Related papers: Simple post-translational circadian clock models f…
Regular measurements allow predicting the future and retrodicting the past of quantum systems. Time-non-local measurements can leave the future and the past uncertain, yet establish a relation between them. We show that continuous…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
Biological systems have the unique ability to self-organize and generate autonomous motion and work. Motivated by this, we investigate a 2D model colloidal network that can repeatedly transition between disordered states of low connectivity…
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…
We consider the adiabatic quantum algorithm for systems with "no sign problem", such as the transverse field Ising mode, and analyze the equilibration time for quantum Monte Carlo (QMC) on these systems. We ask: if the spectral gap is only…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
We review the construction and evolution of mathematical models of the Arabidopsis circadian clock, structuring the discussion into two distinct historical phases of modeling strategies: extension and reduction. The extension phase explores…
We demonstrate how a time-dependent dissipative environment may be used as a tool for controlling the quantum state of a two-level atom. In our model system the frequency and coupling strength associated with microscopic reservoir modes are…
Discrete time crystals (DTCs) are nonequilibrium phases of matter with exotic observable dynamics. Among their remarkable features is their response to a periodic drive at a fraction of its frequency. Current successful experiments are…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
Coherent oscillatory activity can arise spontaneously as a result of increased coupling in a system of excitable and passive cells, each being quiescent in isolation. This can potentially explain the appearance of spontaneous rhythmic…
We propose a novel Bayesian methodology for analyzing nonstationary time series that exhibit oscillatory behaviour. We approximate the time series using a piecewise oscillatory model with unknown periodicities, where our goal is to estimate…
The center of mass motion of trapped ions and neutral atoms is suitable for approximation by a time-dependent driven quantum harmonic oscillator whose frequency and driving strength may be controlled with high precision. We show the time…
Whereas the importance of transient dynamics to the functionality and management of complex systems has been increasingly recognized, most of the studies are based on models. Yet in realistic situations the models are often unknown and what…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
We study feedback control of classical Hamiltonian systems with the controlling parameter varying slowly in time. The control aims to change system's energy. We show that the control problems can be solved with help of an adiabatic…
The engineering of new states of matter through Floquet driving has revolutionized the field of condensed matter physics. This technique enables the creation of hybrid topological states and ordered phases that are absent in normal systems.…
Quantum simulation has begun to penetrate the field of quantum chemistry in hopes of efficiently calculating ground state energies and approximating real-time evolution. With modern research highlighting nonadiabatic dynamics, tunably…
Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely,…