E. Scheer, P. Joyez, D. Esteve, C. Urbina, and M. H. Devoret, Conduction Channel Transmissions of Atomic-Size Aluminum Contacts, Physical Review Letters, vol.78, issue.18, p.3535, 1997.
DOI : 10.1103/PhysRevLett.78.3535

Y. Nazarov and Y. M. Blanter, Quantum transport : introduction to nanoscience, 2009.
DOI : 10.1017/CBO9780511626906

R. Cron, M. F. Goffman, D. Esteve, and C. Urbina, Multiple-Charge-Quanta Shot Noise in Superconducting Atomic Contacts, Physical Review Letters, vol.86, issue.18, p.4104, 2001.
DOI : 10.1103/PhysRevLett.86.4104

L. Bretheau, Ç. Ö. Girit, L. Tosi, M. Goffman, P. Joyez et al., Superconducting quantum point contacts, Comptes Rendus Physique, vol.13, issue.1, p.89, 2012.
DOI : 10.1016/j.crhy.2011.12.006
URL : http://arxiv.org/abs/1201.4739

A. A. Golubov, M. Yu, and E. Kupriyanov, The current-phase relation in Josephson junctions, Reviews of Modern Physics, vol.76, issue.2, p.411, 2004.
DOI : 10.1103/RevModPhys.76.411

C. W. Beenakker and H. Van-houten, Josephson current through a superconducting quantum point contact shorter than the coherence length, Physical Review Letters, vol.66, issue.23, p.3056, 1991.
DOI : 10.1103/PhysRevLett.66.3056

L. Bretheau, Ç. Ö. Girit, H. Pothier, D. Esteve, and C. Urbina, Exciting Andreev pairs in a superconducting atomic contact, Nature, vol.336, issue.7458, p.312, 2013.
DOI : 10.1038/nature12315
URL : https://hal.archives-ouvertes.fr/hal-00823378

F. S. Bergeret, P. Virtanen, T. T. Heikkilä, and J. C. Cuevas, Theory of Microwave-Assisted Supercurrent in Quantum Point Contacts, Physical Review Letters, vol.105, issue.11, p.117001, 2010.
DOI : 10.1103/PhysRevLett.105.117001

F. S. Bergeret, P. Virtanen, A. Ozaeta, T. T. Heikkilä, and J. C. Cuevas, Supercurrent and Andreev bound state dynamics in superconducting quantum point contacts under microwave irradiation, Physical Review B, vol.84, issue.5, p.54504, 2011.
DOI : 10.1103/PhysRevB.84.054504
URL : http://arxiv.org/abs/1105.1016

F. Kos, S. E. Nigg, and L. I. Glazman, Frequency-dependent admittance of a short superconducting weak link, Physical Review B, vol.87, issue.17, p.174521, 2013.
DOI : 10.1103/PhysRevB.87.174521

M. Zgirski, L. Bretheau, Q. Le-masne, H. Pothier, D. Esteve et al., Evidence for Long-Lived Quasiparticles Trapped in Superconducting Point Contacts, Physical Review Letters, vol.106, issue.25, p.257003, 2011.
DOI : 10.1103/PhysRevLett.106.257003
URL : https://hal.archives-ouvertes.fr/hal-00595339

D. A. Ivanov and M. V. Feigel-'man, Two-level Hamiltonian of a superconducting quantum point contact, Physical Review B, vol.59, issue.13, p.8444, 1999.
DOI : 10.1103/PhysRevB.59.8444

M. A. Desposito and A. L. Yeyati, Controlled dephasing of Andreev states in superconducting quantum point contacts, Physical Review B, vol.64, issue.14, p.140511, 2001.
DOI : 10.1103/PhysRevB.64.140511

A. Zazunov, V. S. Shumeiko, E. N. Bratus-', J. Lantz, and G. Wendin, Andreev Level Qubit, Physical Review Letters, vol.90, issue.8, p.87003, 2003.
DOI : 10.1103/PhysRevLett.90.087003

A. Zazunov, V. S. Shumeiko, G. Wendin, and E. N. Bratus, Dynamics and phonon-induced decoherence of Andreev level qubit, Physical Review B, vol.71, issue.21, p.214505, 2005.
DOI : 10.1103/PhysRevB.71.214505
URL : http://arxiv.org/abs/cond-mat/0404656

N. M. Chtchelkatchev and Y. V. Nazarov, Andreev Quantum Dots for Spin Manipulation, Physical Review Letters, vol.90, issue.22, p.226806, 2003.
DOI : 10.1103/PhysRevLett.90.226806
URL : http://arxiv.org/abs/cond-mat/0207684

J. Michelsen, V. S. Shumeiko, and G. Wendin, Manipulation with Andreev states in spin active mesoscopic Josephson junctions, Physical Review B, vol.77, issue.18, p.184506, 2008.
DOI : 10.1103/PhysRevB.77.184506

A. Blais, R. Huang, A. Wallraff, S. M. Girvin, and R. J. Schoelkopf, Cavity quantum electrodynamics for superconducting electrical circuits: An architecture for quantum computation, Physical Review A, vol.69, issue.6, p.62320, 2004.
DOI : 10.1103/PhysRevA.69.062320
URL : http://arxiv.org/abs/cond-mat/0402216

A. Blais, J. Gambetta, 1. Wallraff, D. I. Schuster, S. M. Girvin et al., Quantum-information processing with circuit quantum electrodynamics, Physical Review A, vol.75, issue.3, p.32329, 2007.
DOI : 10.1103/PhysRevA.75.032329
URL : http://arxiv.org/abs/cond-mat/0612038

G. Romero, I. Lizuain, V. S. Shumeiko, E. Solano, and F. S. Bergeret, Circuit quantum electrodynamics with a superconducting quantum point contact, Physical Review B, vol.85, issue.18, p.180506, 2012.
DOI : 10.1103/PhysRevB.85.180506
URL : http://arxiv.org/abs/1202.5507

R. Barends, J. Wenner, M. Lenander, Y. Chen, R. C. Bialczak et al., Minimizing quasiparticle generation from stray infrared light in superconducting quantum circuits, Applied Physics Letters, vol.99, issue.11, p.113507, 2011.
DOI : 10.1063/1.3638063

A. D. Córcoles, J. M. Chow, J. M. Gambetta, C. Rigetti, J. R. Rozen et al., Protecting superconducting qubits from radiation, Applied Physics Letters, vol.99, issue.18, p.181906, 2011.
DOI : 10.1063/1.3658630

K. J. Franke, G. Schulze, and J. I. , Competition of Superconducting Phenomena and Kondo Screening at the Nanoscale, Science, vol.332, issue.6032, pp.940-944, 2011.
DOI : 10.1126/science.1202204

C. Caroli, P. G. De-gennes, and J. Matricon, Bound Fermion states on a vortex line in a type II superconductor, Physics Letters, vol.9, issue.4, p.307, 1964.
DOI : 10.1016/0031-9163(64)90375-0

C. W. Beenakker and H. Van-houten, Josephson current through a superconducting quantum point contact shorter than the coherence length, Physical Review Letters, vol.66, issue.23, p.3056, 1991.
DOI : 10.1103/PhysRevLett.66.3056

M. A. Despósito and A. L. Yeyati, Controlled dephasing of Andreev states in superconducting quantum point contacts, Physical Review B, vol.64, issue.14, p.140511, 2001.
DOI : 10.1103/PhysRevB.64.140511

A. Zazunov, V. S. Shumeiko, E. N. Bratus-', J. Lantz, and &. G. Wendin, Andreev Level Qubit, Physical Review Letters, vol.90, issue.8, p.87003, 2003.
DOI : 10.1103/PhysRevLett.90.087003

M. Nikolai, Y. V. Chtchelkatchev, and . Nazarov, Andreev Quantum Dots for Spin Manipulation, Phys. Rev. Lett, vol.90, p.226806, 2003.

A. Zazunov, V. S. Shumeiko, G. Wendin, and E. N. , Dynamics and phonon-induced decoherence of Andreev level qubit, Physical Review B, vol.71, issue.21, p.214505, 2005.
DOI : 10.1103/PhysRevB.71.214505

C. Padurariu and Y. V. Nazarov, Spin blockade qubit in a superconducting junction, EPL (Europhysics Letters), vol.100, issue.5, p.57006, 2012.
DOI : 10.1209/0295-5075/100/57006
URL : http://arxiv.org/abs/1210.5151

J. Pillet, Andreev bound states in supercurrent-carrying carbon nanotubes revealed, Nature Physics, vol.49, issue.12, p.965, 2010.
DOI : 10.1103/PhysRevB.79.134518

M. Zgirski, Evidence for Long-Lived Quasiparticles Trapped in Superconducting Point Contacts, Physical Review Letters, vol.106, issue.25, p.257003, 2011.
DOI : 10.1103/PhysRevLett.106.257003
URL : https://hal.archives-ouvertes.fr/hal-00595339

E. M. Levenson-falk, F. Kos, R. Vijay, L. Glazman, and I. Siddiqi, Single-Quasiparticle Trapping in Aluminum Nanobridge Josephson Junctions, Physical Review Letters, vol.112, issue.4, p.47002, 2014.
DOI : 10.1103/PhysRevLett.112.047002
URL : http://arxiv.org/abs/1310.6996

A. Zazunov, A. Brunetti, A. L. Yeyati, and R. Egger, Quasiparticle trapping, Andreev level population dynamics, and charge imbalance in superconducting weak links, Physical Review B, vol.90, issue.10, p.104508, 2014.
DOI : 10.1103/PhysRevB.90.104508
URL : http://arxiv.org/abs/1407.7991

L. Bretheau, Ç. Ö. Girit, H. Pothier, D. Esteve, and &. C. Urbina, Exciting Andreev pairs in a superconducting atomic contact, Nature, vol.336, issue.7458, p.312, 2013.
DOI : 10.1038/nature12315
URL : https://hal.archives-ouvertes.fr/hal-00823378

L. Bretheau, Ç. Ö. Girit, C. Urbina, D. Esteve, and H. Pothier, Supercurrent Spectroscopy of Andreev States, Physical Review X, vol.3, issue.4, p.41034, 2013.
DOI : 10.1103/PhysRevX.3.041034
URL : https://hal.archives-ouvertes.fr/cea-01479024

E. Scheer, P. Joyez, D. Esteve, C. Urbina, and M. H. Devoret, Conduction Channel Transmissions of Atomic-Size Aluminum Contacts, Physical Review Letters, vol.78, issue.18, p.3535, 1997.
DOI : 10.1103/PhysRevLett.78.3535

J. M. Van-ruitenbeek, Adjustable nanofabricated atomic size contacts, Review of Scientific Instruments, vol.67, issue.1, 1996.
DOI : 10.1063/1.1146558

C. Janvier, Superconducting atomic contacts inductively coupled to a microwave resonator, Journal of Physics: Condensed Matter, vol.26, issue.47, p.474208, 2014.
DOI : 10.1088/0953-8984/26/47/474208
URL : https://hal.archives-ouvertes.fr/cea-01384806

A. Wallraff, Strong coupling of a single photon to a superconducting qubit using circuit quantum electrodynamics, Nature, vol.431, issue.7005, p.162, 2004.
DOI : 10.1038/22275

G. Romero, I. Lizuain, V. S. Shumeiko, E. Solano, and F. S. Bergeret, Circuit quantum electrodynamics with a superconducting quantum point contact, Physical Review B, vol.85, issue.18, p.180506, 2012.
DOI : 10.1103/PhysRevB.85.180506

D. G. Olivares, Dynamics of quasiparticle trapping in Andreev levels, Physical Review B, vol.89, issue.10, p.104504, 2014.
DOI : 10.1103/PhysRevB.89.104504
URL : https://hal.archives-ouvertes.fr/cea-01384760

R. Vijay, D. H. Slichter, and I. Siddiqi, Observation of Quantum Jumps in a Superconducting Artificial Atom, Physical Review Letters, vol.106, issue.11, p.110502, 2011.
DOI : 10.1103/PhysRevLett.106.110502

M. Greenfeld, D. S. Pavlichin, H. Mabuchi, and D. Herschlag, Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data, PLoS ONE, vol.286, issue.2, p.30024, 2012.
DOI : 10.1371/journal.pone.0030024.s001

J. M. Martinis, M. Ansmann, and J. Aumentado, Energy Decay in Superconducting Josephson-Junction Qubits from Nonequilibrium Quasiparticle Excitations, Physical Review Letters, vol.103, issue.9, p.97002, 2009.
DOI : 10.1103/PhysRevLett.103.097002

G. Catelani, R. J. Schoelkopf, M. H. Devoret, and &. L. Glazman, Relaxation and frequency shifts induced by quasiparticles in superconducting qubits, Physical Review B, vol.84, issue.6, p.64517, 2011.
DOI : 10.1103/PhysRevB.84.064517
URL : http://arxiv.org/abs/1106.0829

F. Kos, S. E. Nigg, and L. I. Glazman, Frequency-dependent admittance of a short superconducting weak link, Physical Review B, vol.87, issue.17, p.174521, 2013.
DOI : 10.1103/PhysRevB.87.174521

I. M. Pop, Coherent suppression of electromagnetic dissipation due to superconducting quasiparticles, Nature, vol.87, issue.7496, p.369, 2014.
DOI : 10.1038/nature13017

C. Wang, Measurement and control of quasiparticle dynamics in a superconducting qubit, Nature Communications, vol.4, p.5836, 2014.
DOI : 10.1103/PhysRevB.79.174512

Y. Makhlin and A. Shnirman, Dephasing of Solid-State Qubits at Optimal Points, Physical Review Letters, vol.92, issue.17, p.178301, 2004.
DOI : 10.1103/PhysRevLett.92.178301

J. Clarke and F. K. Wilhelm, Superconducting quantum bits, Nature, vol.31, issue.7198, p.1031, 2008.
DOI : 10.1038/nature07128

U. Vool, Non-Poissonian Quantum Jumps of a Fluxonium Qubit due to Quasiparticle Excitations, Physical Review Letters, vol.113, issue.24, p.247001, 2014.
DOI : 10.1103/PhysRevLett.113.247001
URL : https://hal.archives-ouvertes.fr/hal-01099948

D. Ristè, Millisecond charge-parity fluctuations and induced decoherence in a superconducting transmon qubit, Nature Communications, vol.86, 1913.
DOI : 10.1038/ncomms2936

P. J. De and . Visser, Number Fluctuations of Sparse Quasiparticles in a Superconductor, Phys. Rev. Lett, vol.106, p.167004, 2011.

W. Chang, V. E. Manucharyan, T. S. Jespersen, J. Nygård, and C. M. Marcus, Tunneling Spectroscopy of Quasiparticle Bound States in a Spinful Josephson Junction, Physical Review Letters, vol.110, issue.21, p.217005, 2013.
DOI : 10.1103/PhysRevLett.110.217005

V. Mourik, Signatures of Majorana Fermions in Hybrid Superconductor-Semiconductor Nanowire Devices, Science, vol.336, issue.6084, p.1003, 2012.
DOI : 10.1126/science.1222360

D. Chevallier, P. Simon, and C. Bena, From Andreev bound states to Majorana fermions in topological wires on superconducting substrates: A story of mutation, Physical Review B, vol.88, issue.16, p.165401, 2013.
DOI : 10.1103/PhysRevB.88.165401

D. S. Holmes, A. L. Ripple, and M. A. Manheimer, Energy-Efficient Superconducting Computing—Power Budgets and Requirements, IEEE Transactions on Applied Superconductivity, vol.23, issue.3, pp.1701610-185, 2013.
DOI : 10.1109/TASC.2013.2244634

M. H. Devoret and R. J. Schoelkopf, Superconducting Circuits for Quantum Information: An Outlook, Science, vol.339, issue.6124, pp.1169-185, 2013.
DOI : 10.1126/science.1231930

A. A. Houck, H. E. Türeci, and J. Koch, On-chip quantum simulation with superconducting circuits, Nature Physics, vol.8, issue.4, p.292, 2012.
DOI : 10.1103/PhysRevLett.107.240501

J. Zmuidzinas, Superconducting Microresonators: Physics and Applications, Annual Review of Condensed Matter Physics, vol.3, issue.1, p.185, 2012.
DOI : 10.1146/annurev-conmatphys-020911-125022

G. N. Gol-'tsman, Picosecond superconducting single-photon optical detector, Appl. Phys. Lett, vol.79, issue.1, pp.705-185, 2001.

B. Josephson, Possible new effects in superconductive tunnelling, Physics Letters, vol.1, issue.7, pp.251-185, 1962.
DOI : 10.1016/0031-9163(62)91369-0

A. F. Andreev, The thermal conductivity of the intermediate state in superconductors, Sov. Phys. JETP, vol.19, issue.2, pp.1228-186, 1964.

C. W. Beenakker and H. Van-houten, Josephson current through a superconducting quantum point contact shorter than the coherence length, Physical Review Letters, vol.66, issue.23, pp.15-17, 1991.
DOI : 10.1103/PhysRevLett.66.3056

R. Cron, Atomic contacts: a test-bed for mesoscopic physics URL https, p.186, 2001.

M. Chauvin, Josephson effect in atomic contacts URL https, p.186, 2005.

B. Huard, Interactions between electrons, mesoscopic Josephson effect and asymmetric current fluctuations URL https, p.186, 2006.
DOI : 10.1051/anphys:2007002

L. Masne and Q. , Asymmetric current fluctuations and Andreev states probed with a Josephson junction URL https, p.186, 2009.

A. Zazunov, V. S. Shumeiko, E. N. Bratus, J. Lantz, and G. Wendin, Andreev Level Qubit, Physical Review Letters, vol.90, issue.8, pp.87003-87033, 2003.
DOI : 10.1103/PhysRevLett.90.087003

A. Zazunov, V. S. Shumeiko, G. Wendin, and E. N. Bratus-;, Dynamics and phonon-induced decoherence of Andreev level qubit, Physical Review B, vol.71, issue.21, pp.214505-214531, 2005.
DOI : 10.1103/PhysRevB.71.214505

C. Padurariu and Y. Nazarov, Spin blockade qubit in a superconducting junction, EPL (Europhysics Letters), vol.100, issue.5, pp.57006-186, 2012.
DOI : 10.1209/0295-5075/100/57006

L. Bretheau, Localized excitations in superconducting atomic contacts: probing the Andreev doublet Ecole Polytechnique X (2013) URL https, pp.25-93

J. Pillet, Tunneling spectroscopy of the Andreev Bound States in a Carbon Nanotube URL https, p.186, 2011.

E. J. Lee, Spin-resolved Andreev levels and parity crossings in hybrid superconductor???semiconductor nanostructures, Nature Nanotechnology, vol.49, issue.1, pp.79-186, 2014.
DOI : 10.1021/nl072024a
URL : http://arxiv.org/abs/1302.2611

F. Chiodi, Probing the dynamics of Andreev states in a coherent Normal/Superconducting ring, Scientific Reports, vol.10, issue.1, p.186, 2011.
DOI : 10.1088/1367-2630/10/9/093005

B. Dassonneville, M. Ferrier, S. Guéron, and H. Bouchiat, Dissipation and Supercurrent Fluctuations in a Diffusive Normal-Metal???Superconductor Ring, Physical Review Letters, vol.110, issue.21, pp.217001-186, 2013.
DOI : 10.1103/PhysRevLett.110.217001

N. Agraït, A. L. Yeyati, and J. M. Van-ruitenbeek, Quantum properties of atomic-sized conductors, Physics Reports, vol.377, issue.2-3, pp.51-52, 2003.
DOI : 10.1016/S0370-1573(02)00633-6

S. Haroche, J. Raimond, A. Blais, R. Huang, A. Wallraff et al., Exploring the quantum: atoms, cavities , and photons Exploring the quantum: atoms, cavities, and photons Cavity quantum electrodynamics for superconducting electrical circuits: An architecture for quantum computation, Phys. Rev. A, vol.2, issue.186, pp.158-62320, 2004.
DOI : 10.1093/acprof:oso/9780198509141.001.0001

I. Chiorescu, Coherent dynamics of a flux qubit coupled to a harmonic oscillator, Nature, vol.431, issue.7005, 2004.
DOI : 10.1126/science.290.5492.773

A. Wallraff, Strong coupling of a single photon to a superconducting qubit using circuit quantum electrodynamics, Nature, vol.431, issue.7005, p.59, 2004.
DOI : 10.1038/22275

Y. Kubo, Strong Coupling of a Spin Ensemble to a Superconducting Resonator, Physical Review Letters, vol.105, issue.14, p.140502, 2010.
DOI : 10.1103/PhysRevLett.105.140502
URL : https://hal.archives-ouvertes.fr/hal-00710240

K. D. Petersson, Circuit quantum electrodynamics with a spin qubit, Nature, vol.84, issue.7420, 2012.
DOI : 10.1038/nature11559

J. J. Viennot, M. C. Dartiailh, A. Cottet, and T. Kontos, Coherent coupling of a single spin to microwave cavity photons, Science, vol.349, issue.6246, p.151, 2015.
DOI : 10.1126/science.aaa3786
URL : https://hal.archives-ouvertes.fr/hal-01310665

T. Frey, Dipole Coupling of a Double Quantum Dot to a Microwave Resonator, Physical Review Letters, vol.108, issue.4, p.46807, 2012.
DOI : 10.1103/PhysRevLett.108.046807

J. Bochmann, A. Vainsencher, D. D. Awschalom, and A. N. Cleland, Nanomechanical coupling between microwave and optical photons, Nature Physics, vol.459, issue.11, p.712, 2013.
DOI : 10.1038/nphys2748

N. M. Chtchelkatchev and Y. Nazarov, Andreev Quantum Dots for Spin Manipulation, Physical Review Letters, vol.90, issue.22, pp.226806-187, 2003.
DOI : 10.1103/PhysRevLett.90.226806
URL : http://arxiv.org/abs/cond-mat/0207684

J. Lantz, V. S. Shumeiko, E. Bratus, and G. Wendin, Flux qubit with a quantum point contact, Physica C: Superconductivity, vol.368, issue.1-4, pp.315-188, 2002.
DOI : 10.1016/S0921-4534(01)01188-1

M. Devoret, A. Wallraff, and J. Martinis, Superconducting qubits: A short review, arXiv, issue.3, 2004.

E. Scheer, P. Joyez, D. Esteve, C. Urbina, and M. Devoret, Conduction Channel Transmissions of Atomic-Size Aluminum Contacts, Physical Review Letters, vol.78, issue.18, pp.72-73, 1997.
DOI : 10.1103/PhysRevLett.78.3535
URL : http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-25334

J. K. Gimzewski and R. Möller, Transition from the tunneling regime to point contact studied using scanning tunneling microscopy, Physical Review B, vol.36, issue.2, pp.1284-189, 1987.
DOI : 10.1103/PhysRevB.36.1284

M. L. Trouwborst, S. J. Van-der-molen, and B. J. Van-wees, The role of Joule heating in the formation of nanogaps by electromigration, Journal of Applied Physics, vol.99, issue.11
DOI : 10.1063/1.2203410

C. Zhou, C. J. Muller, M. R. Deshpande, J. W. Sleight, and M. A. Reed, Microfabrication of a mechanically controllable break junction in silicon, Applied Physics Letters, vol.67, issue.8, pp.1160-189, 1995.
DOI : 10.1063/1.114994

J. M. Van-ruitenbeek, Adjustable nanofabricated atomic size contacts, Review of Scientific Instruments, vol.67, issue.1, p.189, 1996.
DOI : 10.1063/1.1146558

G. Romero, I. Lizuain, V. S. Shumeiko, E. Solano, and F. S. Bergeret, Circuit quantum electrodynamics with a superconducting quantum point contact, Physical Review B, vol.85, issue.18, pp.180506-190, 2012.
DOI : 10.1103/PhysRevB.85.180506

H. Paik, Observation of High Coherence in Josephson Junction Qubits Measured in a Three-Dimensional Circuit QED Architecture, Physical Review Letters, vol.107, issue.24, pp.240501-240532, 2011.
DOI : 10.1103/PhysRevLett.107.240501

M. Stern, Flux Qubits with Long Coherence Times for Hybrid Quantum Circuits, Physical Review Letters, vol.113, issue.12, pp.123601-123632, 2014.
DOI : 10.1103/PhysRevLett.113.123601
URL : https://hal.archives-ouvertes.fr/cea-01384637

J. Gambetta, Quantum trajectory approach to circuit QED: Quantum jumps and the Zeno effect, Physical Review A, vol.77, issue.1, pp.12112-195, 2008.
DOI : 10.1103/PhysRevA.77.012112

D. I. Schuster, Resolving photon number states in a superconducting circuit, Nature, vol.75, issue.7127, 0195.
DOI : 10.1038/nature05461

M. Zgirski, Evidence for Long-Lived Quasiparticles Trapped in Superconducting Point Contacts, Physical Review Letters, vol.106, issue.25, pp.257003-257030, 2011.
DOI : 10.1103/PhysRevLett.106.257003
URL : https://hal.archives-ouvertes.fr/hal-00595339

O. Naaman and J. Aumentado, Time-domain measurements of quasiparticle tunneling rates in a single-Cooper-pair transistor, Physical Review B, vol.73, issue.17, p.172504, 0196.
DOI : 10.1103/PhysRevB.73.172504

K. J. Stone, Real time quasiparticle tunneling measurements on an illuminated quantum capacitance detector, Applied Physics Letters, vol.100, issue.26, p.263509, 0196.
DOI : 10.1063/1.4731880

U. Vool, Non-Poissonian Quantum Jumps of a Fluxonium Qubit due to Quasiparticle Excitations, Physical Review Letters, vol.113, issue.24, pp.247001-196, 2014.
DOI : 10.1103/PhysRevLett.113.247001
URL : https://hal.archives-ouvertes.fr/hal-01099948

J. M. Martinis, M. Ansmann, and J. Aumentado, Energy Decay in Superconducting Josephson-Junction Qubits from Nonequilibrium Quasiparticle Excitations, Physical Review Letters, vol.103, issue.9, p.97002, 0196.
DOI : 10.1103/PhysRevLett.103.097002

I. M. Pop, Coherent suppression of electromagnetic dissipation due to superconducting quasiparticles Observation of parity-induced suppression of Josephson tunneling in the superconducting single electron transistor, Nature Phys. Rev. Lett, vol.508, issue.135, pp.196-2458, 1994.

M. D. Shaw, R. M. Lutchyn, P. Delsing, and P. M. Echternach, Kinetics of nonequilibrium quasiparticle tunneling in superconducting charge qubits, Physical Review B, vol.78, issue.2, pp.24503-196, 2008.
DOI : 10.1103/PhysRevB.78.024503

J. Wenner, Excitation of Superconducting Qubits from Hot Nonequilibrium Quasiparticles, Physical Review Letters, vol.110, issue.15, pp.150502-196, 2013.
DOI : 10.1103/PhysRevLett.110.150502

M. Greenfeld, D. S. Pavlichin, H. Mabuchi, and D. Herschlag, Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data, PLoS ONE, vol.286, issue.2, pp.30024-179, 2012.
DOI : 10.1371/journal.pone.0030024.s001

S. Gammelmark, K. Molmer, W. Alt, T. Kampschulte, and D. Meschede, Hidden Markov model of atomic quantum jump dynamics in an optically probed cavity, Physical Review A, vol.89, issue.4, pp.43839-197, 2014.
DOI : 10.1103/PhysRevA.89.043839

M. C. Koops, G. V. Van-duyneveldt, and R. De-bruyn-ouboter, Direct Observation of the Current-Phase Relation of an Adjustable Superconducting Point Contact, Physical Review Letters, vol.77, issue.12, pp.2542-2562, 1996.
DOI : 10.1103/PhysRevLett.77.2542

D. Rocca and M. L. , Measurement of the Current-Phase Relation of Superconducting Atomic Contacts, Physical Review Letters, vol.99, issue.12, pp.127005-127026, 2007.
DOI : 10.1103/PhysRevLett.99.127005
URL : https://hal.archives-ouvertes.fr/hal-00186792

J. Basset, Joint measurement of current-phase relations and transport properties of hybrid junctions using a three junctions superconducting quantum interference device, Journal of Applied Physics, vol.116, issue.2, pp.24311-24332, 2014.
DOI : 10.1063/1.4887354

R. Delagrange, quantum transition in a carbon nanotube Josephson junction: Universal phase dependence and orbital degeneracy, Physical Review B, vol.93, issue.19, pp.195437-195458, 2016.
DOI : 10.1103/PhysRevB.93.195437

T. Yokoyama, M. Eto, and Y. Nazarov, Anomalous Josephson effect induced by spin-orbit interaction and Zeeman effect in semiconductor nanowires, Physical Review B, vol.89, issue.19, pp.195407-195428, 2014.
DOI : 10.1103/PhysRevB.89.195407

T. Klapwijk, G. Blonder, and M. Tinkham, Explanation of subharmonic energy gap structure, Phys. B, vol.109, pp.1657-1679, 1982.

L. D. Landau, A theory of energy transer II, Phys.Z. Sowjetunion, vol.2, pp.46-68, 1932.

C. Zener, Non-Adiabatic Crossing of Energy Levels, Proc. R. Soc A, pp.696-718, 1932.
DOI : 10.1098/rspa.1932.0165

M. Chauvin, Crossover from Josephson to Multiple Andreev Reflection Currents in Atomic Contacts, Physical Review Letters, vol.99, issue.6, pp.67008-67030, 2007.
DOI : 10.1103/PhysRevLett.99.067008

E. J. Lee, Zero-Bias Anomaly in a Nanowire Quantum Dot Coupled to Superconductors, Physical Review Letters, vol.109, issue.18, pp.186802-186824, 2012.
DOI : 10.1103/PhysRevLett.109.186802

T. Dirks, Transport through Andreev bound states in a graphene quantum dot, Nature Physics, vol.25, issue.5, pp.25-47, 2010.
DOI : 10.1038/nphys1911

R. S. Deacon, Tunneling Spectroscopy of Andreev Energy Levels in a Quantum Dot Coupled to a Superconductor, Physical Review Letters, vol.104, issue.7, pp.76805-76827, 2010.
DOI : 10.1103/PhysRevLett.104.076805

L. Bretheau, Ç. Ö. Girit, H. Pothier, D. Esteve, and C. Urbina, Exciting Andreev pairs in a superconducting atomic contact, Nature, vol.336, issue.7458, pp.312-335, 2013.
DOI : 10.1038/nature12315
URL : https://hal.archives-ouvertes.fr/hal-00823378

M. H. Devoret, Effect of the electromagnetic environment on the Coulomb blockade in ultrasmall tunnel junctions, Physical Review Letters, vol.64, issue.15, pp.4559-4582, 1990.
DOI : 10.1103/PhysRevLett.64.1824

A. Geresdi, Private communication, p.153, 2016.

D. G. Olivares, Dynamics of quasiparticle trapping in Andreev levels, Physical Review B, vol.89, issue.10, pp.136-145, 2014.
DOI : 10.1103/PhysRevB.89.104504
URL : https://hal.archives-ouvertes.fr/cea-01384760

E. M. Levenson-falk, F. Kos, R. Vijay, L. Glazman, and I. Siddiqi, Single-Quasiparticle Trapping in Aluminum Nanobridge Josephson Junctions, Physical Review Letters, vol.112, issue.4, pp.47002-47028, 2014.
DOI : 10.1103/PhysRevLett.112.047002

A. P. Higginbotham, Parity lifetime of bound states in a proximitized semiconductor nanowire, Nature Physics, vol.90, issue.12, pp.1017-1043, 2015.
DOI : 10.1038/nphys3461

A. A. Golubov, M. Y. Kupriyanov, and E. Il-'ichev, The current-phase relation in Josephson junctions, Reviews of Modern Physics, vol.76, issue.2, pp.411-438, 2004.
DOI : 10.1103/RevModPhys.76.411

M. Tinkham, Introduction to superconductivity: second edition, p.29, 2004.

A. Anthore, J. M. Martinis, S. Nam, J. Aumentado, and C. Urbina, Decoherence mechanisms in mesoscopic conductors URL https://tel.archives-ouvertes.fr/tel-00003518v1 Rabi oscillations in a large Josephson-junction qubit, Phys. Rev. Lett, vol.28, issue.89, pp.93-117901, 2002.

Y. Nakamura, Y. A. Pashkin, and J. S. Tsai, Coherent control of macroscopic quantum states in a single-Cooper-pair box, Nature, vol.398, issue.6730, pp.786-816, 1999.
DOI : 10.1038/19718

D. Vion, Manipulating the Quantum State of an Electrical Circuit, Science, vol.296, issue.5569, p.31, 2002.
DOI : 10.1126/science.1069372
URL : https://hal.archives-ouvertes.fr/hal-00021251

J. E. Mooij, T. P. Orlando, L. Levitov, and L. Tian, Josephson Persistent-Current Qubit, Science, vol.285, issue.5430, pp.1036-1067, 1999.
DOI : 10.1126/science.285.5430.1036
URL : https://www.rug.nl/research/portal/files/3156486/1999ScienceMooij.pdf

I. Chiorescu, Y. Nakamura, C. J. Harmans, and J. Mooij, Coherent Quantum Dynamics of a Superconducting Flux Qubit, Science, vol.299, issue.5614, pp.1869-1900, 2003.
DOI : 10.1126/science.1081045

J. Koch, Charge-insensitive qubit design derived from the Cooper pair box, Physical Review A, vol.76, issue.4, pp.42319-42350, 2007.
DOI : 10.1103/PhysRevA.76.042319

C. Rigetti, Superconducting qubit in a waveguide cavity with a coherence time approaching 0.1 ms, Physical Review B, vol.86, issue.10, pp.100506-100537, 2012.
DOI : 10.1103/PhysRevB.86.100506

E. Jeffrey, Fast Accurate State Measurement with Superconducting Qubits, Physical Review Letters, vol.112, issue.19, pp.31-47, 2014.
DOI : 10.1103/PhysRevLett.112.190504

D. Lange and G. , Realization of Microwave Quantum Circuits Using Hybrid Superconducting-Semiconducting Nanowire Josephson Elements, Physical Review Letters, vol.115, issue.12, pp.127002-127033, 2015.
DOI : 10.1103/PhysRevLett.115.127002

T. W. Larsen, Semiconductor-Nanowire-Based Superconducting Qubit, Physical Review Letters, vol.115, issue.12, pp.127001-127032, 2015.
DOI : 10.1103/PhysRevLett.115.127001
URL : http://arxiv.org/abs/1503.08339

J. Kelly, State preservation by repetitive error detection in a superconducting quantum circuit, Nature, vol.113, issue.7541, p.59, 2015.
DOI : 10.1038/nature14270

J. Bylander, Noise spectroscopy through dynamical decoupling with a superconducting flux qubit, Nature Physics, vol.7, issue.7, pp.565-98, 2011.
DOI : 10.1103/PhysRevB.70.064517

S. Deléglise, Reconstruction of non-classical cavity field states with snapshots of their decoherence, Nature, vol.32, issue.7212, pp.510-544, 2008.
DOI : 10.1038/nature07288

A. Megrant, Planar superconducting resonators with internal quality factors above one million, Applied Physics Letters, vol.100, issue.11, pp.113510-113546, 2012.
DOI : 10.1063/1.3693409

E. T. Jaynes and F. W. Cummings, Comparison of quantum and semiclassical radiation theories with application to the beam maser, Proc. IEEE 51, pp.89-129, 1963.
DOI : 10.1109/PROC.1963.1664

A. N. Omelyanchouk, S. N. Shevchenko, Y. S. Greenberg, O. Astafiev, and E. Il-'ichev, Quantum behavior of a flux qubit coupled to a resonator, Low Temperature Physics, vol.36, issue.10, pp.893-934, 2010.
DOI : 10.1063/1.3515520

V. Schmitt, Multiplexed readout of transmon qubits with Josephson bifurcation amplifiers, Physical Review A, vol.90, issue.6, pp.62333-62380, 2014.
DOI : 10.1103/PhysRevA.90.062333
URL : https://hal.archives-ouvertes.fr/cea-01384732

A. Palacios-laloy, Superconducting qubit in a resonator : test of the Leggett-Garg inequality and single-shot readout URL https, 2010.

J. Moreland and J. W. Ekin, Electron tunneling experiments using Nb???Sn ??????break?????? junctions, Journal of Applied Physics, vol.58, issue.10, pp.3888-51, 1985.
DOI : 10.1063/1.335608

A. N. Cleland, [101] DuPont. Summary of properties for Kapton polyimide films, Foundations of Nanomechanics Tech. Rep, vol.53, issue.170, p.171, 2003.

R. Simons, Coplanar waveguide circuits, components, and systems, p.58, 2001.
DOI : 10.1002/0471224758

M. Sandberg, Radiation-suppressed superconducting quantum bit in a planar geometry, Applied Physics Letters, vol.102, issue.7, p.59, 2013.
DOI : 10.1063/1.4792698

S. S. Gevorgian, T. Martinsson, P. L. Linnér, and E. L. Kollberg, CAD models for multilayered substrate interdigital capacitors, IEEE Transactions on Microwave Theory and Techniques, vol.44, issue.6, pp.896-60, 1996.
DOI : 10.1109/22.506449

G. Ithier, Decoherence in a superconducting quantum bit circuit, Physical Review B, vol.72, issue.13, pp.134519-108, 1977.
DOI : 10.1103/PhysRevB.72.134519

M. A. Despósito and A. Levy-yeyati, Controlled dephasing of Andreev states in superconducting quantum point contacts, Physical Review B, vol.64, issue.14, pp.140511-94, 2001.
DOI : 10.1103/PhysRevB.64.140511

H. Y. Carr and E. M. Purcell, Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments, Physical Review, vol.94, issue.3, pp.630-99, 1954.
DOI : 10.1103/PhysRev.94.630

S. Meiboom and D. Gill, Modified Spin???Echo Method for Measuring Nuclear Relaxation Times, Review of Scientific Instruments, vol.29, issue.8, pp.688-99, 1958.
DOI : 10.1063/1.1716296

?. Cywi?ski, R. M. Lutchyn, C. P. Nave, and S. Das-sarma, How to enhance dephasing time in superconducting qubits, Physical Review B, vol.77, issue.17, pp.174509-99, 2008.
DOI : 10.1103/PhysRevB.77.174509

S. Lasic, J. Stepisnik, and A. Mohoric, Displacement power spectrum measurement by CPMG in constant gradient, Journal of Magnetic Resonance, vol.182, issue.2, pp.208-99, 2006.
DOI : 10.1016/j.jmr.2006.06.030

P. Kumar, Origin and suppression of 1/f magnetic flux noise, Arxiv, p.109, 2016.

R. H. Koch, Flicker (1/f) noise in tunnel junction dc SQUIDS, Journal of Low Temperature Physics, vol.38, issue.1-2, pp.207-108, 1983.
DOI : 10.1007/BF00683423

Y. Makhlin and A. Shnirman, Dephasing of Solid-State Qubits at Optimal Points, Physical Review Letters, vol.92, issue.17, pp.178301-109, 2004.
DOI : 10.1103/PhysRevLett.92.178301

R. Wynands and S. Weyers, Atomic fountain clocks, Metrologia, vol.42, issue.3, pp.64-112, 2005.
DOI : 10.1088/0026-1394/42/3/S08

R. J. Glauber, Coherent and Incoherent States of the Radiation Field, Physical Review, vol.131, issue.6, pp.2766-120, 1963.
DOI : 10.1103/PhysRev.131.2766

K. Geerlings, Demonstrating a Driven Reset Protocol for a Superconducting Qubit, Physical Review Letters, vol.110, issue.12, pp.120501-121, 2013.
DOI : 10.1103/PhysRevLett.110.120501

J. R. Johansson, P. D. Nation, and F. Nori, QuTiP: An open-source Python framework for the dynamics of open quantum systems, Computer Physics Communications, vol.183, issue.8, pp.1760-127, 2012.
DOI : 10.1016/j.cpc.2012.02.021

J. R. Johansson, P. D. Nation, and F. Nori, QuTiP 2: A Python framework for the dynamics of open quantum systems, Computer Physics Communications, vol.184, issue.4, pp.1234-127, 2013.
DOI : 10.1016/j.cpc.2012.11.019

M. Boissonneault, J. M. Gambetta, and A. Blais, Dispersive regime of circuit QED: Photon-dependent qubit dephasing and relaxation rates, Physical Review A, vol.79, issue.1, pp.13819-134, 2009.
DOI : 10.1103/PhysRevA.79.013819

W. Nagourney, J. Sandberg, and H. Dehmelt, Shelved optical electron amplifier: Observation of quantum jumps, Physical Review Letters, vol.56, issue.26, pp.2797-135, 1986.
DOI : 10.1103/PhysRevLett.56.2797

A. Delteil, W. B. Gao, P. Fallahi, J. Miguel-sanchez, and A. Imamoglu, Observation of Quantum Jumps of a Single Quantum Dot Spin Using Submicrosecond Single-Shot Optical Readout, Physical Review Letters, vol.112, issue.11, pp.116802-135, 2014.
DOI : 10.1103/PhysRevLett.112.116802

R. Vijay, D. H. Slichter, and I. Siddiqi, Observation of Quantum Jumps in a Superconducting Artificial Atom, Physical Review Letters, vol.106, issue.11, pp.110502-135, 2011.
DOI : 10.1103/PhysRevLett.106.110502

A. Zazunov, A. Brunetti, A. L. Yeyati, and R. Egger, Quasiparticle trapping, Andreev level population dynamics, and charge imbalance in superconducting weak links, Physical Review B, vol.90, issue.10, pp.104508-136, 2014.
DOI : 10.1103/PhysRevB.90.104508

G. Zhu, D. G. Ferguson, V. E. Manucharyan, and J. Koch, Circuit QED with fluxonium qubits: Theory of the dispersive regime, Physical Review B, vol.87, issue.2, pp.24510-149, 2013.
DOI : 10.1103/PhysRevB.87.024510

U. Vool, Suplementary material: Non-poissonian quantum jumps of a fluxonium qubit due to quasiparticle excitations, Phys. Rev. Lett, vol.113, p.149, 2014.

N. Roch, Widely Tunable, Nondegenerate Three-Wave Mixing Microwave Device Operating near the Quantum Limit, Physical Review Letters, vol.108, issue.14, pp.147701-153, 2012.
DOI : 10.1103/PhysRevLett.108.147701
URL : https://hal.archives-ouvertes.fr/hal-00700677

M. R. Delbecq, Photon-mediated interaction between distant quantum dot circuits, Nature Communications, vol.66, pp.1400-151, 2013.
DOI : 10.1038/ncomms2407
URL : https://hal.archives-ouvertes.fr/hal-01310661

V. Ranjan, Clean carbon nanotubes coupled to superconducting impedance-matching circuits, Nature Communications, vol.280, pp.7165-151, 2015.
DOI : 10.1038/ncomms8165
URL : http://doi.org/10.1038/ncomms8165

A. Dewes, Demonstrating quantum speed-up with a two-transmon quantum processor URL https, 2012.

Y. Dappe, C. Urbina, C. Janvier, H. Pothier, and M. Goffman, Transmission fluctuations in an atomic junction : an atomistic study, p.152, 2016.

R. Riwar, M. Houzet, J. S. Meyer, and Y. Nazarov, Multiterminal Josephson junctions as topological materials 153 [133] Chang, W. et al. Hard gap in epitaxial semiconductor-superconductor nanowires, Nat. Commun. Nat. Nanotechnol, vol.7, issue.10, pp.232-153, 2015.
DOI : 10.1038/ncomms11167
URL : http://doi.org/10.1038/ncomms11167

S. M. Albrecht, Exponential protection of zero modes in Majorana islands, Nature, vol.92, issue.7593, p.153, 2016.
DOI : 10.1038/nature17162

C. Li, Magnetic field resistant quantum interferences in Josephson junctions based on bismuth nanowires, Physical Review B, vol.90, issue.24, pp.245427-153, 2014.
DOI : 10.1103/PhysRevB.90.245427
URL : https://hal.archives-ouvertes.fr/in2p3-01115787

B. J. Van-wees, Quantized conductance of point contacts in a two-dimensional electron gas, Physical Review Letters, vol.60, issue.9, pp.848-154, 1988.
DOI : 10.1103/PhysRevLett.60.848

M. Kjaergaard, Transparent Semiconductor-Superconductor Interface and Induced Gap in an Epitaxial Heterostructure Josephson Junction, Physical Review Applied, vol.7, issue.3, p.154, 2016.
DOI : 10.1103/PhysRevApplied.7.034029

B. Béri, J. H. Bardarson, and C. W. Beenakker, Splitting of Andreev levels in a Josephson junction by spin-orbit coupling, Physical Review B, vol.77, issue.4, pp.45311-154, 2008.
DOI : 10.1103/PhysRevB.77.045311

A. A. Reynoso, G. Usaj, C. A. Balseiro, D. Feinberg, and M. Avignon, Spin-orbit-induced chirality of Andreev states in Josephson junctions, Physical Review B, vol.86, issue.21, pp.214519-154, 2012.
DOI : 10.1103/PhysRevB.86.214519
URL : https://hal.archives-ouvertes.fr/hal-00997152

L. Fu and C. L. Kane, Superconducting Proximity Effect and Majorana Fermions at the Surface of a Topological Insulator, Physical Review Letters, vol.100, issue.9, pp.96407-154, 2008.
DOI : 10.1103/PhysRevLett.100.096407

R. M. Lutchyn, J. D. Sau, and S. Das-sarma, Majorana Fermions and a Topological Phase Transition in Semiconductor-Superconductor Heterostructures, Physical Review Letters, vol.105, issue.7, pp.77001-154, 2010.
DOI : 10.1103/PhysRevLett.105.077001

L. Rabiner and B. Juang, An introduction to hidden Markov models, IEEE ASSP Magazine, vol.3, issue.1, p.180, 1986.
DOI : 10.1109/MASSP.1986.1165342

R. Dugad and U. B. Desai, A tutorial on hidden Markov models, Tech. Rep, p.179, 1996.