Thermodynamic cost of external control

Artificial molecular machines are often driven by the periodic variation of an external parameter. This external control exerts work on the system of which a part can be extracted as output if the system runs against an applied load. Usually, the thermodynamic cost of the process that generates the external control is ignored. Here, we derive a refined second law for such small machines that include this cost, which is, for example, generated by free energy consumption of a chemical reaction that modifies the energy landscape for such a machine. In the limit of irreversible control, this refined second law becomes the standard one. Beyond this ideal limiting case, our analysis shows that due to a new entropic term unexpected regimes can occur: The control work can be smaller than the extracted work and the work required to generate the control can be smaller than this control work. Our general inequalities are illustrated by a paradigmatic three-state system.Comment: 11 pages, 3 figure

Coherence of Biochemical Oscillations is Bounded by Driving Force and Network Topology

Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the number of coherent oscillations that quantifies the precision of the oscillator is universally bounded by the thermodynamic force that drives the system out of equilibrium and by the topology of the underlying biochemical network of states. Our results are valid for arbitrary Markov processes, which are commonly used to model biochemical reactions. We apply our results to a model for a single KaiC protein and to an activator-inhibitor model that consists of several molecules. From a mathematical perspective, based on strong numerical evidence, we conjecture a universal constraint relating the imaginary and real parts of the first non-trivial eigenvalue of a stochastic matrix.Comment: 12 pages, 13 figure

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

Dispersion of the time spent in a state: General expression for unicyclic model and dissipation-less precision

We compare the relation between dispersion and dissipation for two random variables that can be used to characterize the precision of a Brownian clock. The first random variable is the current between states. In this case, a certain precision requires a minimal energetic cost determined by a known thermodynamic uncertainty relation. We introduce a second random variable that is a certain linear combination of two random variables, each of which is the time a stochastic trajectory spends in a state. Whereas the first moment of this random variable is equal to the average probability current, its dispersion is generally different from the dispersion associated with the current. Remarkably, for this second random variable a certain precision can be obtained with an arbitrarily low energy dissipation, in contrast to the thermodynamic uncertainty relation for the current. As a main technical achievement, we provide an exact expression for the dispersion related to the time that a stochastic trajectory spends in a cluster of states for a general unicyclic network.Comment: 17 pages, 1 figur