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The in vivo circadian clock in single cyanobacteria is studied here by time-lapse fluorescence microscopy when the temperature is lowered below 25{\deg}C . We first disentangle the circadian clock behavior from the bacterial cold shock…
Rhythms in electrical activity in the membrane of cells in the suprachiasmatic nucleus (SCN) are crucial for the function of the circadian timing system, which is characterized by the expression of the so-called clock genes. Intracellular…
Polyelectrolytes, such as polyacrylic acid (PAA), can effectively mitigate $\mathrm{CaCO_3}$ scale formation. Despite their success as antiscalants, the underlying mechanism of $\mathrm{Ca^{2+}}$ binding to polyelectrolyte chains remains…
In this Supporting Information, we provide background information on our model of the in vitro Kai system and the calculations that we have performed. We will closely follow the outline of the main text.
Quantum systems driven by time-dependent Hamiltonians are considered here within the framework of steepest-entropy-ascent quantum thermodynamics (SEAQT) and used to study the thermodynamic characteristics of such systems. In doing so, a…
We consider a harmonic oscillator under periodic driving and coupled to two harmonic-oscillator heat baths at different temperatures. We use the thermofield transformation with chain mapping for this setup, which allows us to study the…
The green microscopic alga Ostreococcus tauri has recently emerged as a promising model for understanding how circadian clocks, which drive the daily biological rythms of many organisms, synchronize to the day/night cycle in changing…
Many organisms repartition their proteome in a circadian fashion in response to the daily nutrient changes in their environment. A striking example is provided by cyanobacteria, which perform photosynthesis during the day to fix carbon.…
Mitochondrial adenine nucleotide (AdN) content is regulated through the Ca2+-activated, electroneutral ATP-Mg/Pi carrier (APC). The APC is a protein in the mitochondrial carrier super family that localizes to the inner mitochondrial…
Temperature compensation is a notable property of circadian oscillators that indicates the insensitivity of the oscillator system's period to temperature changes; the underlying mechanism, however, is still unclear. We investigated the…
Synchronisation is a collective phenomenon widely investigated in classical oscillators and, more recently, in quantum systems. However, it remains unclear what features distinguish synchronous behaviour in these two scenarios. Recent works…
Autonomous circadian clocks drive daily rhythms in physiology and behaviour. A network of coupled neurons, the suprachiasmatic nucleus (SCN), serves as a robust self-sustained circadian pacemaker. Synchronization of this timer to the…
An ultra-stable optical clock based on coherent population trapping effect of alkaline-earth ions, such as Ca$^+$, Sr$^+$, Ba$^+$, is analyzed here. The proposed transitions use the odd isotopes, so that the frequency shift is insensitive…
Thermal machines are physical systems designed to convert thermal energy into practical work through cyclic state transformations. A key component in such a machine is a clock-equipped control element that dictates which interaction…
In classical physics, clocks are open dissipative systems driven from thermal equilibrium and necessarily subject to thermal noise. We describe a quantum clock driven by entropy reduction through measurement. The mechanism consists of a…
Quantum hydrodynamics is a formulation of quantum mechanics based on the probability density and flux (current) density of a quantum system. It can be used to define trajectories which allow for a particle-based interpretation of quantum…
We consider a periodic quantum clock based on cooperative resonance fluorescence at zero temperature. In the quantum case, this system has an exact steady state and the limit cycle appears in conditional quantum dynamics under homodyne…
Living organisms need to be sensitive to a changing environment while also ignoring uninformative environmental fluctuations. Here, we show that the circadian clock in \textit{Synechococcus elongatus} can naturally tune its environmental…
Recent experimental evidence for collective protein vibrations in the terahertz (THz) domain indicates that energy in biomolecular systems can self-organize in an orderly manner, as anticipated by Fr\"ohlich's theory of condensates within a…
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…