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

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

An autonomous and reversible Maxwell's demon

Building on a model introduced by Mandal and Jarzynski [Proc. Natl. Acad. Sci. U. S. A., {\bf 109}, (2012) 11641], we present a simple version of an autonomous reversible Maxwell's demon. By changing the entropy of a tape consisting of a sequence of bits passing through the demon, the demon can lift a mass using the coupling to a heat bath. Our model becomes reversible by allowing the tape to move in both directions. In this thermodynamically consistent model, total entropy production consists of three terms one of which recovers the irreversible limit studied by MJ. Our demon allows an interpretation in terms of an enzyme transporting and transforming molecules between compartments. Moreover, both genuine equilibrium and a linear response regime with corresponding Onsager coefficients are well defined. Efficiency and efficiency at maximum power are calculated. In linear response, the latter is shown to be bounded by 1/2 if the demon operates as a machine and by 1/3 if it is operated as an eraser.Comment: 6 pages, 3 figure

Fluctuation spectra of free and supported membrane pairs

Fluctuation spectra of fluid compound membrane systems are calculated. The systems addressed contain two (or more) almost parallel membranes that are connected by harmonic tethers or by a continuous, harmonic confining potential. Additionally, such a compound system can be attached to a supporting substrate. We compare quasi-analytical results for tethers with analytical results for corresponding continuous models and investigate under what circumstances the discrete nature of the tethers actually influences the fluctuations. A tethered, supported membrane pair with similar bending rigidities and stiff tethers can possess a nonmonotonic fluctuation spectrum with a maximum. A nonmonotonic spectrum with a maximum and a minimum can occur for an either free or supported membrane pair of rather different bending rigidities and for stiff tethers. Typical membrane displacements are calculated for supported membrane pairs with discrete or continuous interacting potentials. Thereby an estimate of how close the constituent two membranes and the substrate typically approach each other is given. For a supported membrane pair with discrete or continuous interactions, the typical displacements of each membrane are altered with respect to a single supported membrane, where those of the membrane near the substrate are diminished and those of the membrane further away are enhanced.Comment: 14 pages, 8 figure