title: Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates.
abstract: We present a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. The formalism is based on combining Transition Path Theory with the results of nonequilibrium work relations, and shows that the equilibrium and nonequilibrium transition rates are in fact related. Aside from its fundamental importance, this allows for the calculation of relative equilibrium reaction rates with driven nonequilibrium simulations such as Steered Molecular Dynamics. The workings of the formalism are illustrated with a few typical numerical examples.
authors: Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors: Mahmoud
authors: M
authors: Moradi
authors: Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors: Celeste
authors: C
authors: Sagui
authors: Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors: Christopher
authors: C
authors: Roland
mesh_terms: D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011336:Probability; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; C002956:alanylalanine