F. Ample, S. Ami, C. Joachim, F. Thiemann, and G. Rapenne, A Morse manipulator molecule for the modulation of metallic shockley surface states, Chemical Physics Letters, vol.434, issue.4-6, pp.434-280, 2007.
DOI : 10.1016/j.cplett.2006.12.021

H. Dietz, S. M. Douglas, and W. M. Shih, Folding DNA into Twisted and Curved Nanoscale Shapes, Science, vol.325, issue.5941, pp.725-730, 2009.
DOI : 10.1126/science.1174251

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737683

L. Grill, K. Rieder, F. Moresco, G. Rapenne, S. Stojkovic et al., Rolling a single molecular wheel at the atomic scale, Nature Nanotechnology, vol.185, issue.2, pp.95-98, 2007.
DOI : 10.1038/nnano.2006.210

C. Joachim, H. Tang, F. Moresco, G. Rapenne, and G. Meyer, The design of a nanoscale molecular barrow, Nanotechnology, vol.13, issue.3, pp.330-335, 2002.
DOI : 10.1088/0957-4484/13/3/318

J. M. Kelly and . Tour, Surface-rolling molecules, J. Am. Chem. Soc, vol.128, pp.4854-4864, 2006.

A. C. Van-duin, S. Dasgupta, F. Lorant, W. A. Goddard, and I. , ReaxFF:?? A Reactive Force Field for Hydrocarbons, The Journal of Physical Chemistry A, vol.105, issue.41, pp.9396-9409, 2001.
DOI : 10.1021/jp004368u

D. W. Brenner, Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films, Physical Review B, vol.42, issue.15, pp.9458-9471, 1990.
DOI : 10.1103/PhysRevB.42.9458

D. W. Brenner, The Art and Science of an Analytic Potential, physica status solidi (b), vol.217, issue.1, pp.23-40, 2000.
DOI : 10.1002/(SICI)1521-3951(200001)217:1<23::AID-PSSB23>3.0.CO;2-N

S. B. Sinnott, R. Andrews, D. Qian, A. M. Rao, Z. Mao et al., Model of carbon nanotube growth through chemical vapor deposition, Chemical Physics Letters, vol.315, issue.1-2, pp.315-340, 1999.
DOI : 10.1016/S0009-2614(99)01216-6

S. J. Harris and D. G. Goodwin, Growth on the reconstructed diamond (100) surface, The Journal of Physical Chemistry, vol.97, issue.1, pp.23-28, 1993.
DOI : 10.1021/j100103a007

T. Belytschko, S. P. Xiao, G. C. Schatz, and R. S. Ruoff, Atomistic simulations of nanotube fracture, Physical Review B, vol.65, issue.23, p.235430, 2002.
DOI : 10.1103/PhysRevB.65.235430

D. W. Brenner, J. A. Harrison, C. T. White, and R. J. Colton, Molecular dynamics simulations of the nanometer-scale mechanical properties of compressed Buckminsterfullerene, Thin Solid Films, vol.206, issue.1-2, pp.220-223, 1991.
DOI : 10.1016/0040-6090(91)90425-W

D. W. Brenner, O. A. Shenderova, J. A. Harrison, S. J. Stuart, B. Ni et al., A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons, Journal of Physics: Condensed Matter, vol.14, issue.4, pp.14-783, 2002.
DOI : 10.1088/0953-8984/14/4/312

A. J. Dyson and P. V. Smith, Extension of the Brenner empirical interatomic potential to C???Si???H systems, Surface Science, vol.355, issue.1-3, pp.140-150, 1996.
DOI : 10.1016/0039-6028(96)00004-0

J. H. Los and A. Fasolino, Intrinsic long-range bond-order potential for carbon: Performance in Monte Carlo simulations of graphitization, Physical Review B, vol.68, issue.2, p.24107, 2003.
DOI : 10.1103/PhysRevB.68.024107

S. J. Stuart, A. B. Tutein, and J. A. Harrison, A reactive potential for hydrocarbons with intermolecular interactions, The Journal of Chemical Physics, vol.112, issue.14, 2000.
DOI : 10.1063/1.481208

R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam et al., Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design, Bioinformatics, vol.23, issue.13, pp.408-417, 2007.
DOI : 10.1093/bioinformatics/btm191

URL : https://hal.archives-ouvertes.fr/inria-00390312

J. H. Los and A. Fasolino, Monte Carlo simulations of carbon-based structures based on an extended Brenner potential, Computer Physics Communications, vol.147, issue.1-2, pp.178-181, 2002.
DOI : 10.1016/S0010-4655(02)00240-0

J. H. Los, L. M. Ghiringhelli, E. J. Meijer, and A. Fasolino, Improved long-range reactive bond-order potential for carbon. I. Construction, Physical Review B, vol.72, issue.21, p.214102, 2005.
DOI : 10.1103/PhysRevB.72.214102

URL : http://repository.ubn.ru.nl/bitstream/2066/32617/1/32617.pdf

L. M. Ghiringhelli, J. H. Los, A. Fasolino, and E. J. Meijer, Improved longrange reactive bond-order potential for carbon. II. Molecular simulation of liquid carbon, Phys. Rev. B, vol.72, 2005.

L. J. Karssemeijer and A. Fasolino, Phonons of graphene and graphitic materials derived from the empirical potential LCBOPII, Surface Science, vol.605, issue.17-18, pp.1611-1615, 2011.
DOI : 10.1016/j.susc.2010.10.036

P. A. Gravil, M. Devel, P. Lambin, X. Bouju, C. Girard et al., Adsorption of C 60 molecules, J. Chem. Phys, pp.53-1622, 1996.

Y. J. Dappe, M. A. Basanta, F. Flores, and J. Ortega, Weak chemical interaction and van der Waals forces between graphene layers: A combined density functional and intermolecular perturbation theory approach, Physical Review B, vol.74, issue.20, 2006.
DOI : 10.1103/PhysRevB.74.205434

Y. J. Dappe, J. Ortega, and F. Flores, Intermolecular interaction in density functional theory: Application to carbon nanotubes and fullerenes, Physical Review B, vol.79, issue.16, p.165409, 2009.
DOI : 10.1103/PhysRevB.79.165409

. Aimé, Atomic force microscope measurements and LCAO-S 2 + vdW calculations of contact length between carbon nanotube and graphene surface, Phys. Rev. B, vol.83, p.45410, 2011.

Y. V. Shtogun and L. M. Woods, Many-Body van der Waals Interactions between Graphitic Nanostructures, The Journal of Physical Chemistry Letters, vol.1, issue.9, pp.1356-1362, 2010.
DOI : 10.1021/jz100309m

J. Björk, F. Hanke, C. Palma, P. Samori, M. Cecchini et al., Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through ??????? Stacking, The Journal of Physical Chemistry Letters, vol.1, issue.23, pp.3407-3412, 2010.
DOI : 10.1021/jz101360k

T. Hertel, R. E. Walkup, and P. , Deformation of carbon nanotubes by surface van der Waals forces, Physical Review B, vol.58, issue.20, pp.13870-13873, 1998.
DOI : 10.1103/PhysRevB.58.13870

S. Lebègue, J. Harl, T. Gould, J. G. Angyán, G. Kresse et al., Cohesive Properties and Asymptotics of the Dispersion Interaction in Graphite by the Random Phase Approximation, Physical Review Letters, vol.105, issue.19, 2010.
DOI : 10.1103/PhysRevLett.105.196401

N. R. Wilson and J. V. Macpherson, Carbon nanotube tips for atomic force microscopy, Nature Nanotechnology, vol.79, issue.3, pp.483-491, 2009.
DOI : 10.1038/nnano.2009.154

M. Seydou, S. Marsaudon, J. Buchoux, J. Aimé, and A. Bonnot, Molecular mechanics investigations of carbon nanotube and graphene sheet interaction, Physical Review B, vol.80, issue.24, p.245421, 2009.
DOI : 10.1103/PhysRevB.80.245421

URL : https://hal.archives-ouvertes.fr/hal-01075297

M. Delmas, M. Monthioux, and T. Ondarçuhu, Contact Angle Hysteresis at the Nanometer Scale, Physical Review Letters, vol.106, issue.13, p.136102, 2011.
DOI : 10.1103/PhysRevLett.106.136102

S. Redon, N. Galoppo, and M. C. Lin, Adaptive dynamics of articulated bodies, ACM Transactions on Graphics (TOG), vol.24, p.936945, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00390315

W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical recipes in FORTRAN: The art of scientific computing, 1992.

O. Hod, E. Rabani, and R. Baer, Carbon nanotube closed-ring structures, Physical Review B, vol.67, issue.19, 2003.
DOI : 10.1103/PhysRevB.67.195408

Y. Huang, J. Wu, and K. C. Hwang, Thickness of graphene and single-wall carbon nanotubes, Physical Review B, vol.74, issue.24, p.245413, 2006.
DOI : 10.1103/PhysRevB.74.245413

C. D. Reddy, S. Rajendran, and K. M. Liew, Equilibrium configuration and continuum elastic properties of finite sized graphene, Nanotechnology, vol.17, issue.3, pp.864-870, 2006.
DOI : 10.1088/0957-4484/17/3/042

D. L. Theobald, Rapid calculation of RMSDs using a quaternion-based characteristic polynomial, Acta Cryst, pp.61-478, 2005.

A. V. Petukhov and A. Fasolino, Reconstructions of Diamond (100) and (111) Surfaces: Accuracy of the Brenner Potential, physica status solidi (a), vol.61, issue.1, pp.109-114, 2000.
DOI : 10.1002/1521-396X(200009)181:1<109::AID-PSSA109>3.0.CO;2-W

Z. Liu, K. Suenaga, P. J. Harris, and S. Iijima, Open and Closed Edges of Graphene Layers, Physical Review Letters, vol.102, issue.1, p.15501, 2009.
DOI : 10.1103/PhysRevLett.102.015501

T. W. Chamberlain, J. C. Meyer, J. Biskupek, J. Leschner, A. Santana et al., Reactions of the inner surface of carbon nanotubes and nanoprotrusion processes imaged at the atomic scale, Nature Chemistry, vol.29, issue.9, pp.732-737, 2011.
DOI : 10.1038/nchem.1115

I. Rosenblum, J. Adler, and S. Brandon, MULTI-PROCESSOR MOLECULAR DYNAMICS USING THE BRENNER POTENTIAL: PARALLELIZATION OF AN IMPLICIT MULTI-BODY POTENTIAL, International Journal of Modern Physics C, vol.10, issue.01, pp.189-203, 1999.
DOI : 10.1142/S0129183199000139

A. Omeltchenko, J. Yu, R. K. Kalia, and P. Vashishta, Crack Front Propagation and Fracture in a Graphite Sheet: A Molecular-Dynamics Study on Parallel Computers, Physical Review Letters, vol.78, issue.11, pp.78-2148, 1997.
DOI : 10.1103/PhysRevLett.78.2148

D. Srivastava and S. T. Barnard, Molecular dynamics simulation of largescale carbon nanotubes on a shared-memory architecture, Supercomputing '97: Proceedings of the 1997 ACM/IEEE conference on Supercomputing, pp.1-10, 1997.

J. Pikunic, C. Clinard, N. Cohaut, K. E. Gubbins, J. Guet et al., Structural Modeling of Porous Carbons:?? Constrained Reverse Monte Carlo Method, Langmuir, vol.19, issue.20, pp.8565-8582, 2003.
DOI : 10.1021/la034595y

J. Que, M. W. Radny, P. V. Smith, and A. J. Dyson, Application of the extended Brenner potential to the Si(111)7??7:H system I: cluster calculations, Surface Science, vol.444, issue.1-3, pp.444-123, 2000.
DOI : 10.1016/S0039-6028(99)00994-2

J. Que, M. W. Radny, P. V. Smith, and A. J. Dyson, Application of the extended Brenner potential to the Si(111)7×7:H system II: periodic calculations, Surf. Sci, pp.444-140, 2000.

J. D. Schall, G. Gao, and J. A. Harrison, Elastic constants of silicon materials calculated as a function of temperature using a parametrization of the second-generation reactive empirical bond-order potential, Physical Review B, vol.77, issue.11, p.115209, 2008.
DOI : 10.1103/PhysRevB.77.115209