Biochemical oscillations, regulating the timing of life processes, need consume energy to achieve good performance on crucial functions, such as high accuracy of phase period and high sensitivity to external signals. However, it is a great challenge to precisely estimate the energy dissipation in such systems. Here, based on the stochastic normal form theory (SNFT), we calculate the Pearson correlation coefficient between the oscillatory amplitude and phase, and a trade-off relation between transport efficiency and phase sensitivity can then be derived, which serves as a tighter form than the estimator resulting from the conventional thermodynamic uncertainty relation (TUR). Our findings demonstrate that a more precise energy dissipation estimation can be obtained by enhancing the sensitivity of the biochemical oscillations. Moreover, the internal noise and amplitude power effects have also been discovered.
Biochemical oscillations are ubiquitous in living organisms. In an autonomous system, not influenced by an external signal, they can only occur out of equilibrium. We show that they emerge through a generic nonequilibrium phase transition, with a characteristic qualitative behavior at criticality. The control parameter is the thermodynamic force, which must be above a certain threshold for the onset of biochemical oscillations. This critical behavior is characterized by the thermodynamic flux associated with the thermodynamic force, its diffusion coefficient, and the stationary distribution of…
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 r…
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 $\mathcal{N}$ oscillations has a minimal free energy cost per oscillati…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We obtain analytical expressions for the coherence and period of oscillations in these networks. These quantities are expected to depend on all details of the transition rates in the Markov state model. However, our analytical calculations reveal that driving the system out of equilibrium makes many of these details - specifically, the location and arrangement o…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic. Understanding the physical basis for robust biochemical oscillations in the presence of fluctuations has thus emerged as an important problem. In a previous paper [C. del Junco and S. Vaikuntanathan, Phys. Rev. E 101, 012410 (2020)], we explored this question using the non-equilibrium statistical mechanics of single-ring Markov state models of biochemical network…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration of a full oscillation cycle is random. Their success in carrying out their biological function is thought to depend on the degree to which these fluctuations in the cycle period can be suppressed. Biochemical oscillators also require a constant supply of free energy in order to break detailed balance and maintain their cyclic dynamics. For a given free energy…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations, fail to exhibit oscillations for any values of rate constants. The mechanism relies on amplification of the underlying stochasticity of reaction kinetics within a narrow window of frequencies. This amplification allows fluctuations to beat the central limit theorem, having a dominant effect even though the number of molecules in the system is relatively large.…
A formalism is developed which describes the extent to which stochastic oscillations in biochemical models are synchronised. It is based on the calculation of the complex coherence function within the linear noise approximation. The method is illustrated on a simple example and then applied to study the synchronisation of chemical concentrations in social amoeba. The degree to which variation of rate constants in different cells and the volume of the cells affects synchronisation of the oscillations is explored, and the phase lag calculated. In all cases the analytical results are shown to be …
Accurate and robust spatial orders are ubiquitous in living systems. In 1952, Alan Turing proposed an elegant mechanism for pattern formation based on spontaneous breaking of the spatial translational symmetry in the underlying reaction-diffusion system. Much is understood about dynamics and structure of Turing patterns. However, little is known about the energetic cost of Turing pattern. Here, we study nonequilibrium thermodynamics of a small spatially extended biochemical reaction-diffusion system by using analytical and numerical methods. We find that the onset of Turing pattern requires a …
Living and non-living active matter consumes energy at the microscopic scale to drive emergent, macroscopic behavior including traveling waves and coherent oscillations. Recent work has characterized non-equilibrium systems by their total energy dissipation, but little has been said about how dissipation manifests in distinct spatiotemporal patterns. We introduce a novel measure of irreversibility we term the entropy production factor (EPF) to quantify how time reversal symmetry is broken in field theories across scales. We use the EPF to characterize a dynamical phase transition in simulation…
Characteristic oscillations in frequency-resolved heat dissipation of linear time-delayed Langevin systems: Approach from the violation of the fluctuation-response relation
We perform a detailed field theoretical study of nonequilibrium Josephson oscillations between interacting Bose-Einstein condensates confined in a finite-size double-well trap. We find that the Josephson junction can sustain multiple undamped Josephson oscillations up to a characteristic time scale $τ_c$ without quasipartcles being excited in the system. This may explain recent related experiments. At larger times the dynamics of the junction is governed by fast Rabi oscillations between the descrete quasiparticle levels. We predict that a selftrapped BEC state will be destroyed by these Rabi …
The spontaneously oscillating hair bundle of sensory cells in the inner ear is an example of a stochastic, nonlinear oscillator driven by internal active processes. Moreover, this internal activity is adaptive -- its power input depends on the current state of the system. We study fluctuation dissipation relations in such adaptively-driven, nonequilibrium limit-cycle oscillators. We observe the expected violation of the well-known, equilibrium fluctuation-dissipation theorem (FDT), and verify the existence of a generalized fluctuation-dissipation theorem (GFDT) in the non-adaptively driven mod…
In $N$-body systems with long-range interactions mean-field effects dominate over binary interactions (collisions), so that relaxation to thermal equilibrium occurs on time scales that grow with $N$, diverging in the $N\to\infty$ limit. However, a faster and non-collisional relaxation process, referred to as violent relaxation, sets in when starting from generic initial conditions: collective oscillations (referred to as virial oscillations) develop and damp out on timescales not depending on the system's size. After the damping of such oscillations the system is found in a quasi-stationary st…
A phenomenon of energy dissipation in Bose-Einstein condensates is studied based on a microscopic model for the motion of impurity. Critical velocities for onset of energy dissipation are obtained for periodic motions, such as a dipole-like oscillation and a circular motion. The first example is similar to a series of MIT group experiments settings where the critical velocity was observed much below the Landau critical velocity. The appearance of the smaller values for the critical velocity is also found in our model, even in the homogeneous condensate in the thermodynamic limit. This suggests…
We investigate the conditions under which periodically driven quantum systems subject to dissipation exhibit a stable subharmonic response. Noting that coupling to a bath introduces not only cooling but also noise, we point out that a system subject to the latter for the entire cycle tends to lose coherence of the subharmonic oscillations, and thereby the long-time temporal symmetry breaking. We provide an example of a short-ranged two-dimensional system which does not suffer from this and therefore displays persistent subharmonic oscillations stabilised by the dissipation. We also show that t…
The interplay of synchronization and topological band structures with symmetry protected midgap states under the influence of driving and dissipation is largely unexplored. Here we consider a trimer chain of electron shuttles, each consisting of a harmonic oscillator coupled to a quantum dot positioned between two electronic leads. Each shuttle is subject to thermal dissipation and undergoes a bifurcation towards self-oscillation with a stable limit cycle if driven by a bias voltage between the leads. By mechanically coupling the oscillators together, we observe synchronized motion at the ends…
