title: Equilibrium binding energies from fluctuation theorems and force spectroscopy simulations.
abstract: Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead that is weakly bound to a cell and then removed by an optical tweezer. The external driving force arises from the combined optical tweezer and substrate potentials, and thermal fluctuations are taken into account by a Brownian force. The Jarzynski equality and Crooks fluctuation theorem are applied to obtain the equilibrium free energy difference between the final and initial states. To this end, we sample non-equilibrium work trajectories for various tweezer pulling rates. We argue that this methodology should also be feasible experimentally for the envisioned system. Furthermore, we outline how the measurement of a whole free energy profile would allow the experimentalist to retrieve the unknown substrate potential by means of a suitable deconvolution. The influence of the pulling rate on the accuracy of the results is investigated, and umbrella sampling is used to obtain the equilibrium probability of particle escape for a variety of trap potentials.
authors.affiliation: Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia. ravi.jagadeeshan@monash.edu and Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia.
authors.forename: Emma
authors.initials: E
authors.lastname: Hodges
authors.affiliation: Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia.
authors.forename: B M
authors.initials: BM
authors.lastname: Cooke
authors.affiliation: Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
authors.forename: E M
authors.initials: EM
authors.lastname: Sevick
authors.affiliation: AIBN Centre for Theoretical and Computational Molecular Science, University of Queensland, Brisbane, QLD 4072, Australia and School of Chemical and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
authors.forename: Debra J
authors.identifier: http://orcid.org/0000-0003-1346-8318
authors.initials: DJ
authors.lastname: Searles
authors.affiliation: Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia. ravi.jagadeeshan@monash.edu and Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany and Condensed Matter Physics, TU Darmstadt, Hochschulstraße 12, 64289 Darmstadt, Germany.
authors.forename: B
authors.initials: B
authors.lastname: Dünweg
authors.affiliation: Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia. ravi.jagadeeshan@monash.edu.
authors.forename: J Ravi
authors.identifier: http://orcid.org/0000-0002-1702-6392
authors.initials: JR
authors.lastname: Prakash