W. Poon, Colloids as Big Atoms, Science, vol.304, pp.830-831, 2004.

Z. Wang, F. Wang, Y. Peng, Z. Zheng, and Y. Han, Imaging the homogeneous nucleation during the melting of superheated colloidal crystals, Science, vol.338, pp.87-90, 2012.

J. Russo and H. Tanaka, The microscopic pathway to crystallization in supercooled liquids, Sci. Rep, vol.2, p.505, 2012.

P. N. Pusey and W. Van-megen, Observation of a Glass Transition in Suspensions of Spherical Colloidal Particles, Phys. Rev. Lett, vol.59, pp.2083-2086, 1987.

P. N. Pusey and W. Van-megen, Phase behaviour of concentrated suspensions of nearly hard colloidal spheres, Nature, vol.320, pp.340-342, 1986.

P. N. Pusey, W. Van-megen, P. Bartlett, B. J. Ackerson, J. G. Rarity et al., Structure of crystals of hard colloidal spheres, Phys. Rev. Lett, vol.63, pp.2753-2756, 1989.

E. Grelet, Hexagonal order in crystalline and columnar phases of hard rods, Phys. Rev. Lett, vol.100, p.168301, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00276351

Z. Dogic and S. Fraden, Smectic Phase in a Colloidal Suspension of Semi exible Virus Particles, Phys. Rev. Lett, vol.78, pp.2417-2420, 1997.

J. Tang and S. Fraden, Isotropic-cholesteric phase transition in colloidal suspensions of filamentous bacteriophaeg fd, Liq. Cryst, vol.19, pp.459-467, 1995.

O. D. Velev and S. Gupta, Materials fabricated by micro-and nanoparticle assembly -The challenging path from science to engineering, Adv. Mater, vol.21, pp.1897-1905, 2009.

G. A. Ozin, Nanofabrication by self-assembly, Mater. Today, vol.12, pp.12-23, 2009.

V. N. Manoharan, Colloidal matter: Packing, geometry, and entropy, Science, vol.349, p.1253751, 2015.

G. M. Whitesides, Self-Assembly at All Scales, Science, vol.295, pp.2418-2421, 2002.

M. R. Jones and C. A. Mirkin, Materials science: Self-assembly gets new direction, Nature, vol.491, pp.42-43, 2012.

J. Zhang, Z. Sun, and B. Yang, Self-assembly of photonic crystals from polymer colloids, Curr. Opin. Colloid Interface Sci, vol.14, pp.103-114, 2009.

J. F. Galisteo-lópez, M. Ibisate, R. Sapienza, L. S. Froufe-pérez, Ú. Blanco et al., Self-Chapter 0: General introduction assembled photonic structures, Adv. Mater, vol.23, pp.30-69, 2011.

D. Morphew, J. Shaw, C. Avins, and D. Chakrabarti, Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules, ACS Nano, vol.12, pp.2355-2364, 2018.

G. R. Yi, D. J. Pine, and S. Sacanna, Recent progress on patchy colloids and their self-assembly, J. Phys. Condens. Matter, vol.25, 2013.

S. Sacanna and D. J. Pine, Shape-anisotropic colloids: Building blocks for complex assemblies, Curr. Opin. Colloid Interface Sci, vol.16, pp.96-105, 2011.

G. Van-anders, N. K. Ahmed, R. Smith, M. Engel, and S. C. Glotzer, Entropically patchy particles: Engineering valence through shape entropy, ACS Nano, vol.8, pp.931-940, 2014.

K. T. Nam, Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes, Science, vol.312, pp.885-888, 2006.

X. Dang, Virus-templated self-assembled single-walled carbon nanotubes for highly efficient electron collection in photovoltaic devices, Nat. Nanotechnol, vol.6, pp.377-84, 2011.

T. Mirkovic, N. S. Zacharia, G. D. Scholes, and G. A. Ozin, Nanolocomotion -Catalytic nanomotors and nanorotors, Small, vol.6, pp.159-167, 2010.

A. Van-blaaderen, Colloidal Molecules and Beyond. Science, vol.301, pp.470-471, 2003.

E. Duguet, A. Désert, A. Perro, and S. Ravaine, Design and elaboration of colloidal molecules: an overview, Chem. Soc. Rev, vol.40, p.941, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00560351

F. Li, W. C. Yoo, M. B. Beernink, and A. Stein, Site-specific functionalization of anisotropic nanoparticles: From colloidal atoms to colloidal molecules, J. Am. Chem. Soc, vol.131, pp.18548-18555, 2009.

M. Grzelczak, J. Vermant, E. M. Furst, L. M. Liz-marz-n, and .. Iz-marzá, Directed Self-Assembly of Nanoparticles, ACS Nano, vol.4, pp.3591-3605, 2010.

U. Jeong, Y. Wang, M. Ibisate, and Y. Xia, Some new developments in the synthesis, functionalization, and utilization of monodisperse colloidal spheres, Adv. Funct. Mater, vol.15, pp.1907-1921, 2005.

D. J. Norris, E. G. Arlinghaus, L. Meng, R. Heiny, and L. E. Scriven, Opaline photonic crystals: How does self-assembly work?, Adv. Mater, vol.16, pp.1393-1399, 2004.

E. W. Seelig, B. Tang, A. Yamilov, H. Cao, and R. P. Chang, Self-assembled 3D photonic crystals from ZnO colloidal spheres, Mater. Chem. Phys, vol.80, pp.257-263, 2003.

E. Yablonovitch, Inhibited spontaneous emission in solid-state physics and electronics, Phys. Rev. Lett, vol.58, pp.2059-2062, 1987.

. Guez, Photonic crystal properties of packed submicrometric SiO2 spheres, Appl. Phys. Lett, vol.71, pp.1148-1150, 1997.

A. P. Hynninen, C. G. Christova, R. Van-roij, A. Van-blaaderen, and M. Dijkstra, Prediction and observation of crystal structures of oppositely charged colloids, Phys. Rev. Lett, vol.96, p.138308, 2006.

F. Li, D. P. Josephson, and A. Stein, Colloidal assembly: The road from particles to colloidal molecules and crystals, Angew. Chem. Int. Ed, vol.50, pp.360-388, 2011.

S. C. Glotzer and M. J. Solomon, Anisotropy of building blocks and their assembly into complex 0.7 References structures, Nat. Mater, vol.6, pp.557-562, 2007.

J. A. Millan, D. Ortiz, G. Van-anders, and S. C. Glotzer, Self-assembly of archimedean tilings with enthalpically and entropically patchy polygons, ACS Nano, vol.8, pp.2918-2928, 2014.

A. , Pawar and I. Kretzschmar. Fabrication, assembly, and application of patchy particles, Macromol. Rapid Commun, vol.31, pp.150-168, 2010.

S. Sacanna, W. T. Irvine, P. M. Chaikin, and D. J. Pine, Lock and key colloids, Nature, vol.464, pp.575-578, 2010.

Y. Wang, Three-dimensional lock and key colloids, J. Am. Chem. Soc, vol.136, pp.6866-6869, 2014.

A. Kuijk, D. Byelov, A. Petukhov, A. Van-blaaderen, and A. Imhof, Phase behavior of colloidal silica rods, Faraday Discuss, vol.159, pp.181-199, 2012.

M. A. Bates, D. Frenkel, M. A. Bates, and D. Frenkel, Phase behavior of two-dimensional hard rod fluids Phase behavior of two-dimensional hard rod fluids, J. Chem. Phys, vol.112, pp.10033-10041, 2000.

J. Viamontes, P. W. Oakes, and J. X. Tang, Isotropic to nematic liquid cystalline phase transition of F-actin varies from continuous to first oder, Phys. Rev. Lett, vol.97, p.118103, 2006.

M. P. Lettinga, E. Barry, and Z. Dogic, Self-diffusion of rod-like viruses in the nematic phase, Europhys. Lett, vol.71, pp.692-698, 2005.

K. R. Purdy and S. Fraden, Isotropic-cholesteric phase transition of filamentous virus suspensions as a function of rod length and charge, Phys. Rev. E, vol.70, p.61703, 2004.

Z. Dogic and S. Fraden, Ordered phases of filamentous viruses, Curr. Opin. Colloid Interface Sci, vol.11, pp.47-55, 2006.

E. Grelet, Hard-rod behavior in dense mesophases of semiflexible and rigid charged viruses, Phys. Rev. X, vol.4, p.21053, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01011713

E. Barry, D. Beller, and Z. Dogic, A model liquid crystalline system based on rodlike viruses with variable chirality and persistence length, Soft Matter, vol.5, pp.2563-2570, 2009.

J. H. Lee, Phage-Based Structural Color Sensors and Their Pattern Recognition Sensing System, ACS Nano, vol.11, pp.3632-3641, 2017.

Y. S. Nam, Virus-templated assembly of porphyrins into light-harvesting nanoantennae, J. Am. Chem. Soc, vol.132, pp.1462-1463, 2010.

L. Rossi, S. Sacanna, W. T. Irvine, P. M. Chaikin, D. J. Pine et al., Cubic crystals from cubic colloids, Soft Matter, vol.7, pp.4139-4142, 2011.

S. Adireddy, C. Lin, B. Cao, W. Zhou, and G. Caruntu, Solution-based growth of monodisperse cube-like BaTiO3 colloidal nanocrystals, Chem. Mater, vol.22, pp.1946-1948, 2010.

T. Sugimoto, M. M. Khan, A. Muramatsu, and H. Itoh, Formation mechanism of monodisperse peanut-type ?-Fe2O3 particles from condensed ferric hydroxide gel, Colloids Surf. A, vol.70, pp.167-169, 1993.

Y. Yin, C. Erdonmez, S. Aloni, and A. P. Alivisatos, Faceting of nanocrystals during chemical transformation: From solid silver spheres to hollow gold octahedra, J. Am. Chem. Soc, vol.128, pp.12671-12673, 2006.

Q. Chen, J. Yan, J. Zhang, S. C. Bae, and S. Granick, Janus and Multiblock Colloidal Particles, General introduction Langmuir, vol.28, pp.13555-13561, 2012.

H. Takei and N. Shimizu, Gradient Sensitive Microscopic Probes Prepared by Gold Evaporation and Chemisorption on Latex Spheres, Langmuir, vol.13, pp.1865-1868, 1997.

A. Perro, S. Reculusa, S. Ravaine, E. Bourgeat-lami, and E. Duguet, Design and synthesis of Janus micro-and nanoparticles, J. Mater. Chem, vol.15, p.3745, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00096043

G. Zhang, D. Wang, and H. Möhwald, Patterning microsphere surfaces by templating colloidal crystals, Nano Lett, vol.5, pp.143-146, 2005.

A. B. Pawar and I. Kretzschmar, Multifunctional patchy particles by glancing angle deposition, Langmuir, vol.25, pp.9057-9063, 2009.

Y. P. Zhao, D. X. Ye, G. C. Wang, and T. M. Lu, Novel Nano-Column and Nano-Flower Arrays by Glancing Angle Deposition, Nano Lett, vol.2, pp.351-354, 2002.

A. B. , Pawar and I. Kretzschmar. Patchy particles by glancing angle deposition, Langmuir, vol.24, pp.355-358, 2008.

Y. Wang, Colloids with valence and specific directional bonding, Nature, vol.491, pp.51-56, 2012.

V. N. Manoharan, M. T. Elsesser, and D. J. Pine, Dense Packing and Symmetry in Small Clusters of Microspheres, Science, vol.301, pp.483-487, 2003.

K. Chaudhary, Q. Chen, J. J. Juárez, S. Granick, and J. A. Lewis, Janus colloidal matchsticks. J. Am. Chem. Soc, vol.134, pp.12901-12903, 2012.

D. Morphew and D. Chakrabarti, Clusters of anisotropic colloidal particles: From colloidal molecules to supracolloidal structures, Curr. Opin. Colloid Interface Sci, vol.30, pp.70-80, 2017.

A. F. Demirörs, P. P. Pillai, B. Kowalczyk, and B. A. Grzybowski, Colloidal assembly directed by virtual magnetic moulds, Nature, vol.503, pp.99-103, 2013.

A. Perro, E. Duguet, O. Lambert, J. C. Taveau, E. Bourgeat-lami et al., A chemical synthetic route towards "Colloidal molecules, Angew. Chem. Int. Ed, vol.48, pp.361-365, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00350952

D. J. Kraft, W. S. Vlug, C. M. Van-kats, A. Van-blaaderen, A. Imhof et al., Selfassembly of colloids with liquid protrusions, J. Am. Chem. Soc, vol.131, pp.1182-1186, 2009.

S. H. Kim, G. R. Yi, K. H. Kim, and S. M. Yang, Photocurable pickering emulsion for colloidal particles with structural complexity, Langmuir, vol.24, pp.2365-2371, 2008.

G. R. Yi, V. N. Manoharan, E. Michel, M. T. Elsesser, S. M. Yang et al., Colloidal clusters of silica or polymer microspheres, Adv. Mater, vol.16, pp.1204-1208, 2004.

Y. Xia, Y. Yin, Y. Lu, and J. Mclellan, Template-Assisted Self-Assembly of Spherical Colloids into Complex and Controllable Structures, Adv. Funct. Mater, vol.13, pp.907-918, 2003.

Y. Yin, Y. Lu, B. Gates, and Y. Xia, Template-assisted self-assembly: A practical route to complex aggregates of monodispersed colloids with well-defined sizes, shapes, and structures, J. Am. Chem. Soc, vol.123, pp.8718-8729, 2001.

D. Luo, C. Yan, and T. Wang, Interparticle Forces Underlying Nanoparticle Self-Assemblies, Small, vol.11, pp.5984-6008, 2015.

Z. Dogic, P. Sharma, and M. J. Zakhary, Hypercomplex Liquid Crystals, Annu. Rev. Condens. Matter Phys, vol.5, pp.137-157, 2014.

H. N. Lekkerkerker and R. Tuinier, Colloids and the Depletion Interaction, 2011.

C. Hubert, Synthesis of multivalent silica nanoparticles combining both enthalpic and entropic patchiness, Faraday Discuss, vol.181, pp.139-146, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01187264

Q. Chen, S. C. Bae, and S. Granick, Directed self-assembly of a colloidal kagome lattice, Nature, vol.469, pp.381-384, 2011.

Q. Chen, S. C. Bae, and S. Granick, Staged self-assembly of colloidal metastructures, J. Am. Chem. Soc, vol.134, pp.11080-11083, 2012.

H. Qiu, Z. M. Hudson, M. A. Winnik, and I. Manners, Multidimensional hierarchical selfassembly of amphiphilic cylindrical block comicelles, Science, vol.347, pp.1329-1332, 2015.

H. Qiu, G. Russo, P. A. Rupar, L. Chabanne, M. A. Winnik et al., Tunable supermicelle architectures from the hierarchical self-assembly of amphiphilic cylindrical B-A-B triblock Co-micelles, Angew. Chem. Int. Ed, vol.51, pp.11882-11885, 2012.

F. Oosawa, Interaction between parallel rodlike macroions, Biopolymers, vol.6, pp.1633-1647, 1968.

B. Shaughnessy and Q. Yang, anning-Oosawa counterion condensation, Phys. Rev. Lett, vol.94, p.48302, 2005.

A. Naji, S. Jungblut, A. G. Moreira, and R. R. Netz, Electrostatic interactions in strongly coupled soft matter, Physica A, vol.352, pp.131-170, 2005.

R. R. Netz, Electrostatistics of counter-ions at and between planar charged walls: From Poisson-Boltzmann to the strong-coupling theory, Eur. Phys. J. E, vol.5, pp.557-574, 2001.

A. Naji and R. R. Netz, Attraction of like-charged macroions in the strong-coupling limit, Eur. Phys. J. E, vol.13, pp.43-59, 2004.

E. ?amaj and . Trizac, Wigner-crystal formulation of strong-coupling theory for counterions near planar charged interfaces, Phys. Rev. E, vol.84, p.41401, 2011.

A. Naji, M. Kanduc, J. Forsman, and R. Podgornik, Perspective: Coulomb fluids--weak coupling, strong coupling, in between and beyond, J. Chem. Phys, vol.139, p.150901, 2013.

J. L. Sikorav, J. Pelta, and F. Livolant, A Liquid Crystalline Phase in Spermidine-Condensed DNA, Biophys. J, vol.67, pp.1387-1392, 1994.

J. Pelta, F. Livolant, and J. L. Sikorav, DNA aggregation induced by polyamines and cobalthexamine, J. Biol. Chem, vol.271, pp.5656-5662, 1996.

J. Pelta, D. Durand, J. Doucet, and F. Livolant, DNA mesophases induced by spermidine: structural properties and biological implications, Biophys. J, vol.71, pp.48-63, 1996.

E. Raspaud, D. Durand, and F. Livolant, Interhelical spacing in liquid crystalline spermine and spermidine-DNA precipitates, Biophys. J, vol.88, pp.392-403, 2005.

J. X. Tang, P. A. Janmey, A. Lyubartsev, and L. Nordenskiöld, Metal ion-induced lateral aggregation of filamentous viruses fd and M13, Biophys. J, vol.83, pp.566-581, 2002.

J. C. Butler, T. Angelini, J. X. Tang, and G. C. Wong, Ion multivalence and like-charge polyelectrolyte attraction, Phys. Rev. Lett, vol.91, p.28301, 2003.

P. F. Damasceno, M. Engel, and S. C. Glotzer, Predictive Self-Assembly of Polyhedra into Complex Structures, Science, vol.453, pp.453-458, 2012.

G. Van-anders, D. Klotsa, N. K. Ahmed, M. Engel, and S. C. Glotzer, Understanding shape entropy through local dense packing, Proc. Natl. Acad. Sci, vol.111, pp.4812-4821, 2014.

E. Grelet and R. Rana, From soft to hard rod behavior in liquid crystalline suspensions of Chapter 0: General introduction sterically stabilized colloidal filamentous particles, Soft Matter, vol.12, pp.4621-4627, 2016.

Y. Yang, G. Chen, L. J. Martinez-miranda, H. Yu, K. Liu et al., Synthesis and Liquid-Crystal Behavior of Bent Colloidal Silica Rods, J. Am. Chem. Soc, vol.138, pp.68-71, 2016.

D. A. Marvin, M. F. Symmons, and S. K. Straus, Structure and assembly of filamentous bacteriophages, Prog. Biophys. Mol. Biol, vol.114, pp.80-122, 2014.

G. P. Smith and V. A. Petrenko, Phage display, Chem. Rev, vol.97, pp.391-410, 1997.
URL : https://hal.archives-ouvertes.fr/hal-01677196

D. Marvin, Filamentous phage structure, infection and assembly, Curr. Opin. Struct. Biol, vol.8, pp.150-158, 1998.

S. Bhattacharjee, M. J. Glucksman, and L. Makowski, Structural polymorphism correlated to surface charge in filamentous bacteriophages, Biophys. J, vol.61, pp.725-735, 1992.

Z. Dogic and S. Fraden, Cholesteric phase in virus suspensions, Langmuir, vol.16, pp.7820-7824, 2000.

Z. Dogic and S. Fraden, Development of model colloidal liquid crystals and the kinetics of the isotropic-smectic transition, Philos. Trans. R. Soc. A, vol.359, pp.997-1015, 2001.

Z. Dogic, Surface freezing and a two-step pathway of the isotropic-smectic phase transition in colloidal rods, Phys. Rev. Lett, vol.91, p.165701, 2003.

E. Pouget, E. Grelet, and M. P. Lettinga, Dynamics in the smectic phase of stiff viral rods, Phys. Rev. E, vol.84, p.41704, 2011.

M. P. Lettinga and E. Grelet, Self-diffusion of rodlike viruses through smectic layers, Phys. Rev. Lett, vol.99, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00257723

E. Grelet, M. Lettinga, M. Bier, R. Van-roij, P. Van-der et al., Dynamical and structural insights into the smectic phase of rod-like particles, J. Phys. Condens. Matter, vol.20, p.494213, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00682030

S. Naderi, E. Pouget, P. Ballesta, P. Van-der, M. P. Schoot et al., Fractional hoppinglike motion in columnar mesophases of semiflexible rodlike particles, Phys. Rev. Lett, vol.111, p.37801, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00932042

L. Alvarez, M. P. Lettinga, and E. Grelet, Fast Diffusion of Long Guest Rods in a Lamellar Phase of Short Host Particles, Phys. Rev. Lett, vol.118, p.178002, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522021

B. Sung, A. De-la-cotte, and E. Grelet, Chirality-controlled crystallization via screw dislocations, Nat. Commun, vol.9, p.1405, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02176429

E. Barry and Z. Dogic, Entropy driven self-assembly of nonamphiphilic colloidal membranes, Proc. Natl. Acad. Sci, vol.107, pp.10348-10353, 2010.

P. Sharma, A. Ward, T. Gibaud, M. F. Hagan, and Z. Dogic, Hierarchical organization of chiral rafts in colloidal membranes, Nature, vol.513, pp.77-80, 2014.

T. Gibaud, Reconfigurable self-assembly through chiral control of interfacial tension, Nature, vol.481, pp.348-351, 2012.

C. Mao, Viral assembly of oriented quantum dot nanowires, Proc. Natl. Acad. Sci, vol.100, pp.6946-6951, 2003.

S. Lee, C. Mao, C. E. Flynn, and A. M. Belcher, Ordering of Quantum Dots Using Genetically Engineered Viruses, Science, vol.296, pp.892-895, 2002.

I. Yacoby, M. Shamis, H. Bar, D. Shabat, and I. Benhar, Targeting antibacterial agents by using drug-carrying filamentous bacteriophages, Antimicrob. Agents Chemother, vol.50, pp.2087-2097, 2006.

Q. Wang, Chemical modification of M13 bacteriophage and its application in cancer cell imaging, Bioconjug. Chem, vol.21, pp.1369-77, 2010.

G. Abbineni, S. Modali, B. Safiejko-mroczka, V. A. Petrenko, and C. Mao, Evolutionary selection of new breast cancer cell-targeting peptides and phages with the cell-targeting peptides fully displayed on the major coat and their effects on actin dynamics during cell internalization, Mol. Pharm, vol.7, pp.1629-1642, 2010.

D. J. Rodi and L. Makowski, Phage-display technology -Finding a needle in a vast molecular haystack, Curr. Opin. Biotechnol, vol.10, pp.87-93, 1999.

S. S. Sidhu, Phage display in pharmaceutical biotechnology, Curr. Opin. Biotechnol, vol.11, pp.610-616, 2000.

S. F. Parmley and G. P. Smith, Antibody-selectable filamentous fd phage vectors: affinity purification of target genes, Gene, vol.73, pp.305-318, 1988.

B. P. Gray and K. C. Brown, Combinatorial peptide libraries: Mining for cell-binding peptides, Chem. Rev, vol.114, pp.1020-1081, 2014.

S. R. Whaley, D. S. English, E. L. Hu, P. F. Barbara, and A. M. Belcher, Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly, Nature, vol.405, pp.665-673, 2000.

B. D. Reiss, C. Mao, D. J. Solis, K. S. Ryan, T. Thomson et al., Biological routes to metal alloy ferromagnetic nanostructures, Nano Lett, vol.4, pp.1127-1132, 2004.

K. T. Nam, B. R. Reelle, S. W. Lee, and A. M. Belcher, Genetically Driven Assembly of Nanorings Based on the M13 Virus, Nano Lett, vol.4, pp.23-27, 2004.

S. W. Lee, S. K. Lee, and A. M. Belcher, Virus-based alignment of inorganic, organic, and biological nanosized materials, Adv. Mater, vol.15, pp.689-692, 2003.

Y. Huang, Programmable Assembly of Nanoarchitectures Using Genetically Engineered Viruses, Nano Lett, vol.5, pp.1429-1463, 2005.

C. Mao, Virus-Based Toolkit for the Directed Synthesis of Magnetic and Semiconducting Nanowires, Science, vol.303, pp.213-217, 2004.

G. Winter, A. D. Griffiths, R. E. Hawkins, and H. R. Hoogenboom, Making Antibodies by Phage Display Technology, Annu. Rev. Immunol, vol.12, pp.433-455, 1994.

I. Yacoby, H. Bar, and I. Benhar, Targeted drug-carrying bacteriophages as antibacterial nanomedicines, Antimicrob. Agents Chemother, vol.51, pp.2156-2163, 2007.

I. Yacoby and I. Benhar, Targeted filamentous bacteriophages as therapeutic agents, Expert Opin. Drug Deliv, vol.5, pp.321-330, 2008.

H. Bar, I. Yacoby, and I. Benhar, Killing cancer cells by targeted drug-carrying phage nanomedicines, BMC Biotechnol, vol.8, pp.1-14, 2008.

J. Rong, Oriented cell growth on self-assembled bacteriophage M13 thin films, Chem. Commun, pp.5185-5187, 2008.

D. L. Jaye, C. M. Geigerman, R. E. Fuller, A. Akyildiz, and C. A. Parkos, Direct fluorochrome labeling of phage display library clones for studying binding specificities: Applications in flow cytometry and fluorescence microscopy, J. Immunol. Methods, vol.295, pp.119-127, 2004.

Z. Ruff, Designing disordered materials using DNA-coated colloids of bacteriophage fd and gold, Faraday Discuss, vol.186, pp.473-488, 2016.

, General introduction

M. Chiappini, E. Eiser, and F. Sciortino, Phase behaviour in complementary DNA-coated gold nanoparticles and fd-viruses mixtures: a numerical study, Eur. Phys. J. E, vol.40, p.7, 2017.

F. Huang, Pair potential of charged colloidal stars, Phys. Rev. Lett, vol.102, p.108302, 2009.

K. E. Sapsford, Functionalizing nanoparticles with biological molecules: Developing chemistries that facilitate nanotechnology, Chem. Rev, vol.113, pp.1904-2074, 2013.

D. Montalvan-sorrosa, J. L. González-solis, J. Mas-oliva, and R. Castillo, Filamentous virus decoration with gold nanoparticles: global fingerprints of bionanocomposites acquired with SERS, RSC Adv, vol.4, pp.57329-57336, 2014.

R. Bott, Fundamental Studies of the Chemisorption of Organosulfur Compounds on Au( 111), J. Am. Chem. Soc, vol.109, pp.733-740, 1987.

A. S. Khalil, Single M13 bacteriophage tethering and stretching, Proc. Natl. Acad. Sci, vol.104, pp.4892-4897, 2007.

R. Y. Sweeney, E. Y. Park, B. L. Iverson, and G. Georgiou, Assembly of Multimeric Phage Nanostructures Through Leucine Zipper Interactions, Biotechnol. Bioeng, vol.95, pp.539-545, 2006.

F. Huang, Interactions and Collective Behavior of Attractive Colloidal Rods and Microspheres Grafted with Filamentous Bacteriophage, 2009.

G. T. Hess, C. P. Guimaraes, E. Spooner, H. L. Ploegh, and A. M. Belcher, Orthogonal labeling of M13 minor capsid proteins with DNA to self-assemble end-to-end multiphage structures, ACS Synth. Biol, vol.2, pp.490-496, 2013.

C. Mao, Virus-Based Toolkit for the Directed Synthesis of Magnetic and Semiconducting Nanowires, Science, vol.303, pp.213-217, 2004.

W. Konigsberg, Reduction of Disulfide Bonds in Proteins with Dithiothreitol, Methods Enzymol, vol.25, pp.185-188, 1972.

J. C. Bardwell, K. Mcgovern, and J. Beckwith, Identification of a protein required for disulfide bond formation in vivo, Cell, vol.67, pp.581-589, 1991.

W. R. Gray and W. R. Gray, Disulfide structures of highly bridged peptides : A new strategy for analysis Disulfide structures of highly bridged peptides : A new strategy for analysis, Protein Sci, vol.2, pp.1732-1748, 1993.

T. G. Senkevich, C. L. White, E. Koonin, and B. Moss, A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation, Proc. Natl. Acad. Sci, vol.97, pp.12068-12073, 2000.

J. Wu and J. T. Watson, A novel methodology for assignment of disulfide bond pairings in proteins, Protein Sci, vol.6, pp.391-398, 1997.

I. , R. Rebollo, and C. Heinis, Phage selection of bicyclic peptides, Methods, vol.60, pp.46-54, 2013.

S. Kalhor-monfared, Rapid Biocompatible Macrocyclization of Peptides with Decafluorosulfone, Chem. Sci, vol.9, pp.1-6, 2016.

M. R. Jafari, Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library, ACS Chem. Biol, vol.9, pp.443-450, 2014.

S. Bellotto, S. Chen, I. Rebollo, H. A. Wegner, and C. Heinis, Phage selection of photoswitchable peptide ligands, J. Am. Chem. Soc, vol.136, pp.5880-5883, 2014.

E. Pretzer and J. E. Wiktorowicz, Saturation fluorescence labeling of proteins for proteomic analyses, Anal. Biochem, vol.374, pp.250-262, 2008.

P. D. Tzanavaras, C. Mitani, A. Anthemidis, and D. G. Themelis, On-line cleavage of disulfide bonds by soluble and immobilized tris-(2-carboxyethyl)phosphine using sequential injection analysis, Talanta, vol.96, pp.21-25, 2012.

, Chapter 2: Reduction of disulfide groups at proximal end of M13C7C viruses by TCEP/iTCEP and labeling with maleimide activated fluorescent dyes 66

D. Montalvan-sorrosa, J. L. González-solis, J. Mas-oliva, and R. Castillo, Filamentous virus decoration with gold nanoparticles: global fingerprints of bionanocomposites acquired with SERS, RSC Adv, vol.4, pp.57329-57336, 2014.

P. Liu, A Tris (2-Carboxyethyl) Phosphine (TCEP) Related Cleavage on Cysteine-Containing Proteins, J. Am. Soc. Mass Spectrom, vol.21, pp.837-844, 2010.

J. C. Han and G. Y. Han, A procedure for quantitative determination of tris(2-carboxyethyl)phosphine, an odorless reducing agent more stable and effective than dithiothreitol, Anal. Biochem, vol.220, pp.5-10, 1994.

G. T. Hermanson, Bioconjugate Techniques, 2013.

, 3.3.1 Influence of M13 virus strains on the reaction with AuNBs

, Influence of metal species on the nanoparticle-M13 reaction, 3.4 Roles of capping reagent and ionic strength on the reaction between M13C7C and

. .. Aunbs, 3.5 Influence of molar excess on the reaction between M13C7C and AuNBs, vol.87

. .. Conclusions,

. .. References,

, Introducing patchiness to the tip of rod-like viruses by grafting metallic nanoparticles, Chapter

G. T. Hess, C. P. Guimaraes, E. Spooner, H. L. Ploegh, and A. M. Belcher, Orthogonal labeling of M13 minor capsid proteins with DNA to self-assemble end-to-end multiphage structures, ACS Synth. Biol, vol.2, pp.490-496, 2013.

R. Y. Sweeney, E. Y. Park, B. L. Iverson, and G. Georgiou, Assembly of Multimeric Phage Nanostructures Through Leucine Zipper Interactions, Biotechnol. Bioeng, vol.95, pp.539-545, 2006.

Y. Huang, Programmable Assembly of Nanoarchitectures Using Genetically Engineered Viruses, Nano Lett, vol.5, pp.1429-1463, 2005.

K. T. Nam, B. R. Reelle, S. W. Lee, and A. M. Belcher, Genetically Driven Assembly of Nanorings Based on the M13 Virus, Nano Lett, vol.4, pp.23-27, 2004.

R. , D. Felice, and A. Selloni, Adsorption modes of cysteine on Au(111): Thiolate, amino-thiolate, disulfide, J. Chem. Phys, vol.120, pp.4906-4914, 2004.

R. G. Nuzzo and D. L. Allara, Adsorption of Bifunctional Organic Disulfides on Gold Surfaces, J. Am. Chem. Soc, vol.105, pp.4481-4483, 1983.

J. L. Burt, C. Gutiérrez-wing, M. Miki-yoshida, and M. José-yacamán, Noble-metal nanoparticles directly conjugated to globular proteins, Langmuir, vol.20, pp.11778-11783, 2004.

H. Grönbeck, A. Curioni, and W. Andreoni, Thiols and disulfides on the Au(111) surface: The headgroup-gold interaction, J. Am. Chem. Soc, vol.122, pp.3839-3842, 2000.

Z. Huang, F. Chen, P. A. Bennett, and N. Tao, Single Molecule Junctions Formed via Au?Thiol Contact: Stability and Breakdown Mechanism, J. Am. Chem. Soc, vol.129, pp.13225-13231, 2007.

Z. Li, S. C. Chang, and R. S. Williams, Self-assembly of alkanethiol molecules onto platinum and platinum oxide surfaces, Langmuir, vol.19, pp.6744-6749, 2003.

Y. J. Lee, I. C. Jeon, W. Paik, and K. Kim, Self-Assembly of 1,2-Benzenedithiol on Gold and Silver: Fourier Transform Infrared Spectroscopy and Quartz Crystal Microbalance Study, Langmuir, vol.12, pp.5830-5837, 1996.

J. C. Love, D. B. Wolfe, M. L. Chabinyc, K. E. Paul, and G. M. Whitesides, Self-assembled monolayers of alkanethiolates on palladium are good etch resists, J. Am. Chem. Soc, vol.124, pp.1576-1577, 2002.

P. Kohli, K. K. Taylor, J. J. Harris, and G. J. Blanchard, Assembly of covalently-coupled disulfide multilayers on gold, J. Am. Chem. Soc, vol.120, pp.11962-11968, 1998.

Y. Xue, X. Li, H. Li, and W. Zhang, Quantifying thiol-gold interactions towards the efficient strength control, Nat. Commun, vol.5, p.4348, 2014.

T. Sainsbury, T. Ikuno, D. Okawa, D. Pacilé, J. M. Fréchet et al., Self-assembly of gold nanoparticles at the surface of amine-and thiol-functionalized boron nitride nanotubes, J. Phys. Chem. C, vol.111, pp.12992-12999, 2007.

A. Ulman, Self-assembled monolayers of rigid thiols, J. Biotechnol, vol.74, pp.175-188, 2000.

D. Montalvan-sorrosa, J. L. González-solis, J. Mas-oliva, and R. Castillo, Filamentous virus decoration with gold nanoparticles: global fingerprints of bionanocomposites acquired with SERS, RSC Adv, vol.4, pp.57329-57336, 2014.

J. Sambrook and W. D. , Molecular Cloning A LaboratoryManual, 2012.

T. Hendel, M. Wuithschick, F. Kettemann, A. Birnbaum, K. Rademann et al., Situ Determination of Colloidal Gold Concentrations with UV?Vis Spectroscopy: Limitations and Perspectives, vol.86, pp.11115-11124, 2014.

S. Kalhor-monfared, Rapid Biocompatible Macrocyclization of Peptides with Decafluorosulfone, Chem. Sci, vol.9, pp.1-6, 2016.

B. Xu, G. Gonella, B. G. Delacy, and H. L. Dai, Adsorption of anionic thiols on silver nanoparticles, J. Phys. Chem. C, vol.119, pp.5454-5461, 2015.

P. E. Laibinis, G. M. Whitesides, D. L. Allara, Y. T. Tao, A. N. Parikh et al., Comparison of the structures and wetting properties of self-assembled monolayers of nalkanethiols on the coinage metal surfaces, copper, silver, and gold, J. Am. Chem. Soc, vol.113, pp.7152-7167, 1991.

D. A. Stern, Adsorbed Thiophenol and Related Compounds Studied at Pt(111) Electrodes by EELS, Auger Spectroscopy, and Cyclic Voltammetry, J. Am. Chem. Soc, vol.110, pp.4885-4893, 1988.

J. A. Williams and C. B. Gorman, Alkanethiol reductive desorption from self-assembled monolayers on gold, platinum, and palladium substrates, J. Phys. Chem. C, vol.111, pp.12804-12810, 2007.

, Introducing patchiness to the tip of rod-like viruses by grafting metallic nanoparticles, Chapter

J. C. Love, L. A. Estroff, J. K. Kriebel, R. G. Nuzzo, and G. M. Whitesides, Self-assembled monolayers of thiolates on metals as a form of nanotechnology, Chem. Rev, vol.105, pp.1103-1169, 2005.

W. Wang, W. Duan, S. Ahmed, A. Sen, and T. E. Mallouk, From one to many: Dynamic assembly and collective behavior of self-propelled colloidal motors, Acc. Chem. Res, vol.48, pp.1938-1946, 2015.

S. Sanchez, L. Soler, and J. Katuri, Chemically powered micro-and nanomotors, Angew. Chem. Int. Ed, vol.54, pp.1414-1444, 2015.

W. F. Paxton, P. T. Baker, T. R. Kline, Y. Wang, T. E. Mallouk et al., Catalytically induced electrokinetics for motors and micropumps, J. Am. Chem. Soc, vol.128, pp.14881-14888, 2006.

H. T. Britton, A. R. Robinson, and . Cxcviii, Universal buffer solutions and the dissociation constant of veronal, J. Chem. Soc, pp.1456-1462, 1931.

H. Endemann and P. Model, Location of filamentous phage minor coat proteins in phage and in infected cells, J. Mol. Biol, vol.250, pp.496-506, 1995.

T. Ahmad, Reviewing the tannic acid mediated synthesis of metal nanoparticles, J. Nanotechnol, pp.1-11, 2014.

, 3.1 Influence of ionic strength on the valency of self-assembled colloidal molecules, Self-assembly of rod-like viruses into colloidal molecules with controlled valency Contents 4.1 Introduction

, Quantitative Model for the valency of colloidal molecules

. .. Conclusions,

. .. References,

, Self-assembly of rod-like viruses into colloidal molecules with

J. Turkevich, P. C. Stevenson, and J. Hiller, A Study of the Nucleation and Growth Processes in the Synthesis of Colloidal Gold, Discuss. Faraday Soc, vol.11, pp.55-75, 1951.

C. Ziegler and A. Eychmüller, Seeded growth synthesis of uniform gold nanoparticles with diameters of 15-300 nm, J. Phys. Chem. C, vol.115, pp.4502-4506, 2011.

N. G. Bastús, J. Comenge, and V. Puntes, Kinetically controlled seeded growth synthesis of citrate-stabilized gold nanoparticles of up to 200 nm: Size focusing versus ostwald ripening, Langmuir, vol.27, pp.11098-11105, 2011.

S. K. Sivaraman, S. Kumar, and V. Santhanam, Room-temperature synthesis of gold nanoparticles -Size-control by slow addition, Gold Bull, vol.43, pp.275-286, 2010.

T. Hendel, M. Wuithschick, F. Kettemann, A. Birnbaum, K. Rademann et al., Self-assembly of rod-like viruses into colloidal molecules with controlled valency Determination of Colloidal Gold Concentrations with UV?Vis Spectroscopy: Limitations and Perspectives, Situ Chapter, vol.4, pp.11115-11124, 2014.

T. Ahmad, Reviewing the tannic acid mediated synthesis of metal nanoparticles, J. Nanotechnol, pp.1-11, 2014.

L. Onsager, 110 5.2.1 Labeling of M13C7C viruses with red and green fluorescent dyes, The Effects of Shape on the Interaction of Colloidal Particles, vol.51, pp.627-659, 1949.

, 112 5.2.4 Diffusion coefficients and angle fluctuations of the diblocks

D. .. Results,

. .. Conclusions,

. .. References,

, Heterobifunctional colloidal diblocks from directional self-assembly of rod-shaped viruses, Chapter

C. Mao, Virus-Based Toolkit for the Directed Synthesis of Magnetic and Semiconducting Nanowires, Science, vol.303, pp.213-217, 2004.

Y. Huang, Programmable Assembly of Nanoarchitectures Using Genetically Engineered Viruses, Nano Lett, vol.5, pp.1429-1463, 2005.

Y. S. Nam, Virus-templated assembly of porphyrins into light-harvesting nanoantennae, J. Am. Chem. Soc, vol.132, pp.1462-1463, 2010.

K. T. Nam, Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes, Science, vol.312, pp.885-888, 2006.

D. Oh, J. Qi, Y. C. Lu, Y. Zhang, Y. Shao-horn et al., Biologically enhanced cathode design for improved capacity and cycle life for lithium-oxygen batteries, Nat. Commun, vol.4, pp.1-8, 2013.

D. Montalvan-sorrosa, J. L. González-solis, J. Mas-oliva, and R. Castillo, Filamentous virus decoration with gold nanoparticles: global fingerprints of bionanocomposites acquired with SERS, RSC Adv, vol.4, pp.57329-57336, 2014.

Z. Ruff, Designing disordered materials using DNA-coated colloids of bacteriophage fd and gold, Faraday Discuss, vol.186, pp.473-488, 2016.

M. Moradi, Improving the capacity of sodium ion battery using a virus-templated nanostructured composite cathode, Nano Lett, vol.15, pp.2917-2921, 2015.

S. Lee, C. Mao, C. E. Flynn, and A. M. Belcher, Ordering of Quantum Dots Using Genetically Engineered Viruses, Science, vol.296, pp.892-895, 2002.

S. W. Lee, S. K. Lee, and A. M. Belcher, Virus-based alignment of inorganic, organic, and biological nanosized materials, Adv. Mater, vol.15, pp.689-692, 2003.

S. R. Whaley, D. S. English, E. L. Hu, P. F. Barbara, and A. M. Belcher, Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly, Nature, vol.405, pp.665-673, 2000.

J. Sambrook and W. D. , Molecular Cloning A LaboratoryManual, 2012.

Q. Wang, Chemical modification of M13 bacteriophage and its application in cancer cell imaging, Bioconjug. Chem, vol.21, pp.1369-77, 2010.

L. A. Frances, Single particle dynamics in liquid crystalline phases formed by filamentous viruses, 2017.
URL : https://hal.archives-ouvertes.fr/tel-01534484

W. Andreoni, W. Andreoni, A. Curioni, A. Curioni, H. Grönbeck et al., Density 5.5 References functional theory approach to thiols and disulfides on gold: Au (111) surface and clusters, Int. J. Quant. Chem, vol.80, pp.598-608, 2000.

H. Grönbeck, A. Curioni, and W. Andreoni, Thiols and disulfides on the Au(111) surface: The headgroup-gold interaction, J. Am. Chem. Soc, vol.122, pp.3839-3842, 2000.

R. Bott, Fundamental Studies of the Chemisorption of Organosulfur Compounds on Au( 111), J. Am. Chem. Soc, vol.109, pp.733-740, 1987.

, Heterobifunctional colloidal diblocks from directional self-assembly of rod-shaped viruses References, Chapter

P. Kohli, K. K. Taylor, J. J. Harris, and G. J. Blanchard, Assembly of covalently-coupled disulfide multilayers on gold, J. Am. Chem. Soc, vol.120, pp.11962-11968, 1998.

Y. Xue, X. Li, H. Li, and W. Zhang, Quantifying thiol-gold interactions towards the efficient strength control, Nat. Commun, vol.5, p.4348, 2014.

W. Wang, W. Duan, S. Ahmed, A. Sen, and T. E. Mallouk, From one to many: Dynamic assembly and collective behavior of self-propelled colloidal motors, Acc. Chem. Res, vol.48, pp.1938-1946, 2015.

S. Sanchez, L. Soler, and J. Katuri, Chemically powered micro-and nanomotors, Angew. Chem. Int. Ed, vol.54, pp.1414-1444, 2015.

W. F. Paxton, P. T. Baker, T. R. Kline, Y. Wang, T. E. Mallouk et al., Catalytically induced electrokinetics for motors and micropumps, J. Am. Chem. Soc, vol.128, pp.14881-14888, 2006.

, Conclusion and perspectives References

D. A. Marvin, M. F. Symmons, and S. K. Straus, Structure and assembly of filamentous bacteriophages, Prog. Biophys. Mol. Biol, vol.114, pp.80-122, 2014.

H. Endemann and P. Model, Location of filamentous phage minor coat proteins in phage and in infected cells, J. Mol. Biol, vol.250, pp.496-506, 1995.

, Peptide Property Calculator

D. Marvin, Filamentous phage structure, infection and assembly, Curr. Opin. Struct. Biol, vol.8, pp.150-158, 1998.

K. Zimmermann, H. Hagedorn, C. C. Heuck, M. Hirichsen, and H. Ludwig, The ionic properties of the filmentous bacteriophages Pf1 and \textit{fd}, J. Bio. Chem, vol.261, pp.1653-1655, 1986.

Z. Dogic, A. P. Philipse, S. Fraden, and J. K. Dhont, Concentration-dependent sedimentation of colloidal rods, J. Chem. Phys, vol.113, pp.8368-8380, 2000.