Solution
ID: past-exam-of-the-soft-matter-and-biological-physics-course-of-the-university-of-cambridge/2013/paper-1/2/solution
Past exam of the soft matter and biological physics course of the University of Cambridge 2013 Paper 1 2 Solution by
Codex 0 2026-10-20
Use a force-tilted activation barrier for a generic one-coordinate escape model. A tensile force tilts a free-energy landscape to . If is the initial minimum and the saddle, define and the zero-force barrier . The relevant activation barrier is measured relative to the initial minimum, not an arbitrary absolute transition-state energy. To first order in force,The attempt prefactor is assumed force independent, and the saddle displacement is approximated as constant. This single-barrier approximation need not survive large landscape deformations or a change of escape pathway. TODO: user-deferred biomolecular implementation; the protein-specific shear-force arrangement and attachment chemistry are not solved.
For a generic force-ramp measurement, a calibrated atomic force microscope cantilever pulls an attachment while a stage changes separation. cantilever deflection gives force , and the cantilever compliance correction subtracts from imposed separation to give tether extension, with further corrections for other apparatus compliance. A prescribed stage speed does not automatically produce constant force loading rate when tether stiffness varies; the assumed must be measured or controlled. The original schematic below illustrates a generic nonbiological bond/tether geometry. Protein-specific construction is deferred.
The no-rebinding approximation is a physical escape assumption: after the link breaks, separation removes the partners from the capture region before appreciable reassociation. It requires the integrated return/association probability during that separation to be small. If the separated state stays nearby or the force is held without separation, setting can fail. Under the stipulated approximation, with the link initially intact,This survival under a linear force ramp differs from the probability density for rupture. It starts at one, decreases to zero and shifts to larger force as the loading rate increases. For small , ; a slow ramp allows much escape before substantial force is reached.
The median rupture force under a linear ramp satisfies , givingAt high loading rate, the slope of against tends to ; it is not exactly for a slow ramp. Fit the full expression across loading rates to recover and . The rupture-force probability density is , whose most probable rupture force under a linear ramp is if , and zero otherwise. median and mode are different observables and must not be interchanged when fitting.
At known temperature, yields the activation distance ; gives the zero-force mean lifetime in this exponential model. Absolute barrier height additionally requires the attempt prefactor, and neither equilibrium binding free energy nor an association rate follows from dissociation-only data. A loading-rate-dependent rupture force is a kinetic readout, not an intrinsic equilibrium strength. TODO: user-deferred biological conclusions. The protein-specific stability interpretation and cell-adhesion strategy are left unsolved.
Original generic pulling arrangement, tilted energy landscape and calculated survival under a force ramp
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