Publication: Force-extension curves for biomolecules
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Single-molecule atomic force spectroscopy probes elastic properties of proteins such as titin and ubiquitin. We analyze bioprotein folding dynamics under both force and length-clamp conditions by modeling polyprotein modules as particles in a bistable potential, connected by harmonic springs. The study of multistable equilibria in these models explains recorded sawtooth force-extension curves. We show that bifurcations and transitions through quasi-stationary domain configurations modified by thermal noise are involved in observed stepwise and abrupt refolding and unfolding phenomena under force-clamp conditions. These predictions agree with experimental observations.
 L.L. Bonilla, A. Carpio, A. Prados, Protein unfolding and refolding as transitions through virtual states, EPL (Europhysics Letters) 108, 28002, 2014  A. Prados, A. Carpio, L.L. Bonilla, Sawtooth patterns in force-extension curves of biomolecules: an equilibrium-statistical-mechanics theory, Physical Review E 88, 012704, 2013  A. Prados, A. Carpio, L.L. Bonilla, Spin-oscillator model for the unzipping of biomolecules by mechanical force, Physical Review E 86, 021919, 2012  A. Carpio, LL Bonilla, Wave front depinning transition in discrete one-dimensional reaction-diffusion systems, Physical Review Letters 86, 6034-6037, 2001  Effects of disorder on the wave front depinning transition in spatially discrete systems, A. Carpio, L.L. Bonilla, A. Luzon, Physical Review E 65, 035207, 2002  A. Carpio, L.L. Bonilla, Depinning transitions in discrete reaction-diffusion equations, SIAM Journal on Applied Mathematics 63, 1056-1082, 2003  A. Carpio, Wave trains, self-oscillations and synchronization in discrete media, Physica D-Nonlinear Phenomena 207, 117-136, 2005