Physical insight into the thermodynamic uncertainty relation using Brownian motion in tilted periodic potentials

Thermodynamic uncertainty relation for Langevin dynamics by scaling time

The thermodynamic uncertainty relation (TUR) quantifies a relationship between current fluctuations and dissipation in out-of-equilibrium overdamped Langevin dynamics, making it a natural counterpart of the fluctuation-dissipation theorem in equilibrium statistical mechanics. For underdamped Langevin dynamics, the situation is known to be more complicated with dynamical activity also playing a role in limiting the magnitude of current fluctuations. Progress on those underdamped TUR-like bounds has largely come from applications of the information-theoretic Cramér-Rao inequality. Here, we present an alternative perspective by employing large deviation theory. The approach offers a general unified treatment of TUR-like bounds for both overdamped and underdamped Langevin dynamics built upon current fluctuations achieved by scaling time. The bounds we derive following this approach are similar to known results but with differences we discuss and rationalize.

Universal minimal cost of coherent biochemical oscillations

Biochemical clocks are essential for virtually all living systems. A biochemical clock that is isolated from an external periodic signal and subjected to fluctuations can oscillate coherently only for a finite number of oscillations. Furthermore, such an autonomous clock can oscillate only if it consumes free energy. What is the minimum amount of free-energy consumption required for a certain number of coherent oscillations? We conjecture a universal bound that answers this question. A system that oscillates coherently for N oscillations has a minimal free-energy cost per oscillation of 4π^{2}Nk_{B}T. Our bound is valid for general finite Markov processes, is conjectured based on extensive numerical evidence, is illustrated with numerical simulations of a known model for a biochemical oscillator, and applies to existing experimental data.

Thermodynamic uncertainty relation for quantum work distribution: Exact case study for a perturbed oscillator

Recently, some general relations have been intensively investigated in nonequilibrium mesoscopic systems. In particular, the thermodynamic uncertainty relation (TUR) provides a general bound of the precision for the fluctuation of some currents in terms of the corresponding entropy production. On the other hand, the fluctuation of the work performed is also a significant quantity, which is supposed to satisfy TUR under some conditions, such as symmetric driving protocol. In this paper, we analytically show that the TUR holds for the work performed on an externally perturbed quantum harmonic oscillator interacting with multiple reservoirs in full quantum regime. In this manner, we evaluate how the noncommutativity affects the thermodynamic precision. We also explore its experimental accessibility.

Origin of loose bound of the thermodynamic uncertainty relation in a dissipative two-level quantum system

Thermodynamic uncertainty relations (TURs), originally discovered for classical systems, dictate the tradeoff between dissipation and fluctuations of irreversible current, specifying a minimal bound that constrains the two quantities. In a series of efforts to extend the relation to the one under more generalized conditions, it has been noticed that the bound is less tight in open quantum processes. To study the origin of the loose bounds, we consider an external field-driven transition dynamics of a two-level quantum system weakly coupled to the bosonic bath as a model of an open quantum system. The model makes it explicit that the imaginary part of quantum coherence, which contributes to dissipation to the environment, is responsible for loosening the TUR bound by suppressing the relative fluctuations in the irreversible current of transitions, whereas the real part of the coherence tightens it. Our study offers a better understanding of how quantum nature affects the TUR bound.

Cost-precision trade-off relation determines the optimal morphogen gradient for accurate biological pattern formation

Spatial boundaries formed during animal development originate from the pre-patterning of tissues by signaling molecules, called morphogens. The accuracy of boundary location is limited by the fluctuations of morphogen concentration that thresholds the expression level of target gene. Producing more morphogen molecules, which gives rise to smaller relative fluctuations, would better serve to shape more precise target boundaries; however, it incurs more thermodynamic cost. In the classical diffusion-depletion model of morphogen profile formation, the morphogen molecules synthesized from a local source display an exponentially decaying concentration profile with a characteristic length λ. Our theory suggests that in order to attain a precise profile with the minimal cost, λ should be roughly half the distance to the target boundary position from the source. Remarkably, we find that the profiles of morphogens that pattern the Drosophila embryo and wing imaginal disk are formed with nearly optimal λ. Our finding underscores the cost-effectiveness of precise morphogen profile formation in Drosophila development.

Excess and loss of entropy production for different levels of coarse graining

We investigate the effect of coarse graining on the thermodynamic properties of a system, focusing on entropy production. As a case of study, we consider a one-dimensional colloidal particle in contact with a thermal bath, moving in a sinusoidal potential and driven out of equilibrium by a small constant force. Different levels of coarse graining are evaluated: At first, we compare the results in the underdamped dynamics with those in the overdamped one (first coarse graining). For large values of the friction coefficient, the two dynamics have the same thermodynamics properties, while, for smaller friction values, the overdamped approximation produces an excess of entropy production with respect to that of the underdamped dynamics. Moreover, for further smaller values of the drag coefficient, the excess of entropy production turns into a loss. These regimes are explained by evaluating the jump statistics, observing that the inertia is able to induce multiple jumps and affect the average jump rate. The periodic shape of the potential allows us to approximate the continuous dynamics via a Markov chain after the introduction of a suitable time and space discretization (second level of coarse graining). This discretization procedure is implemented starting both from the underdamped and the overdamped evolution and is analyzed for different values of the friction coefficient.

Thermodynamic uncertainty relation to assess biological processes

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 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 is at the Michaelis constant, and some of the key biological processes are found to work around this condition. We illustrate the utility of 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 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 Q recapitulating the biological processes surveyed here provides glimpses into how biological systems are evolved to optimize and balance the conflicting functional requirements.

Dissipation-recurrence inequalities at the steady state

For Markov jump processes in out-of-equilibrium steady state, we present inequalities which link the average rate of entropy production with the timing of the site-to-site recurrences. Such inequalities are upper bounds on the average rate of entropy production. The combination with the finite-time thermodynamic uncertainty relation (a lower bound) yields inequalities of the pure kinetic kind for the relative precision of a dynamical output. After having derived the main relations for the discrete case, we sketch the possible extension to overdamped Markov dynamics on continuous degrees of freedom, treating explicitly the case of one-dimensional diffusion in tilted periodic potentials; an upper bound on the average velocity is derived, in terms of the average rate of entropy production and the microscopic diffusion coefficient, which corresponds to the finite-time thermodynamic uncertainty relation in the limit of vanishingly small observation time.

Thermodynamic uncertainty relation for energy transport in a transient regime: A model study

We investigate a transient version of the recently discovered thermodynamic uncertainty relation (TUR) which provides a precision-cost trade-off relation for certain out-of-equilibrium thermodynamic observables in terms of net entropy production. We explore this relation in the context of energy transport in a bipartite setting for three exactly solvable toy model systems (two coupled harmonic oscillators, two coupled qubits, and a hybrid coupled oscillator-qubit system) and analyze the role played by the underlying statistics of the transport carriers in the TUR. Interestingly, for all these models, depending on the statistics, the TUR ratio can be expressed as a sum or a difference of a universal term which is always greater than or equal to 2 and a corresponding entropy production term. We find that the generalized version of the TUR, originating from the universal fluctuation symmetry, is always satisfied. However, interestingly, the specialized TUR, a tighter bound, is always satisfied for the coupled harmonic oscillator system obeying Bose-Einstein statistics. Whereas, for both the coupled qubit, obeying Fermi-like statistics, and the hybrid qubit-oscillator system with mixed Fermi-Bose statistics, violation of the tighter bound is observed in certain parameter regimes. We have provided conditions for such violations. We also provide a rigorous proof following the nonequilibrium Green's function approach that the tighter bound is always satisfied in the weak-coupling regime for generic bipartite systems.

Do We Understand the Mechanisms Used by Biological Systems to Correct Their Errors?

Most cellular processes involved in biological information processing display a surprisingly low error rate despite the stochasticity of the underlying biochemical reactions and the presence of competing chemical species. Such high fidelity is the result of nonequilibrium kinetic proofreading mechanisms, i.e., the existence of dissipative pathways for correcting the reactions that went in the wrong direction. While proofreading was often studied from the perspective of error minimization, a number of recent studies have demonstrated that the underlying mechanisms need to consider the interplay of other characteristic properties such as speed, energy dissipation, and noise reduction. Here, we present current views and new insights on the mechanisms of error-correction phenomena and various trade-off scenarios in the optimization of the functionality of biological systems. Existing challenges and future directions are also discussed.

Thermodynamic uncertainty relations and molecular-scale energy conversion

The thermodynamic uncertainty relation (TUR) is a universal constraint for nonequilibrium steady states that requires the entropy production rate to be greater than the relative magnitude of current fluctuations. It has potentially important implications for the thermodynamic efficiency of molecular-scale energy conversion in both biological and artificial systems. An alternative multidimensional thermodynamic uncertainty relation (MTUR) has also been proposed. In this paper we apply the TUR and the MTUR to a description of molecular-scale energy conversion that explicitly contains the degrees of freedom exchanging energy via a time-independent multidimensional periodic potential. The TUR and the MTUR are found to be universal lower bounds on the entropy generation rate and provide upper bounds on the thermodynamic efficiency. The TUR is found to provide only a weak bound while the MTUR provides a much tighter constraint by taking into account correlations between degrees of freedom. The MTUR is found to provide a tight bound in the near or far from equilibrium regimes but not in the intermediate force regime. Collectively, these results demonstrate that the MTUR is more appropriate than the TUR for energy conversion processes, but that both diverge from the actual entropy generation in certain regimes.

Thermodynamic Cost, Speed, Fluctuations, and Error Reduction of Biological Copy Machines

Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is 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 for dissipative processes. We found that the two representative copying processes, DNA replication by the exonuclease-deficient T7 DNA polymerase and mRNA translation by the E. coli ribosome, reduce the error rates to biologically acceptable levels while also optimizing the processes close to the physical limit dictated by TUR.

Inferring Entropy Production from Short Experiments

We provide a strategy for the exact inference of the average as well as the fluctuations of the entropy production in nonequilibrium systems in the steady state, from the measurements of arbitrary current fluctuations. Our results are built upon the finite-time generalization of the thermodynamic uncertainty relation, and require only very short time series data from experiments. We illustrate our results with exact and numerical solutions for two colloidal heat engines.

Kinetic proofreading and the limits of thermodynamic uncertainty

To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively studied KPR circuits, DNA replication by the T7 DNA polymerase and translation by the E. coli ribosome. Using experimental data, we analyze the performance of these two vital systems in light of the fundamental bounds set by the recently discovered thermodynamic uncertainty relation (TUR), which places an inherent trade-off between the precision of a desirable output and the amount of energy dissipation required. We show that the DNA polymerase operates close to the TUR lower bound, while the ribosome operates ∼5 times farther from this bound. This difference originates from the enhanced binding discrimination of the polymerase which allows it to operate effectively as a reduced reaction cycle prioritizing correct product formation. We show that approaching this limit also decouples the thermodynamic uncertainty factor from speed and error, thereby relaxing the accuracy-speed trade-off of the system. Altogether, our results show that operating near this reduced cycle limit not only minimizes thermodynamic uncertainty, but also results in global performance enhancement of KPR circuits.

Thermodynamic uncertainty relation for underdamped Langevin systems driven by a velocity-dependent force

Recently, it has been shown that there is a trade-off relation between thermodynamic cost and current fluctuations, referred to as the thermodynamic uncertainty relation (TUR). The TUR has been derived for various processes, such as discrete-time Markov jump processes and overdamped Langevin dynamics. For underdamped dynamics, it has recently been reported that some modification is necessary for application of the TUR. However, the previous TUR for underdamped dynamics is not applicable to a system driven by a velocity-dependent force. In this study, we present a TUR, applicable to a system driven by a velocity-dependent force in the context of underdamped Langevin dynamics, by extending the theory of Vu and Hasegawa [Phys. Rev. E 100, 032130 (2019)2470-004510.1103/PhysRevE.100.032130]. We show that our TUR accurately describes the trade-off properties of a molecular refrigerator (cold damping), Brownian dynamics in a magnetic field, and an active particle system.

Thermodynamic uncertainty relation in thermal transport

We use the fundamental nonequilibrium steady-state fluctuation symmetry and derive a condition on the validity of the thermodynamic uncertainty relation (TUR) in thermal transport problems, classical and quantum alike. We test this condition and study the breakdown of the TUR in different thermal transport junctions of bosonic and electronic degrees of freedom. We prove that the TUR is valid in harmonic oscillator junctions. In contrast, in the nonequilibrium spin-boson model, which realizes many-body effects, it is satisfied in the Markovian limit, but violations arise as we tune (reduce) the cutoff frequency of the thermal baths, thus observing non-Markovian dynamics. We consider heat transport by noninteracting electrons in a tight-binding chain model. We show that the TUR is feasibly violated by tuning, e.g., the hybridization energy of the chain to the metal leads. These results manifest that the validity of the TUR relies on the statistics of the participating carriers, their interaction, and the nature of their couplings to the macroscopic contacts (metal electrodes and phonon baths).

Uncertainty relations for underdamped Langevin dynamics

A trade-off between the precision of an arbitrary current and the dissipation, known as the thermodynamic uncertainty relation, has been investigated for various Markovian systems. Here, we study the thermodynamic uncertainty relation for underdamped Langevin dynamics. By employing information inequalities, we prove that for such systems, the relative fluctuation of a current at a steady state is constrained by both the entropy production and the average dynamical activity. We find that unlike what is the case for overdamped dynamics, the dynamical activity plays an important role in the bound. We illustrate our results with two systems, a single-well potential system and a periodically driven Brownian particle model, and numerically verify the inequalities.

Fluctuation Theorem Uncertainty Relation

The fluctuation theorem is the fundamental equality in nonequilibrium thermodynamics that is used to derive many important thermodynamic relations, such as the second law of thermodynamics and the Jarzynski equality. Recently, the thermodynamic uncertainty relation was discovered, which states that the fluctuation of observables is lower bounded by the entropy production. In the present Letter, we derive a thermodynamic uncertainty relation from the fluctuation theorem. We refer to the obtained relation as the fluctuation theorem uncertainty relation, and it is valid for arbitrary dynamics, stochastic as well as deterministic, and for arbitrary antisymmetric observables for which a fluctuation theorem holds. We apply the fluctuation theorem uncertainty relation to an overdamped Langevin dynamics for an antisymmetric observable. We demonstrate that the antisymmetric observable satisfies the fluctuation theorem uncertainty relation but does not satisfy the relation reported for current-type observables in continuous-time Markov chains. Moreover, we show that the fluctuation theorem uncertainty relation can handle systems controlled by time-symmetric external protocols, in which the lower bound is given by the work exerted on the systems.

Theory of Nonequilibrium Free Energy Transduction by Molecular Machines

Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.

Uncertainty relations for time-delayed Langevin systems

The thermodynamic uncertainty relation, which establishes a universal trade-off between nonequilibrium current fluctuations and dissipation, has been found for various Markovian systems. However, this relation has not been revealed for non-Markovian systems; therefore, we investigate the thermodynamic uncertainty relation for time-delayed Langevin systems. We prove that the fluctuation of arbitrary dynamical observables is constrained by the Kullback-Leibler divergence between the distributions of the forward path and its reversed counterpart. Specifically, for observables that are antisymmetric under time reversal, the fluctuation is bounded from below by a function of a quantity that can be identified as a generalization of the total entropy production in Markovian systems. We also provide a lower bound for arbitrary observables that are odd under position reversal. The term in this bound reflects the extent to which the position symmetry has been broken in the system and can be positive even in equilibrium. Our results hold for finite observation times and a large class of time-delayed systems because detailed underlying dynamics are not required for the derivation. We numerically verify the derived uncertainty relations using two single time-delay systems and one distributed time-delay system.

Thermodynamic uncertainty relation in quantum thermoelectric junctions

Recently, a thermodynamic uncertainty relation (TUR) has been formulated for classical Markovian systems demonstrating trade-off between precision (current fluctuation) and cost (dissipation). Systems that violate the TUR are interesting as they overcome another trade-off relation concerning the efficiency of a heat engine, its power, and its stability (power fluctuations). Here, we analyze the root, extent, and impact on performance of TUR violations in quantum thermoelectric junctions at steady state. Considering noninteracting electrons, first we show that only the "classical" component of the current noise, arising from single-electron transfer events, follows the TUR. The remaining, "quantum" part of current noise is therefore responsible for the potential violation of the TUR in such quantum systems. Next, focusing on the resonant transport regime we determine the parameter range in which the violation of the TUR can be observed-for both voltage-biased junctions and thermoelectric engines. We illustrate our findings with exact numerical simulations of a serial double quantum dot system. Most significantly, we demonstrate that the TUR always holds in noninteracting thermoelectric generators when approaching the thermodynamic efficiency limit.

Unified Thermodynamic Uncertainty Relations in Linear Response

Thermodynamic uncertainty relations (TURs) are recently established relations between the relative uncertainty of time-integrated currents and entropy production in nonequilibrium systems. For small perturbations away from equilibrium, linear response (LR) theory provides the natural framework to study generic nonequilibrium processes. Here, we use LR to derive TURs in a straightforward and unified way. Our approach allows us to generalize TURs to systems without local time-reversal symmetry, including, e.g., ballistic transport and periodically driven classical and quantum systems. We find that, for broken time reversal, the bounds on the relative uncertainty are controlled both by dissipation and by a parameter encoding the asymmetry of the Onsager matrix. We illustrate our results with an example from mesoscopic physics. We also extend our approach beyond linear response: for Markovian dynamics, it reveals a connection between the TUR and current fluctuation theorems.

Large deviation function for a driven underdamped particle in a periodic potential

Employing large deviation theory, we explore current fluctuations of underdamped Brownian motion for the paradigmatic example of a single particle in a one-dimensional periodic potential. Two different approaches to the large deviation function of the particle current are presented. First, we derive an explicit expression for the large deviation functional of the empirical phase space density, which replaces the level 2.5 functional used for overdamped dynamics. Using this approach, we obtain several bounds on the large deviation function of the particle current. We compare these to bounds for overdamped dynamics that have recently been derived, motivated by the thermodynamic uncertainty relation. Second, we provide a method to calculate the large deviation function via the cumulant generating function. We use this method to assess the tightness of the bounds in a numerical case study for a cosine potential.

Thermodynamic Bounds on Precision in Ballistic Multiterminal Transport

For classical ballistic transport in a multiterminal geometry, we derive a universal trade-off relation between total dissipation and the precision, at which particles are extracted from individual reservoirs. Remarkably, this bound becomes significantly weaker in the presence of a magnetic field breaking time-reversal symmetry. By working out an explicit model for chiral transport enforced by a strong magnetic field, we show that our bounds are tight. Beyond the classical regime, we find that, in quantum systems far from equilibrium, the correlated exchange of particles makes it possible to exponentially reduce the thermodynamic cost of precision.

Derivation of Markov processes that violate detailed balance

Time-reversal symmetry of the microscopic laws dictates that the equilibrium distribution of a stochastic process must obey the condition of detailed balance. However, cyclic Markov processes that do not admit equilibrium distributions with detailed balance are often used to model systems driven out of equilibrium by external agents. I show that for a Markov model without detailed balance, an extended Markov model can be constructed, which explicitly includes the degrees of freedom for the driving agent and satisfies the detailed balance condition. The original cyclic Markov model for the driven system is then recovered as an approximation at early times by summing over the degrees of freedom for the driving agent. I also show that the widely accepted expression for the entropy production in a cyclic Markov model is actually a time derivative of an entropy component in the extended model. Further, I present an analytic expression for the entropy component that is hidden in the cyclic Markov model.

Energetic Costs, Precision, and Transport Efficiency of Molecular Motors

An efficient molecular motor would deliver cargo to the target site at a high speed and in a punctual manner while consuming a minimal amount of energy. According to a recently formulated thermodynamic principle, referred to as the thermodynamic uncertainty relation, the travel distance of a motor and its variance are, however, constrained by the free energy being consumed. Here we use the principle underlying the uncertainty relation to quantify the transport efficiency of molecular motors for varying ATP concentration ([ATP]) and applied load (f). Our analyses of experimental data find that transport efficiencies of the motors studied here are semioptimized under the cellular condition. The efficiency is significantly deteriorated for a kinesin-1 mutant that has a longer neck-linker, which underscores the importance of molecular structure. It is remarkable to recognize that, among many possible directions for optimization, biological motors have evolved to optimize the transport efficiency in particular.

Frenetic Bounds on the Entropy Production

We give a systematic derivation of positive lower bounds for the expected entropy production (EP) rate in classical statistical mechanical systems obeying a dynamical large deviation principle. The logic is the same for the return to thermodynamic equilibrium as it is for steady nonequilibria working under the condition of local detailed balance. We recover there recently studied "uncertainty" relations for the EP, appearing in studies about the effectiveness of mesoscopic machines. In general our refinement of the positivity of the expected EP rate is obtained in terms of a positive and even function of the expected current(s) which measures the dynamical activity in the system, a time-symmetric estimate of the changes in the system's configuration. Also underdamped diffusions can be included in the analysis.

Proof of the finite-time thermodynamic uncertainty relation for steady-state currents

The thermodynamic uncertainty relation offers a universal energetic constraint on the relative magnitude of current fluctuations in nonequilibrium steady states. However, it has only been derived for long observation times. Here, we prove a recently conjectured finite-time thermodynamic uncertainty relation for steady-state current fluctuations. Our proof is based on a quadratic bound to the large deviation rate function for currents in the limit of a large ensemble of many copies.