Nonlinear irreversible thermodynamics of single-molecule experiments

Thermodynamics for single-molecule stretching experiments.

We show how to construct nonequilibrium thermodynamics for systems too small to be considered thermodynamically in a traditional sense. Through the use of a nonequilibrium ensemble of many replicas of the system which can be viewed as a large thermodynamic system, we discuss the validity of nonequilibrium thermodynamics relations and analyze the nature of dissipation in small systems through th...

Irreversible Thermodynamics

There are alternative sets of postulates which yield entirely equivalent results for several important theories. In such cases the choice of a particular set of postulates may be based upon mathematical simplicity, close relationship to experiments or to the nature of the theory, or merely personal taste. While the postulate of conservation of energy is usually presented in similar form for the...

Basics of Irreversible Thermodynamics

Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments.

The nonequilibrium work relation allows for the calculation of equilibrium free energy differences between states based on the exponential average of accumulated work from irreversible transitions. Here, we compare two distinct approaches of calculating free energy surfaces from unidirectional single-molecule pulling experiments: the stiff spring approximation and the Hummer-Szabo method. First...

Relating single-molecule measurements to thermodynamics.

Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and whi...