title: Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols.
abstract: The Jarzynski-relation-based free-energy calculation is limited by the very slow convergence of the estimate when dissipation is high. We present two novel perturbation protocols able to significantly improve the quality of the potential of mean force (PMF) calculation by reducing the estimate's bias without increasing the number of samples. The protocols are directly applicable with both numerical simulations and real-life experiments. The improvement is achieved through the intentional but controlled widening of the distribution of the external work used to perturb a given system. Our protocols can achieve the same accuracy in PMF estimation as the normal constant velocity pulling with less than 10% of the required samples.
authors.affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
authors.forename: Ognjen
authors.initials: O
authors.lastname: Perišić
authors.forename: Hui
authors.initials: H
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D015233:Models, Statistical; D009010:Monte Carlo Method; D016011:Normal Distribution; D011846:Radio Waves; D015203:Reproducibility of Results; D013269:Stochastic Processes; D013816:Thermodynamics