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Periodic forcing of nonlinear oscillators leads to a large number of dynamic behaviors. The coupling of the cell-cycle to the circadian clock provides a biological realization of such forcing. Using high throughput single-cell microscopy,…
With the advent of optical clocks featuring fractional frequency uncertainties on the order of $10^{-17}$ and below, new applications such as chronometric levelling with few-cm height resolution emerge. We are developing a transportable…
The ability of a circadian system to entrain to the 24-hour light-dark cycle is one of its most important properties. A new tool, called the entrainment map, was recently introduced to study this process for a single oscillator. Here we…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the…
Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…
The sinoatrial-node (SAN) is a complex heterogeneous tissue that generates a stable rhythm in healthy hearts, yet a general mechanistic explanation for when and how this tissue remains stable is lacking. Although computational and…
We study the dynamics of a circadian oscillator model which was proposed by Tyson, Hong, Thron and Novak. This model indicates a molecular mechanism for the circadian rhythm in Drosophila. After giving a detailed study of the equilibria, we…
Circadian rhythms are biological rhythms of approximately 24 h that persist even under constant conditions without environmental daily cues. The molecular circadian clock machinery generates the physiological rhythms, which can be…
All clocks, classical or quantum, are open non equilibrium irreversible systems subject to the constraints of thermodynamics. Using examples I show that these constraints necessarily limit the performance of clocks and that good clocks…
We analyse the correlated back and forth dynamics and dynamic heterogeneities, i.e. the presence of fast and slow ions, for a lithium metasilicate system via computer simulations. For this purpose we define, in analogy to previous work in…
The quantum harmonic oscillator is the fundamental building block to compute thermal properties of virtually any dielectric crystal at low temperatures in terms of phonons, extended further to cases with anharmonic couplings, or even…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
From a thermodynamic point of view, all clocks are driven by irreversible processes. Additionally, one can use oscillatory systems to temporally modulate the thermodynamic flux towards equilibrium. Focusing on the most elementary…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
In this paper and its sequel, we study non-equilibrium dynamics in driven 1+1D conformal field theories (CFTs) with periodic, quasi-periodic, and random driving. We study a soluble family of drives in which the Hamiltonian only involves the…
We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics…
We study the time evolution of entanglement in a quantum version of the Kac ring. Our model consists of two spin chains and quantum gates instead of the classical markers. The gates take one qubit from each ring at a time as an input and…
Indoor air quality (IAQ) forecasting plays a critical role in safeguarding occupant health, ensuring thermal comfort, and supporting intelligent building control. However, predicting future concentrations of key pollutants such as carbon…