caa a22 4500 445391502 CHVBK 20180317143048.0 cr unu---uuuuu 170323e20110701xx s 000 0 eng 10.1007/s10955-011-0242-7 doi (NATIONALLICENCE)springer-10.1007/s10955-011-0242-7 Reconstructing Free Energy Profiles from Nonequilibrium Relaxation Trajectories [Elektronische Daten] [Qi Zhang, Jasna Brujić, Eric Vanden-Eijnden] Reconstructing free energy profiles is an important problem in bimolecular reactions, protein folding or allosteric conformational changes. Nonequilibrium trajectories are readily measured experimentally, but their statistical significance and relation to equilibrium system properties still call for rigorous methods of assessment and interpretation. Here we introduce methods to compute the equilibrium free energy profile of a given variable from a set of short nonequilibrium trajectories, obtained by externally driving a system out of equilibrium and subsequently observing its relaxation. This protocol is not suitable for the Jarzynski equality since the irreversible work on the system is instantaneous. Assuming that the variable of interest satisfies an overdamped Langevin equation, which is frequently used for modeling biomolecular processes, we show that the trajectories sample a nonequilibrium stationary distribution that can be calculated in closed form. This allows for the estimation of the free energy via an inversion procedure that is analogous to that used in equilibrium and bypasses more complicated path integral methods, which we derive for comparison. We generalize the inversion procedure to systems with a diffusion constant that depends on the reaction coordinate, as is the case in protein folding, as well as to protocols in which the trajectories are initiated at random points. Using only a statistical pool of tens of synthetic trajectories, we demonstrate the versatility of these methods by reconstructing double and multi-well potentials, as well as a proposed profile for the hydrophobic collapse of a protein. Springer Science+Business Media, LLC, 2011 Free energy calculation nationallicence Nonequilibrium sampling nationallicence Maximum likelihood nationallicence Bayesian sampling nationallicence Zhang Qi Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, 10012, New York, NY, USA aut Brujić Jasna Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, 10003, New York, NY, USA aut Vanden-Eijnden Eric Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, 10012, New York, NY, USA aut Journal of Statistical Physics Springer US; http://www.springer-ny.com 144/2(2011-07-01), 344-366 0022-4715 144:2<344 2011 144 10955 https://doi.org/10.1007/s10955-011-0242-7 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10955-011-0242-7 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Zhang Qi Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, 10012, New York, NY, USA aut NATIONALLICENCE 700 1- Brujić Jasna Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, 10003, New York, NY, USA aut NATIONALLICENCE 700 1- Vanden-Eijnden Eric Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, 10012, New York, NY, USA aut NATIONALLICENCE 773 0- Journal of Statistical Physics Springer US; http://www.springer-ny.com 144/2(2011-07-01), 344-366 0022-4715 144:2<344 2011 144 10955 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer