C. Bechinger, R. Di-leonardo, H. Lwen, C. Reichhardt, G. Volpe et al., Active Particles in Complex and Crowded Environments, Reviews of Modern Physics, vol.46, issue.4, p.45006, 2016.
DOI : 10.1103/PhysRevLett.112.118101
URL : http://repository.bilkent.edu.tr/bitstream/11693/36533/1/Active%20particles%20in%20complex%20and%20crowded%20environments.pdf

T. Vicsek and A. Zafeiris, Collective motion, Physics Reports, vol.517, issue.3-4, p.71, 2012.
DOI : 10.1016/j.physrep.2012.03.004

Y. Sumino, K. H. Nagai, Y. Shitaka, D. Tanaka, K. Yoshikawa et al., Large-scale vortex lattice emerging from collectively moving microtubules, Nature, vol.16, issue.7390, p.448, 2012.
DOI : 10.1105/tpc.104.026930
URL : https://hal.archives-ouvertes.fr/cea-00881343

F. Peruani, Active Brownian rods, The European Physical Journal Special Topics, vol.109, issue.11-12, p.2301, 2016.
DOI : 10.1103/PhysRevLett.109.268701
URL : http://arxiv.org/pdf/1512.07567

M. E. Cates and J. Tailleur, Motility-Induced Phase Separation, Annual Review of Condensed Matter Physics, vol.6, issue.1, p.219, 2015.
DOI : 10.1146/annurev-conmatphys-031214-014710
URL : https://hal.archives-ouvertes.fr/hal-00903637

A. P. Solon, Y. Fily, A. Baskaran, M. E. Cates, Y. Kafri et al., Pressure is not a state function for generic active??fluids, Nature Physics, vol.5, issue.8, p.673, 2015.
DOI : 10.1103/PhysRevLett.101.038102
URL : http://arxiv.org/pdf/1412.3952

N. Kumar, H. Soni, S. Ramaswamy, and A. K. Sood, Flocking at a distance in active granular matter, Nature Communications, vol.74, issue.1, p.4688, 2014.
DOI : 10.1103/PhysRevE.74.022101
URL : http://www.nature.com/articles/ncomms5688.pdf

J. Deseigne, O. Dauchot, and H. Chaté, Collective Motion of Vibrated Polar Disks, Physical Review Letters, vol.105, issue.9, p.98001, 2010.
DOI : 10.1088/1751-8113/42/44/445001
URL : https://hal.archives-ouvertes.fr/hal-01422397

A. Kudrolli, G. Lumay, D. Volfson, and L. S. Tsimring, Swarming and Swirling in Self-Propelled Polar Granular Rods, Physical Review Letters, vol.100, issue.5, p.58001, 2008.
DOI : 10.1103/PhysRevE.75.040901
URL : http://arxiv.org/pdf/0710.5101

H. Wioland, F. G. Woodhouse, J. Dunkel, J. O. Kessler, and R. E. Goldstein, Confinement Stabilizes a Bacterial Suspension into a Spiral Vortex, Physical Review Letters, vol.110, issue.26, p.268102, 2013.
DOI : 10.1103/PhysRevLett.101.198101
URL : http://doi.org/10.1103/physrevlett.110.268102

E. Lushi, H. Wioland, and R. Goldstein, Fluid flows created by swimming bacteria drive self-organization in confined suspensions, Proceedings of the National Academy of Sciences, vol.111, issue.27, p.9733, 2014.
DOI : 10.1016/0022-2836(74)90448-3
URL : http://www.pnas.org/content/111/27/9733.full.pdf

F. Peruani, J. Starruss, V. Jakovljevic, L. Sogaard-andersen, A. Deutsch et al., Collective Motion and Nonequilibrium Cluster Formation in Colonies of Gliding Bacteria, Physical Review Letters, vol.108, issue.9, p.98102, 2012.
DOI : 10.1103/PhysRevLett.78.5018
URL : https://hal.archives-ouvertes.fr/hal-00905217

T. Sanchez, D. T. Chen, S. J. Decamp, M. Heymann, and Z. Dogic, Spontaneous motion in hierarchically assembled active matter, Nature, vol.8, issue.7424, p.431, 2012.
DOI : 10.1039/b806706f
URL : http://europepmc.org/articles/pmc3499644?pdf=render

A. Bricard, J. Caussin, N. Desreumaux, O. Dauchot, and D. Bartolo, Emergence of macroscopic directed motion in populations of motile colloids, Nature, vol.179, issue.7474, p.95, 2013.
DOI : 10.1006/jcis.1996.0217
URL : https://hal.archives-ouvertes.fr/hal-01422384

A. Bricard, J. Caussin, D. Das, C. Savoie, V. Chikkadi et al., Emergent vortices in populations of colloidal rollers, Nature Communications, vol.4, issue.1, p.7470, 2015.
DOI : 10.1006/jcis.1996.0217
URL : https://hal.archives-ouvertes.fr/hal-01292102

]. C. Lozano, B. Hagen, H. Löwen, and C. Bechinger, Phototaxis of synthetic microswimmers in optical landscapes, Nature Communications, vol.20, p.12828, 2016.
DOI : 10.1088/0953-8984/20/01/015216
URL : http://www.nature.com/articles/ncomms12828.pdf

I. Theurkauff, C. Cottin-bizonne, J. Palacci, C. Ybert, and L. Bocquet, Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling, Physical Review Letters, vol.108, issue.26, p.268303, 2012.
DOI : 10.1209/epl/i2003-10237-5
URL : https://hal.archives-ouvertes.fr/hal-01628778

H. H. Wensink and H. Löwen, Aggregation of self-propelled colloidal rods near confining walls, Physical Review E, vol.272, issue.3, p.31409, 2008.
DOI : 10.1103/PhysRevE.71.050901
URL : http://arxiv.org/pdf/0809.0633

A. Kaiser, H. H. Wensink, and H. Löwen, How to Capture Active Particles, Physical Review Letters, vol.66, issue.26, p.268307, 2012.
DOI : 10.1103/PhysRevE.82.041921

H. H. Wensink and H. Löwen, Emergent states in dense systems of active rods: from swarming to turbulence, Journal of Physics: Condensed Matter, vol.24, issue.46, p.464130, 2012.
DOI : 10.1088/0953-8984/24/46/464130
URL : http://arxiv.org/pdf/1204.0381

F. Peruani and M. Bar, A kinetic model and scaling properties of non-equilibrium clustering of self-propelled particles, New Journal of Physics, vol.15, issue.6, p.65009, 2013.
DOI : 10.1088/1367-2630/15/6/065009
URL : https://hal.archives-ouvertes.fr/hal-00905157

H. Zhang, A. Be-'er, E. Florin, and H. L. Swinney, Collective motion and density fluctuations in bacterial colonies, Proceedings of the National Academy of Sciences, vol.320, issue.8, p.13626, 2010.
DOI : 10.1073/pnas.96.8.4472
URL : http://www.pnas.org/content/107/31/13626.full.pdf

Y. Yang, V. Marceau, and G. Gompper, Swarm behavior of self-propelled rods and swimming flagella, Physical Review E, vol.221, issue.3, p.31904, 2010.
DOI : 10.1103/PhysRevE.67.066706
URL : http://juser.fz-juelich.de/record/11236/files/PhysRevE.82.031904.pdf

S. Weitz, A. Deutsch, and F. Peruani, Self-propelled rods exhibit a phase-separated state characterized by the presence of active stresses and the ejection of polar clusters, Physical Review E, vol.92, issue.1, p.12322, 2015.
DOI : 10.1143/JPSJ.12.570
URL : https://hal.archives-ouvertes.fr/hal-01254150

A. Stukowski, Visualization and analysis of atomistic simulation data with OVITO???the Open Visualization Tool, Modelling and Simulation in Materials Science and Engineering, vol.18, issue.1, p.15012, 2010.
DOI : 10.1088/0965-0393/18/1/015012
URL : http://iopscience.iop.org/article/10.1088/0965-0393/18/1/015012/pdf

S. Redner, A Guide To First-Passage Processes, 2001.

A. M. Berezhkovskii and A. V. Barzykin, Search for a small hole in a cavity wall by intermittent bulk and surface diffusion, The Journal of Chemical Physics, vol.136, issue.5, p.54115, 2012.
DOI : 10.1137/080733280
URL : http://europepmc.org/articles/pmc3293344?pdf=render

T. Calandre, O. Bénichou, and R. Voituriez, Accelerating search kinetics by following boundaries, Physical Review Letters, vol.112, issue.23, p.230601, 2014.
DOI : 10.1103/PhysRevLett.110.248106

O. Bénichou, D. Grebenkov, P. Levitz, C. Loverdo, and R. Voituriez, Optimal Reaction Time for Surface-Mediated Diffusion, Physical Review Letters, vol.77, issue.15, p.150606, 2010.
DOI : 10.1038/nchem.622

R. Soto and R. Golestanian, Run-and-tumble dynamics in a crowded environment: Persistent exclusion process for swimmers, Physical Review E, vol.89, issue.1, p.12706, 2014.
DOI : 10.1103/PhysRevLett.107.068702
URL : http://arxiv.org/pdf/1306.0481

A. B. Slowman, M. R. Evans, and R. A. Blythe, Jamming and Attraction of Interacting Run-and-Tumble Random Walkers, Physical Review Letters, vol.116, issue.21, p.218101, 2016.
DOI : 10.1073/pnas.0907542106
URL : http://arxiv.org/pdf/1601.00954

E. Altshuler, J. M. Pastor, A. Garcimartín, I. Zuriguel, and D. Maza, Vibrot, a Simple Device for the Conversion of Vibration into Rotation Mediated by Friction: Preliminary Evaluation, PLoS ONE, vol.232, issue.4, p.67838, 2013.
DOI : 10.1371/journal.pone.0067838.s004

G. Junot, G. Briand, R. Ledesma-alonso, and O. Dauchot, Active versus Passive Hard Disks against a Membrane: Mechanical Pressure and Instability, Physical Review Letters, vol.119, issue.2, p.28002, 2017.
DOI : 10.1103/PhysRevLett.110.208001
URL : https://hal.archives-ouvertes.fr/hal-01627495

N. Nikola, A. P. Solon, Y. Kafri, M. Kardar, J. Tailleur et al., Active Particles with Soft and Curved Walls: Equation of State, Ratchets, and Instabilities, Physical Review Letters, vol.117, issue.9, p.98001, 2016.
DOI : 10.1103/PhysRevLett.111.145702
URL : https://link.aps.org/accepted/10.1103/PhysRevLett.117.098001

Y. Fily, A. Baskaran, and M. F. Hagan, Dynamics of self-propelled particles under strong confinement, Soft Matter, vol.28, issue.30, p.5609, 2014.
DOI : 10.1017/CBO9780511606014
URL : http://arxiv.org/pdf/1402.5583