1.210

S. Peter, D. Kim, P. P. Levy, and . Lee, Modeling and Simulation of the Immune System as a Self-Regulating Network, In Methods in Enzymology, vol.467, pp.79-109, 2009.

T. K. Kim, L. S. St, E. D. John, J. Wieder, Q. Khalili et al., Human Late Memory CD8+ T Cells Have a Distinct Cytokine Signature Characterized by CC Chemokine Production without IL-2 Production, The Journal of Immunology, vol.183, issue.10, pp.6167-6174, 2009.
DOI : 10.4049/jimmunol.0902068

D. Kirschner and J. Linderman, Mathematical and computational approaches can complement experimental studies of host-pathogen interactions, Cellular Microbiology, vol.124, issue.4, pp.531-539, 2009.
DOI : 10.4049/jimmunol.166.3.1951

D. E. Kirschner, S. T. Chang, T. W. Riggs, N. Perry, and J. J. Linderman, Toward a multiscale model of antigen presentation in immunity, Immunological Reviews, vol.22, issue.1, pp.93-118, 2007.
DOI : 10.1093/bioinformatics/btl479

Y. Kuang, Delay Differential Equations with Applications in Population Dynamics, p.143, 1993.

A. Lanzavecchia and F. Sallusto, Lead and follow: the dance of the dendritic cell and T cell, Nature Immunology, vol.156, issue.12, pp.1201-1203, 2004.
DOI : 10.1038/79758

E. Larsson, C. Sander, and D. Marks, mrna turnover rate limits sirna and microrna efficacy, Mol Syst Biol, vol.6, p.67, 2010.
DOI : 10.1038/msb.2010.89
URL : http://doi.org/10.1038/msb.2010.89

L. L. Lau, B. D. Jamieson, T. Somasundaram, and R. Ahmed, Cytotoxic T-cell memory without antigen, Nature, vol.369, issue.6482, pp.648-652, 1994.
DOI : 10.1038/369648a0

Q. Li, P. J. Skinner, S. J. Ha, L. Duan, T. L. Mattila et al., Visualizing Antigen-Specific and Infected Cells in Situ Predicts Outcomes in Early Viral Infection, Science, vol.104, issue.39, pp.1726-1735, 2009.
DOI : 10.1073/pnas.0702579104
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753492

W. Liao, J. X. Lin, and W. J. Leonard, Interleukin-2 at the Crossroads of Effector Responses, Tolerance, and Immunotherapy, Immunity, vol.38, issue.1, pp.13-25, 2013.
DOI : 10.1016/j.immuni.2013.01.004

J. J. Linderman, T. Riggs, M. Pande, M. Miller, S. Marino et al., Characterizing the Dynamics of CD4+ T Cell Priming within a Lymph Node, The Journal of Immunology, vol.184, issue.6, pp.65-78, 2010.
DOI : 10.4049/jimmunol.0903117

R. L. Lindquist, G. Shakhar, D. Dudziak, H. Wardemann, T. Eisenreich et al., Visualizing dendritic cell networks in vivo, Nature Immunology, vol.7, issue.12, pp.1243-50, 2004.
DOI : 10.1186/1472-6750-2-11

T. Lorenzi, R. H. Chisholm, and J. Clairambault, Tracking the evolution of cancer cell populations through the mathematical lens of phenotypestructured equations, Biology Direct, vol.11, issue.1, p.44, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01355314

A. Gislâine, L. Martins, J. Cimmino, E. Liao, K. Magnusdottir et al., Blimp-1 directly represses Il2 and the Il2 activator Fos , attenuating T cell proliferation and survival, The Journal of Experimental Medicine, vol.205, issue.127, pp.1959-1965, 2008.

D. Masopust, V. Vezys, A. L. Marzo, and L. Lefrançois, Preferential Localization of Effector Memory Cells in Nonlymphoid Tissue, Science, vol.291, issue.5512, pp.2413-2417, 2001.
DOI : 10.1126/science.1058867

G. Matheron, Random Functions and their Application in Geology
DOI : 10.1007/978-1-4615-7103-2_7

M. P. Matheu, J. R. Teijaro, K. B. Walsh, M. L. Greenberg, D. Marsolais et al., Three Phases of CD8 T Cell Response in the Lung Following H1N1 Influenza Infection and Sphingosine 1 Phosphate Agonist Therapy, PLoS ONE, vol.107, issue.3
DOI : 10.1371/journal.pone.0058033.s017

M. D. Mckay, W. J. Conover, and R. J. Beckman, A comparison of three methods for selection values of input variables in the analysis of output from a computer code, Technometrics, vol.15, pp.239-245, 1979.

L. M. Mclane, P. P. Banerjee, G. L. Cosma, G. Makedonas, E. J. Wherry et al., Differential Localization of T-bet and Eomes in CD8 T Cell Memory Populations, The Journal of Immunology, vol.190, issue.7, pp.3207-3222, 2013.
DOI : 10.4049/jimmunol.1201556

T. R. Mempel, S. E. Henrickson, and U. H. Von-andrian, T-cell priming by dendriticcells in lymph nodes occurs in three distinct phases, Nature, vol.427, issue.6970, pp.154-159, 2004.
DOI : 10.1038/nature02238

M. J. Miller, A. S. Hejazi, S. H. Wei, M. D. Cahalan, and I. Parker, T cell repertoire scanning is promoted by dynamic dendritic cell behavior and random T cell motility in the lymph node, Proceedings of the National Academy of Sciences, vol.2, issue.10, pp.998-1003, 2004.
DOI : 10.1038/ni713

P. Henry, M. J. Mirsky, J. J. Miller, D. E. Linderman, and . Kirschner, Systems biology approaches for understanding cellular mechanisms of immunity in lymph nodes during infection, Journal of Theoretical Biology, vol.287, pp.160-170, 2011.

J. Mockus, V. Tiesis, and A. Zilinskas, The application of Bayesian methods for seeking the extremum, p.170, 1978.

S. Motta, F. Castiglione, P. Lollini, and F. Pappalardo, Modelling vaccination schedules for a cancer immunoprevention vaccine, Immunome Research, vol.1, issue.1, p.5, 2005.
DOI : 10.1186/1745-7580-1-5

S. N. Mueller and R. N. Germain, Stromal cell contributions to the homeostasis and functionality of the immune system, Nature Reviews Immunology, vol.171, pp.618-647, 2009.
DOI : 10.4049/jimmunol.171.8.4359

K. Murali-krishna, D. John, . Altman, D. J. Suresh, . Sourdive et al., Counting Antigen-Specific CD8 T BIBLIOGRAPHIE Cells : A Reevaluation of Bystander Activation during Viral Infection, Immunity, p.8

L. N. Murillo, M. S. Murillo, and A. S. Perelson, Towards multiscale modeling of influenza infection, Journal of Theoretical Biology, vol.332, pp.267-290, 2013.
DOI : 10.1016/j.jtbi.2013.03.024
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758892

S. Palsson, P. Timothy, . Hickling, L. Erica, M. Bradshaw-pierce et al., The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models, BMC Systems Biology, vol.7, issue.1, pp.95-138, 2013.
DOI : 10.1371/journal.pcbi.1000403

V. Picheny and D. Ginsbourger, Noisy kriging-based optimization methods: A unified implementation within the DiceOptim package, Computational Statistics & Data Analysis, vol.71, pp.1035-1053, 2014.
DOI : 10.1016/j.csda.2013.03.018

S. Prokopiou, L. Barbarroux, S. Bernard, J. Mafille, Y. Leverrier et al., Multiscale Modeling of the Early CD8 T-Cell Immune Response in Lymph Nodes: An Integrative Study, Computation, vol.145, issue.4, pp.159-181, 2014.
DOI : 10.1084/jem.185.8.1487
URL : https://hal.archives-ouvertes.fr/hal-01074736

L. Pronzato and W. G. Müller, Design of computer experiments: space filling and beyond, Statistics and Computing, vol.44, issue.1, pp.681-701, 0161.
DOI : 10.1007/BF00048668
URL : https://hal.archives-ouvertes.fr/hal-00685876

N. Rapin, O. Lund, M. Bernaschi, and F. Castiglione, Computational immunology BIBLIOGRAPHIE meets bioinformatics : The use of prediction tools for molecular binding in the simulation of the immune system, PLoS ONE, vol.5, issue.4, p.77, 2010.

N. Rapin, O. Lund, and F. Castiglione, Immune system simulation online, Bioinformatics, vol.27, issue.14, pp.2013-2014, 2011.
DOI : 10.1093/bioinformatics/btr335

P. A. Raviart, An analysis of particle methods, Numerical Methods in Fluid Dynamics, pp.243-324, 1985.
DOI : 10.1007/BFb0074532

T. Riggs, A. Walts, N. Perry, L. Bickle, J. N. Lynch et al., A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning, Journal of Theoretical Biology, vol.250, issue.4, pp.732-751, 2008.
DOI : 10.1016/j.jtbi.2007.10.015

I. Rouzine, R. Murali-krishna, and . Ahmed, Generals die in friendly fire, or modeling immune response to HIV, Journal of Computational and Applied Mathematics, vol.184, issue.1, pp.258-274, 2005.
DOI : 10.1016/j.cam.2004.08.018
URL : http://doi.org/10.1016/j.cam.2004.08.018

C. S. Roxburgh and D. C. Mcmillan, The role of the in situ local inflammatory response in predicting recurrence and survival in patients with primary operable colorectal cancer, Cancer Treatment Reviews, vol.38, issue.5, pp.451-466, 2012.
DOI : 10.1016/j.ctrv.2011.09.001

Y. G. Saab and V. B. Rao, Combinatorial optimization by stochastic evolution, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol.10, issue.4, pp.525-535, 1991.
DOI : 10.1109/43.75636

F. Sallusto, D. Lenig, R. Forster, M. Lipp, and A. Lanzavecchia, Two subsets of memory T lymphocytes with distinct homing potentials and effector functions, Nature, vol.9, issue.6754, pp.708-712, 1999.
DOI : 10.1016/S1074-7613(00)80597-X

D. Sayar, M. Ketzinel, L. Gerez, C. Silberberg, A. Reshef et al., Expression of the human IL-2 receptor on lymphocytes involves rapid turnover of its p55 alphasubunit, J Immunol, vol.145, pp.2946-2949, 1990.

H. J. Shin, J. B. Lee, S. H. Park, J. Chang, and L. C. , T-bet expression is regulated by EGR1-mediated signaling in activated T cells, Clinical Immunology, vol.131, issue.3, pp.385-94, 2009.
DOI : 10.1016/j.clim.2009.02.009

K. A. Smith, The structure of IL2 bound to the three chains of the IL2 receptor and how signaling occurs, Med Immunol, vol.5, issue.68, p.78, 2006.

G. C. Starling, J. Bajorath, J. Emswiler, J. A. Ledbetter, A. Aruffo et al., Identification of Amino Acid Residues Important for Ligand Binding to Fas, The Journal of Experimental Medicine, vol.267, issue.8, pp.1487-92, 1997.
DOI : 10.1002/eji.1830240943

A. Stéphanou and V. Volpert, Hybrid Modelling in Biology: a Classification Review, Mathematical Modelling of Natural Phenomena, vol.11, issue.1, pp.37-48, 2016.
DOI : 10.1051/mmnp/201611103

M. V. Stipdonk, E. Lemmens, and S. Schoenberger, Naive CTLs require a single brief period of antigenic stimulation for clonal expansion and differentiation, Nat. Immunol, vol.2, pp.423-429, 2001.

M. Brandon, A. Sullivan, S. J. Juedes, M. V. Szabo, L. H. Herrath et al., Antigen-driven effector CD8 T cell function regulated by T-bet, Proceedings of the National Academy of Sciences of the United States of America, pp.15818-15823, 2003.

S. J. Szabo, S. T. Kim, G. L. Costa, X. Zhang, C. G. Fathman et al., A Novel Transcription Factor, T-bet, Directs Th1 Lineage Commitment, Cell, vol.100, issue.6, pp.655-669, 2000.
DOI : 10.1016/S0092-8674(00)80702-3
URL : http://doi.org/10.1016/s0092-8674(00)80702-3

E. Terry, J. Marvel, C. Arpin, O. Gandrillon, and F. Crauste, Mathematical model of the primary CD8 T cell immune response: stability analysis of a nonlinear age-structured system, Journal of Mathematical Biology, vol.12, issue.22, pp.263-291, 2012.
DOI : 10.1093/intimm/12.4.467
URL : https://hal.archives-ouvertes.fr/hal-00649219

J. Thakar, M. Poss, R. Albert, G. H. Long, and R. Zhang, Dynamic models of immune responses : What is the ideal level of detail ? Theoretical Biology and Medical Modelling, pp.35-42, 2010.

J. Miller and T. , Sturm's Theorem for Multiple Roots, National Mathematics Magazine, vol.15, issue.8, p.391, 0102.

Q. Wang, J. David, Z. Klinke, and . Wang, CD8 + T cell response to adenovirus vaccination and subsequent suppression of tumor growth: modeling, simulation and analysis, BMC Systems Biology, vol.515, issue.81, p.86, 2015.
DOI : 10.1038/nature13954

B. Webster, E. H. Ekland, L. M. Agle, S. Chyou, R. Ruggieri et al., Regulation of lymph node vascular growth by dendritic cells, The Journal of Experimental Medicine, vol.136, issue.8, pp.1903-1916, 2006.
DOI : 10.4049/jimmunol.172.8.5034

M. A. Williams and M. J. Bevan, Effector and Memory CTL Differentiation, Annual Review of Immunology, vol.25, issue.1, pp.171-92, 2007.
DOI : 10.1146/annurev.immunol.25.022106.141548

A. L. Woelke, J. Von-eichborn, M. S. Murgueitio, C. L. Worth, F. Castiglione et al., Development of Immune-Specific Interaction Potentials and Their Application in the Multi-Agent-System VaccImm, PLoS ONE, vol.3, issue.8, pp.23257-86, 2011.
DOI : 10.1371/journal.pone.0023257.s003

J. Wu and E. S. Tzanakakis, Contribution of Stochastic Partitioning at Human Embryonic Stem Cell Division to NANOG Heterogeneity, PLoS ONE, vol.26, issue.11
DOI : 10.1371/journal.pone.0050715.s010

A. Yates, R. Callard, and J. Stark, Combining cytokine signalling with T-bet and GATA-3 regulation in Th1 and Th2 differentiation: a model for cellular decision-making, Journal of Theoretical Biology, vol.231, issue.2, pp.181-96, 2004.
DOI : 10.1016/j.jtbi.2004.06.013

J. J. Crystal, D. T. Yeo, and . Fearon, T-bet-mediated differentiation of the activated CD8+ T cell, European Journal of Immunology, vol.41, issue.60, pp.60-66, 1924.