J. B. Bancroft and A. , The Self-Assembly Of Spherical Plant Viruses, Virus Res, vol.16, p.99, 1970.
DOI : 10.1016/S0065-3527(08)60022-6

A. Zlotnick, R. Aldrich, J. M. Johnson, P. Ceres, and M. J. Young, Mechanism of Capsid Assembly for an Icosahedral Plant Virus, Virology, vol.277, issue.2, p.450, 2000.
DOI : 10.1006/viro.2000.0619

R. F. Garmann, M. Comas-garcia, M. S. Koay, J. J. Cornelissen, C. M. Knobler et al., Role of Electrostatics in the Assembly Pathway of a Single-Stranded RNA Virus, Journal of Virology, vol.88, issue.18, p.10472, 2014.
DOI : 10.1128/JVI.01044-14

M. Comas-garcia, R. F. Garmann, S. W. Singaram, A. Ben-shaul, C. M. Knobler et al., Characterization of Viral Capsid Protein Self-Assembly around Short Single-Stranded RNA, The Journal of Physical Chemistry B, vol.118, issue.27, p.7510, 2014.
DOI : 10.1021/jp503050z

H. K. Lin, P. Van-der-schoot, and R. Zandi, Impact of charge variation on the encapsulation of nanoparticles by virus coat proteins, Physical Biology, vol.9, issue.6, p.66004, 2012.
DOI : 10.1088/1478-3975/9/6/066004

L. Zhang, L. H. Lua, A. P. Middelberg, Y. Suna, and N. K. Connors, Biomolecular engineering of virus-like particles aided by computational chemistry methods, Chem. Soc. Rev., vol.510, issue.23, p.8608, 2015.
DOI : 10.1038/nature13404

B. Bottcher, S. A. Wynne, and R. A. Crowther, Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy, Nature, vol.386, issue.6620, p.88, 1997.
DOI : 10.1038/386088a0

X. Yu, L. Jin, and Z. H. Zhou, 3.88????? structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy, Nature, vol.24, issue.7193, p.415, 2008.
DOI : 10.1099/0022-1317-81-4-1143

URL : https://hal.archives-ouvertes.fr/inria-00587377

Y. Liu, M. G. Hill, T. Klose, Z. Chen, K. Watters et al., Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma, Proceedings of the National Academy of Sciences, vol.73, issue.11, p.8997, 2016.
DOI : 10.1093/nar/gkn840

X. Zhang, E. Settembre, C. Xu, P. R. Dormitzer, R. Bellamy et al., Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction, Proceedings of the National Academy of Sciences, vol.25, issue.13, p.1867, 2008.
DOI : 10.1002/jcc.20084

URL : http://www.pnas.org/content/105/6/1867.full.pdf

R. I. Koning, J. Gomez-blanco, I. Akopjana, J. Vargas, A. Kazaks et al., Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ, Nature Communications, vol.527, p.12524, 2016.
DOI : 10.1038/nature15767

R. Kuhn, W. Zhang, M. G. Rossmann, S. V. Pletnev, J. Corver et al., Structure of Dengue Virus, Cell, vol.108, issue.5, p.717, 2002.
DOI : 10.1016/S0092-8674(02)00660-8

W. Zhang, S. Mukhopadhyay, S. V. Pletnev, T. S. Baker, R. J. Kuhn et al., Placement of the Structural Proteins in Sindbis Virus, Journal of Virology, vol.76, issue.22, p.11645, 2002.
DOI : 10.1128/JVI.76.22.11645-11658.2002

H. Tsuruta, V. S. Reddy, W. R. Wikoff, and J. E. Johnson, Imaging RNA and dynamic protein segments with low-resolution virus crystallography: experimental design, data processing and implications of electron density maps 1 1Edited by D. Rees, Journal of Molecular Biology, vol.284, issue.5, p.1439, 1998.
DOI : 10.1006/jmbi.1998.2231

K. Toropova, G. Basnak, R. Twarock, P. G. Stockley, and N. A. Ranson, The Three-dimensional Structure of Genomic RNA in Bacteriophage MS2: Implications for Assembly, Journal of Molecular Biology, vol.375, issue.3, p.824, 2008.
DOI : 10.1016/j.jmb.2007.08.067

J. M. Fox, G. Wang, J. A. Speir, N. H. Olson, J. E. Johnson et al., Comparison of the Native CCMV Virion within VitroAssembled CCMV Virions by Cryoelectron Microscopy and Image Reconstruction, Virology, vol.244, issue.1, p.212, 1998.
DOI : 10.1006/viro.1998.9107

Y. Hu, R. Zandi, A. Anavitarte, C. M. Knobler, and W. M. Gelbart, Packaging of a Polymer by a Viral Capsid: The Interplay between Polymer Length and Capsid Size, Biophysical Journal, vol.94, issue.4, p.1428, 2008.
DOI : 10.1529/biophysj.107.117473

Y. Zeng, S. B. Larson, C. E. Heitsch, A. Mcpherson, and S. C. Harvey, A model for the structure of satellite tobacco mosaic virus, Journal of Structural Biology, vol.180, issue.1, p.110, 2012.
DOI : 10.1016/j.jsb.2012.06.008

N. A. Ranson and P. G. Stockley, Emerging Topics in Physical Virology, p.1, 2010.

B. R. Linger, L. Kunovska, R. J. Kuhn, and B. L. Golden, Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization, RNA, vol.10, issue.1, p.128, 2004.
DOI : 10.1261/rna.5127104

B. D. Lindenbach, J. Sgro, and P. Ahlquist, Long-Distance Base Pairing in Flock House Virus RNA1 Regulates Subgenomic RNA3 Synthesis and RNA2 Replication, Journal of Virology, vol.76, issue.8, p.3905, 2002.
DOI : 10.1128/JVI.76.8.3905-3919.2002

A. Siber and R. Podgornik, Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses, Physical Review E, vol.63, issue.5, p.51915, 2008.
DOI : 10.1006/viro.2000.0619

A. Siber, R. Zandi, and R. Podgornik, Thermodynamics of nanospheres encapsulated in virus capsids, Physical Review E, vol.27, issue.5, p.51919, 2010.
DOI : 10.1103/PhysRevE.80.021910

P. Van-der-schoot and R. Zandi, Impact of the topology of viral RNAs on their encapsulation by virus coat proteins, Journal of Biological Physics, vol.393, issue.2, p.289, 2013.
DOI : 10.1016/j.jmb.2009.08.044

G. Erdemci-tandogan, J. Wagner, P. Van-der-schoot, R. Podgornik, and R. Zandi, RNA topology remolds electrostatic stabilization of viruses, Physical Review E, vol.155, issue.3, p.32707, 2014.
DOI : 10.1007/BF00818163

J. Wagner, G. Erdemci-tandogan, and R. Zandi, Adsorption of annealed branched polymers on curved surfaces, Journal of Physics: Condensed Matter, vol.27, issue.49, p.495101, 2015.
DOI : 10.1088/0953-8984/27/49/495101

S. W. Singaram, R. F. Garmann, C. M. Knobler, W. M. Gelbart, and A. Ben, Role of RNA Branchedness in the Competition for Viral Capsid Proteins, The Journal of Physical Chemistry B, vol.119, issue.44, p.13991, 2015.
DOI : 10.1021/acs.jpcb.5b06445

G. Erdemci-tandogan, J. Wagner, P. Van-der-schoot, R. Podgornik, and R. Zandi, Effects of RNA branching on the electrostatic stabilization of viruses, Physical Review E, vol.94, issue.2, p.22408, 2016.
DOI : 10.1093/nar/gkg595

V. Sivanandam, D. Mathews, R. Garmann, G. Erdemci-tandogan, R. Zandi et al., Functional analysis of the N-terminal basic motif of a eukaryotic satellite RNA virus capsid protein in replication and packaging, Scientific Reports, vol.23, issue.1, p.26328, 2016.
DOI : 10.1038/sj.emboj.7600096

R. F. Bruinsma, M. Comas-garcia, R. F. Garmann, and A. Y. Grosberg, Equilibrium self-assembly of small RNA viruses, Physical Review E, vol.93, issue.3, p.32405, 2016.
DOI : 10.1063/1.3212694

G. Erdemci-tandogan, J. Wagner, P. Van-der-schoot, and R. Zandi, Role of Genome in the Formation of Conical Retroviral Shells, The Journal of Physical Chemistry B, vol.120, issue.26, p.6298, 2016.
DOI : 10.1021/acs.jpcb.6b02712

C. Hyeon, R. I. Dima, and D. Thirumalai, Size, shape, and flexibility of RNA structures, The Journal of Chemical Physics, vol.125, issue.19, p.194905, 2006.
DOI : 10.1002/jcc.20084

S. I. Lee and T. T. Nguyen, Radial Distribution of RNA Genomes Packaged inside Spherical Viruses, Physical Review Letters, vol.100, issue.19, p.198102, 2008.
DOI : 10.1051/jphys:0198100420100135900

K. M. Elsawy, L. S. Caves, and R. Twarock, On the Origin of Order in the Genome Organization of ssRNA Viruses, Biophysical Journal, vol.101, issue.4, p.774, 2011.
DOI : 10.1016/j.bpj.2011.07.005

A. Montanari and M. Mezard, Hairpin Formation and Elongation of Biomolecules, Physical Review Letters, vol.103, issue.10, p.2178, 2001.
DOI : 10.1063/1.470461

A. Gopal, Z. H. Zhou, C. M. Knobler, and W. M. Gelbart, Visualizing large RNA molecules in solution, RNA, vol.18, issue.2, p.284, 2012.
DOI : 10.1261/rna.027557.111

R. Bundschuh and T. Hwa, Statistical mechanics of secondary structures formed by random RNA sequences, Physical Review E, vol.86, issue.3, p.31903, 2002.
DOI : 10.1103/PhysRevLett.86.830

H. Orland and A. Zee, RNA folding and large N matrix theory, Nuclear Physics B, vol.620, issue.3, p.456, 2002.
DOI : 10.1016/S0550-3213(01)00522-3

URL : http://arxiv.org/pdf/cond-mat/0106359v1.pdf

G. Vernizzi, H. Orland, and A. Zee, Enumeration of RNA Structures by Matrix Models, Physical Review Letters, vol.1, issue.16, p.168103, 2005.
DOI : 10.1103/PhysRevE.66.040801

URL : https://hal.archives-ouvertes.fr/hal-00020092

H. Ji and D. Hone, Polymer adsorption on rough surfaces. 2. Good solvent conditions, Macromolecules, vol.21, issue.8, p.2600, 1988.
DOI : 10.1021/ma00186a049

M. Sanati and A. Saxena, model, Journal of Physics A: Mathematical and General, vol.32, issue.23, p.4311, 1999.
DOI : 10.1088/0305-4470/32/23/309