Stochastic thermodynamics of single enzymes and molecular motors

For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept of internal energy, intrinsic entropy and free energy for states follows from a microscopic description using one assumption on time-scale separation. A first law energy balance then allows the unique identification of the heat dissipated in one transition. Consistency with the second law on the ensemble level enforces both stochastic entropy as third contribution to the entropy change involved in one transition and the local detailed balance condition for the ratio between forward and backward rates for any transition. These results follow without assuming weak coupling between the enzyme and the solutes, ideal solution behavior or mass action law kinetics. The present approach highlights both the crucial role of the intrinsic entropy of each state and the physically questionable role of chemiostats for deriving the first law for molecular motors subject to an external force under realistic conditions.Comment: 11 page

Efficiency of molecular motors at maximum power

Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the qualitative behaviour depends crucially on the position of the transition state. Specifically, we find a transition state near the initial state (sometimes characterized as a "power stroke") to be most favorable with respect to both high power output and high efficiency at maximum power. In this regime, driving the motor further out of equilibrium by applying higher chemical potential differences can even, counter-intuitively, increase the efficiency.Comment: published in EPL: http://www.iop.org/EJ/abstract/0295-5075/83/3/3000

Multi-terminal Thermoelectric Transport in a Magnetic Field: Bounds on Onsager Coefficients and Efficiency

Thermoelectric transport involving an arbitrary number of terminals is discussed in the presence of a magnetic field breaking time-reversal symmetry within the linear response regime using the Landauer-B\"uttiker formalism. We derive a universal bound on the Onsager coefficients that depends only on the number of terminals. This bound implies bounds on the efficiency and on efficiency at maximum power for heat engines and refrigerators. For isothermal engines pumping particles and for absorption refrigerators these bounds become independent even of the number of terminals. On a technical level, these results follow from an original algebraic analysis of the asymmetry index of doubly substochastic matrices and their Schur complements.Comment: 31 pages, 9 figures, New J. Phys., in pres

Nonexistence of classical diamagnetism and nonequilibrium fluctuation theorems for charged particles on a curved surface

We show that the classical Langevin dynamics for a charged particle on a closed curved surface in a time-independent magnetic field leads to the canonical distribution in the long time limit. Thus the Bohr-van Leeuwen theorem holds even for a finite system without any boundary and the average magnetic moment is zero. This is contrary to the recent claim by Kumar and Kumar (EPL, {\bf 86} (2009) 17001), obtained from numerical analysis of Langevin dynamics, that a classical charged particle on the surface of a sphere in the presence of a magnetic field has a nonzero average diamagnetic moment. We extend our analysis to a many-particle system on a curved surface and show that the nonequilibrium fluctuation theorems also hold in this geometry.Comment: 6 pages; typos correcte