Equilibrium time correlation functions from irreversible transformations in trajectory space

Article Abstract:

A new identity for the statistical mechanics of trajectories is presented, which reflects that a distribution of irreversible transformations between ensembles of trajectories is sufficient to determine equilibrium time correlation functions. The results reveal that connections between the statistical mechanics of trajectories and that of microstates exist even out of equilibrium, and these nonequilibrium relations provide computational savings by allowing fast switching between ensembles.

Protein folding, Nonequilibrium thermodynamics

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Kinetic pathways of ion pair dissociation in water

Article Abstract:

The transition path sampling method is used to examine transition dynamics of a model Na+Cl- ion pair in water. It is shown that a variety of transition pathways are involved in dissociation while the molecular nature of the solvent affects dissociation dynamics. Transition states along pathways involve a wide distribution of ionic separations. Ion pairs in contact also remain associated for an average of 20 ps.

Models, Molecular dynamics, Chemical reaction, Rate of, Chemical kinetics, Dissociation, Dissociation reactions

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Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods?

Article Abstract:

The maximum computational efficiency of reversible work calculations that change control parameters in a finite amount of time is investigated. The findings indicate that in the linear response limit, the only advantage of fast switching simulations compared to thermodynamic integration is the improved error estimation and easier paralelizability.

Science & research, Research, Simulation methods, Simulation, Thermodynamics

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