Related papers: Modeling Transient Changes in Circadian Rhythms
We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We study experimentally the thermal fluctuations of energy input and dissipation in a harmonic oscillator driven out of equilibrium, and search for Fluctuation Relations. We study transient evolution from the equilibrium state, together…
We study the noise characteristics of stochastic oscillations in protein number dynamics of simple genetic oscillatory systems. Using the three-component negative feedback transcription regulatory system called the repressilator as a…
The time-periodic modulation of a temperature gradient can alter the heat transport properties of a physical system. Oscillating thermal gradients give rise to behaviors such as modified thermal conductivity and controllable time-delayed…
When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic…
The fidelity of operations on a solid-state quantum processor is fundamentally bounded by environmental decoherence. Characterizing environmental fluctuations is challenging because the acquisition time of nonadaptive experimental protocols…
The time-dependent optical properties of molecular systems are investigated by step-scan Fourier-transform spectroscopy in order to explore the dynamics at phase transitions and molecular orientation in the milli- and microsecond range. The…
How does soil pollution affect a plant's circadian clock? Are there any differences between how the clock reacts when exposed to different concentrations of elements of the periodic table? If so, can we characterise these differences? We…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Biological systems process information under noisy environment. Sensory adaptation model of E. coli is suitable for investigation because of its simplicity. To understand the adaptation processing quantitatively, stochastic thermodynamic…
By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
We present a rigorous and efficient approach to the calculation of classical lattice-dynamical quantities from simulations that do not require an explicit solution of the time evolution. We focus on the temperature-dependent vibrational…
RNA thermometers are mRNA strands with a temperature dependent secondary structure: depending on the spatial conformation, the mRNA strand can get translated (on-state) or can be inaccessible for ribosomes binding (off-state). These have…
In this theoretical study, we focus on the high-frequency response of the electrothermal NbO2-Mott threshold switch, a real-world electronic device, which has been proved to be relevant in several applications and is classified as a…
Eukaryotic gene regulation is based on stochastic yet controlled promoter switching, during which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies reveal…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…