V. S. Jampani, M. Skarabot, M. Ravnik, S. Copar, S. Zumer et al., Colloidal entanglement in highly twisted chiral nematic colloids: Twisted loops, Hopf links, and trefoil knots, Physical Review E, vol.84, issue.3, p.31703, 2011.
DOI : 10.1051/jphys:01974003503021500

A. Martinez, M. Ravnik, B. Lucero, R. Visvanathan, and S. Zumer, Mutually tangled colloidal knots and induced defect loops in nematic fields, Nature Materials, vol.20, issue.3, pp.258-263, 2014.
DOI : 10.1142/S0217751X05024146

T. Machon and G. P. Alexander, Knots and nonorientable surfaces in chiral nematics, Proc. Natl. Acad. Sci. USA 2013, pp.14174-14179
DOI : 10.1103/RevModPhys.61.385

W. T. Irvine and D. Kleckner, Tangled loops and knots, Nature Materials, vol.12, issue.3, pp.229-231, 2014.
DOI : 10.1038/nmat3583

M. G. Campbell and M. Tasinkevych, Smalyukh, I.I. Topological Polymer Dispersed Liquid Crystals with Bulk Nematic Defect Lines Pinned to Handlebody Surfaces, Phys. Rev. Lett, vol.112, 2014.

C. E. Laing, R. L. Ricca, and D. W. Sumners, Conservation of writhe helicity under anti-parallel reconnection, Scientific Reports, vol.111, issue.1, p.9224, 2015.
DOI : 10.1073/pnas.1407232111

X. Liu and R. L. Ricca, Knots cascade detected by a monotonically decreasing sequence of values. Sci Helicity conservation by flow across scales in reconnecting vortex links and knots, Proc. Natl. Acad. Sci. USA 2014, pp.15350-15355, 2013.

A. J. Taylor, M. R. Dennis, L. H. Kauffman, and W. T. Irvine, Vortex knots in tangled quantum eigenfunctions How superfluid vortex knots untie, Nat. Commun. Nat. Phys, vol.12, pp.650-655, 2016.

K. Shishido, N. Komiyama, and S. Ikawa, Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants, Journal of Molecular Biology, vol.195, issue.1, pp.215-218, 1987.
DOI : 10.1016/0022-2836(87)90338-X

V. V. Rybenkov, C. Ullsperger, A. V. Vologodskii, and N. R. Cozzarelli, Simplification of DNA Topology Below Equilibrium Values by Type II Topoisomerases, Science, vol.277, issue.5326, pp.690-693, 1997.
DOI : 10.1126/science.277.5326.690

X. Hua, D. Nguyen, B. Raghavan, J. Arsuaga, and M. Vazquez, Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases, Topology and its Applications, vol.154, issue.7, pp.1381-1397, 2007.
DOI : 10.1016/j.topol.2006.05.010

I. Grainge, M. Bregu, M. Vazquez, V. Sivanathan, S. C. Ip et al., Unlinking chromosome catenanes in vivo by site-specific recombination, The EMBO Journal, vol.9, issue.19, pp.4228-4238, 2007.
DOI : 10.1038/sj.emboj.7601849

A. Vologodski, Disentangling DNA molecules. Phys. Life Rev, pp.118-134, 2016.

R. Olender and R. Elber, Calculation of classical trajectories with a very large time step: Formalism and numerical examples, The Journal of Chemical Physics, vol.268, issue.20, pp.9299-9315, 1996.
DOI : 10.1021/j100016a003

R. Elber, Reaction Paths and Rates, In Encyclopedia of Biophysics, pp.2186-2191, 2013.
DOI : 10.1007/978-3-642-16712-6_728

J. M. Bello-rivas, R. A. Elber, and D. Sezer, Exact milestoning Roux, B. Finding transition pathways using the string method with swarms of trajectories, J. Chem. Phys. J. Phys. Chem. B, vol.142, issue.112, pp.3432-3440, 2008.
DOI : 10.1063/1.4913399

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352169/pdf

Y. Meng, D. Shukla, V. S. Pande, and B. Roux, Transition path theory analysis of c-Src kinase activation, Proc. Natl. Acad. Sci. USA 2016, pp.9193-9198
DOI : 10.1016/0021-9991(77)90098-5

R. Banisch, N. D. Conrad, and C. Schütte, Reactive flows and unproductive cycles for random walks on complex networks, The European Physical Journal Special Topics, vol.48, issue.12, pp.2369-2387, 2015.
DOI : 10.1063/1.4895044

P. Faccioli, M. Sega, F. Pederiva, and H. Orland, Dominant Pathways in Protein Folding Transition path sampling: throwing ropes over rough mountain passes, in the dark, Phys. Rev. Lett. Annu. Rev. Phys. Chem, vol.97, issue.53, pp.291-318, 2002.

J. O. 30-daldrop, W. K. Kim, and R. R. Netz, Transition paths are hot, EPL (Europhysics Letters), vol.113, issue.1, p.18004, 2016.
DOI : 10.1209/0295-5075/113/18004

J. Schlitter, M. Engels, P. Krüger, E. Jacoby, and A. Wollmer, Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ??? R Transition in Insulin, Molecular Simulation, vol.264, issue.2-6, pp.291-308, 1993.
DOI : 10.1146/annurev.bb.17.060188.002315

H. Grubmüller, B. Heymann, and P. Tavan, Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force, Science, vol.271, issue.5251, pp.997-999, 1996.
DOI : 10.1126/science.271.5251.997

B. 33-isralewitz, M. Gao, and K. Schulten, Steered molecular dynamics and mechanical functions of proteins, Current Opinion in Structural Biology, vol.11, issue.2, pp.224-230, 2001.
DOI : 10.1016/S0959-440X(00)00194-9

N. Halpern and C. Jarzynski, Number of trials required to estimate a free-energy difference, using fluctuation relations, Physical Review E, vol.93, issue.5, p.52144, 2016.
DOI : 10.1038/nature04061

E. Paci and M. Karplus, Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations, Journal of Molecular Biology, vol.288, issue.3, pp.441-459, 1999.
DOI : 10.1006/jmbi.1999.2670

C. Camilloni, R. A. Broglia, and G. Tiana, Hierarchy of folding and unfolding events of protein G, CI 2, and ACBP from explicit-solvent simulations, J. Chem. Phys, vol.134, pp.1-632, 2011.

H. 37-orland, Generating transition paths by Langevin bridges, The Journal of Chemical Physics, vol.134, issue.17, p.174114, 2011.
DOI : 10.1007/978-3-662-21726-9

S. N. Majumdar and H. Orland, Effective Langevin equations for constrained stochastic processes, Journal of Statistical Mechanics: Theory and Experiment, vol.2015, issue.6, p.6039, 2015.
DOI : 10.1088/1742-5468/2015/06/P06039

URL : https://hal.archives-ouvertes.fr/hal-01178100

I. D. Darcy and S. , Applications of topology to DNA, Knot Theory, 1998.
DOI : 10.4064/-42-1-65-75

A. Flammini, A. Maritan, and A. Stasiak, Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots, Biophysical Journal, vol.87, issue.5, pp.2968-2975, 2004.
DOI : 10.1529/biophysj.104.045864

N. Kampen, Stochastic Processes in Physics and Chemistry; North?Holland: Amsterdam, The Netherlands, 1992.

R. 43-zwanzig, Nonequilibrium Statistical Mechanics, 2001.

J. Doob, Conditional brownian motion and the boundary limits of harmonic functions, Bulletin de la Société mathématique de France, vol.79, pp.431-458, 1957.
DOI : 10.24033/bsmf.1494

P. Fitzsimmons, J. Pitman, and M. Yor, Markovian Bridges: Construction, Palm Interpretation, and Splicing, Seminar on Stochastic Processes, 1992.
DOI : 10.1007/978-1-4612-0339-1_5

URL : http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.159.239&rep=rep1&type=pdf