Related papers: Simple post-translational circadian clock models f…
We investigate the emergence of time quasicrystals (TQCs) in the open Dicke model, subjected to a quasi-periodic Fibonacci drive. TQCs are characterized by a robust sub-harmonic quasi-periodic response that is qualitatively distinct from…
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…
Temporal modulation unlocks possibilities to dynamically control and modify the response of electromagnetic systems. Employing explicit dependencies of circuit or surface parameters on time enables the engineering of systems with…
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…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
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…
The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other…
The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced by Earth rotation. However, environmental…
Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are…
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has…
Quantum collision models allow for the dynamics of open quantum systems to be described by breaking the environment into small segments, typically consisting of non-interacting harmonic oscillators or two-level systems. This work introduces…
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…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
Quasi steady state assumptions are often used to simplify complex systems of ordinary differential equations in modelling of biochemical processes. The simplified system is designed to have the same qualitative properties as the original…
A time-dependent vibrational electronic coupled-cluster (VECC) approach is proposed to simulate photoelectron/ UV-VIS absorption spectra, as well as time-dependent properties for non-adiabatic vibronic models, going beyond the…
Open many-body quantum systems can exhibit intriguing nonequilibrium phases of matter, such as time crystals. In these phases, the state of the system spontaneously breaks the time-translation symmetry of the dynamical generator, which…
Discrete (DTCs) and continuous time crystals (CTCs) are novel dynamical many-body states, that are characterized by robust self-sustained oscillations, emerging via spontaneous breaking of discrete or continuous time translation symmetry.…
Many complex systems can spontaneously oscillate under non-periodic forcing. Such self-oscillators are commonplace in biological and technological assemblies where temporal periodicity is needed, such as the beating of a human heart or the…
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically…
Many-body quantum systems, under suitable conditions, exhibit time-translation symmetry breaking and settle in a discrete time crystalline (DTC) phase -- an out-of-equilibrium quantum phase of matter. The defining feature of DTC is a robust…