Related papers: Universal minimal cost of coherent biochemical osc…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
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…
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…
As biochemical systems may frequently suffer from limited energy resources so that internal molecular fluctuation has to be utilized to induce random rhythm, it is still a great theoretical challenge to understand the elementary principles…
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…
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.…
We determine the minimum energy required to control the evolution of any mesoscopic quantum system in the presence of arbitrary Markovian noise processes. This result provides the mesoscopic equivalent of the fundamental cost of…
Circadian rhythms in living organisms are temporal orders emerging from biochemical circuits driven out of equilibrium. Here, considering the KaiABC system, a minimal model in the synthetic biology, we study how the oscillation emerges from…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
Brownian clocks are biomolecular networks that can count time. A paradigmatic example are proteins that go through a cycle thus regulating some oscillatory behaviour in a living system. Typically, such a cycle requires free energy often…
The thermodynamic uncertainty relation sets the minimal bound of the cost-precision trade-off relation for dissipative processes. Examining the dynamics of an internally coupled system that is driven by a constant thermodynamic force, we…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
Temporal order in living matters reflects the self-organizing nature of dynamical processes driven out of thermodynamic equilibrium. Because of functional reason, the period of a biochemical oscillation must be tuned to a specific value…
The living cell uses a variety of molecular receptors to read and process chemical signals that vary in space and time. We model the dynamics of such molecular level measurements as Markov processes in steady state, with a coupling between…
A fundamental description of time can be consistent not only with the usual monotonic behavior but also with a periodic physical clock variable, coupled to the degrees of freedom of a system evolving in time. Generically, one would in fact…
A driven linear oscillator and a feedback mechanism are two necessary elements of any classical periodic clock. Here, we introduce a novel, fully quantum clock using a driven oscillator in the quantum regime and coherent quantum feedback.…
We present a practical method to obtain bounds for the oscillation minima and maxima of large classes of biochemical oscillator models that generate oscillations through a negative feedback. These bounds depend on the feedback nonlinearity…
Hour-glass clocks do not free-run; they keep time by riding an external rhythm. Motivated by the primordial KaiBC system in cyanobacteria, we study a driven, finite-state molecular clock that advances through a small number of biochemical…
Subharmonic response is a well known phenomena in, e.g., deterministic nonlinear dynamical systems. We investigate the conditions under which such subharmonic oscillations can persist for a long time in open systems with stochastic dynamics…
The processing of quantum information always has a cost in terms of physical resources such as energy or time. Determining the resource requirements is not only an indispensable step in the design of practical devices - the resources need…