Unidirectional hopping transport of interacting particles on a finite chain

Network analysis of nanoscale energy conversion processes

Energy conversion in nanosized devices is studied in the framework of state-space models. We use a network representation of the underlying master equation to describe the dynamics by a graph. Particular segments of this network represent input and output processes that provide a way to introduce a coupling to several heat reservoirs and particle reservoirs. In addition, the network representation scheme allows one to decompose the stationary dynamics as cycles. The cycle analysis is a convenient tool for analyse models of machine operations, which are characterized by different nanoscale energy conversion processes. By introducing the cycle affinity, we are able to calculate the zero-current limit. The zero-current limit can be mapped to the zero-affinity limit in a network representation scheme. For example, for systems with competing external driving forces the open-circuit voltage can be determined by setting the cycle affinity zero. This framework is used to derive open-circuit voltage with respect to microscopic material energetics and different coupling to particle and temperature reservoirs.

Energy, Work, Entropy, and Heat Balance in Marcus Molecular Junctions

We present a consistent theory of energy balance and conversion in a single-molecule junction with strong interactions between electrons on the molecular linker (dot) and phonons in the nuclear environment where the Marcus-type electron hopping processes predominate in the electron transport. It is shown that the environmental reorganization and relaxation that accompany electron hopping energy exchange between the electrodes and the nuclear (molecular and solvent) environment may bring a moderate local cooling of the latter in biased systems. The effect of a periodically driven dot level on the heat transport and power generated in the system is analyzed, and energy conservation is demonstrated both within and beyond the quasistatic regime. Finally, a simple model of atomic scale engine based on a Marcus single-molecule junction with a driven electron level is suggested and discussed.

A Kinetic Model of Proton Transport in a Multi-Redox Centre Protein: Cytochrome c Oxidase

We use chemical reaction kinetics to explore the stepwise electron and proton transfer reactions of cytochrome c oxidase (C cO) from R. sphaeroides. Proton transport coupled to electron transport (ET) is investigated in terms of a sequence of protonation-dependent second-order redox reactions. Thereby, we assume fixed rather than shifting dissociation constants of the redox sites. Proton transport can thus be simulated particularly when separate proton uptake and release sites are assumed rather than the same proton pump site for every ET step. In order to test these assumptions, we make use of a model system introduced earlier, which allows us to study direct ET of redox enzymes by electrochemistry. A four-electron transfer model of C cO had been developed before, according to which electrons are transferred from the electrode to CuA. Thereafter, electrons are transferred along the sequence heme a, heme a3 and CuB. In the present investigation, we consider protonation equilibria of the oxidised and reduced species for each of the four centres. Moreover, we add oxygen/H2O as the terminal (fifth) redox couple including protonation of reduced oxygen to water. Finally we arrive at a kinetic model comprising five protonation-dependent redox couples. The results from the simulations are compared with experimental data obtained in the absence and presence of oxygen. As a result, we can show that proton transport can be modelled in terms of protonation-dependent redox kinetics.

Classical driven transport in open systems with particle interactions and general couplings to reservoirs

We study nonequilibrium steady states of lattice gases with nearest-neighbor interactions that are driven between two reservoirs. Density profiles in these systems exhibit oscillations close to the reservoirs. We demonstrate that an approach based on time-dependent density functional theory copes with these oscillations and predicts phase diagrams of bulk densities to a good approximation under arbitrary boundary-reservoir couplings. The minimum or maximum current principles can be applied only for specific bulk-adapted couplings. We show that they generally fail to give the correct topology of phase diagrams but can still be useful for getting insight into the mutual arrangement of different phases.