No Arabic abstract
Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been a subject of active research; however, how error reduction of a process is balanced with its thermodynamic cost and dynamical properties remain largely unexplored. Here, we study the error reducing strategies in light of the recently discovered thermodynamic uncertainty relation (TUR) that sets a physical bound to the cost-precision trade-off relevant in general dissipative processes. We found that the two representative copying processes, DNA replication by the exonuclease-deficient T7 DNA polymerase and mRNA translation by the textit{E. coli} ribosome, reduce the error rates to biologically acceptable levels while also optimizing the processes close to the physical limit dictated by TUR.
We study coupled quantum systems as the working media of thermodynamic machines. Under a suitable phase-space transformation, the coupled systems can be expressed as a composition of independent subsystems. We find that for the coupled systems, the figures of merit, that is the efficiency for engine and the coefficient of performance for refrigerator, are bounded (both from above and from below) by the corresponding figures of merit of the independent subsystems. We also show that the optimum work extractable from a coupled system is upper bounded by the optimum work obtained from the uncoupled system, thereby showing that the quantum correlations do not help in optimal work extraction. Further, we study two explicit examples, coupled spin-$1/2$ systems and coupled quantum oscillators with analogous interactions. Interestingly, for particular kind of interactions, the efficiency of the coupled oscillators outperforms that of the coupled spin-$1/2$ systems when they work as heat engines. However, for the same interaction, the coefficient of performance behaves in a reverse manner, while the systems work as the refrigerator. Thus the same coupling can cause opposite effects in the figures of merit of heat engine and refrigerator.
We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states, and discuss how optimal these processes are in light of the universal bound set by the thermodynamic uncertainty relation (TUR). The values of the uncertainty product $mathcal{Q}$ of TUR, which can be used as a measure of the precision of enzymatic processes realized for a given thermodynamic cost, are suboptimal when the substrate concentration $[S]$ is at the Michaelis constant ($K_text{M}$), and some of the key biological processes are found to work around this condition. We illustrate the utility of $mathcal{Q}$ in assessing how close the molecular motors and biomass producing machineries are to the TUR bound, and for the cases of biomass production (or biological copying processes) we discuss how their optimality quantified in terms of $mathcal{Q}$ is balanced with the error rate in the information transfer process. We also touch upon the trade-offs in other error-minimizing processes in biology, such as gene regulation and chaperone-assisted protein folding. A spectrum of $mathcal{Q}$ recapitulating the biological processes surveyed here provides glimpses into how biological systems are evolved to optimize and balance the conflicting functional requirements.
Thermal machines perform useful tasks--such as producing work, cooling, or heating--by exchanging energy, and possibly additional conserved quantities such as particles, with reservoirs. Here we consider thermal machines that perform more than one useful task simultaneously, terming these hybrid thermal machines. We outline their restrictions imposed by the laws of thermodynamics and we quantify their performance in terms of efficiencies. To illustrate their full potential, reservoirs that feature multiple conserved quantities, described by generalized Gibbs ensembles, are considered. A minimal model for a hybrid thermal machine is introduced, featuring three reservoirs and two conserved quantities, e.g., energy and particle number. This model can be readily implemented in a thermoelectric setup based on quantum dots, and hybrid regimes are accessible considering realistic parameters.
Interesting effects arise in cyclic machines where both heat and ergotropy transfer take place between the energising bath and the system (the working fluid). Such effects correspond to unconventional decompositions of energy exchange between the bath and the system into heat and work, respectively, resulting in efficiency bounds that may surpass the Carnot efficiency. However, these effects are not directly linked with quantumness, but rather with heat and ergotropy, the likes of which can be realised without resorting to quantum mechanics.
A model of coupled molecular oscillators is proposed to study nonequilibrium thermodynamics of synchronization. We find that synchronization of nonequilibrium oscillators costs energy even when the oscillator-oscillator coupling is conservative. By solving the steady state of the many-body system analytically, we show that the system goes through a nonequilibrium phase transition driven by energy dissipation, and the critical energy dissipation depends on both the frequency and strength of the exchange reactions. Moreover, our study reveals the optimal design for achieving maximum synchronization with a fixed energy budget. We apply our general theory to the Kai system in Cyanobacteria circadian clock and predict a relationship between the KaiC ATPase activity and synchronization of the KaiC hexamers. The theoretical framework can be extended to study thermodynamics of collective behaviors in other extended nonequilibrium active systems.