Related papers: Promoter methylation in a mixed feedback loop circ…
In genomic applications, there is often interest in identifying genes whose time-course expression trajectories exhibit periodic oscillations with a period of approximately 24 hours. Such genes are usually referred to as circadian, and…
The model of light-matter interaction in quantum electrodynamics typically relies on the Markovian approximation, which assumes that the system's future evolution depends solely on its current state, effectively treating it as a…
Parametrically modulated optomechanical systems have been recently proposed as a simple and efficient setting for the quantum control of a micromechanical oscillator: relevant possibilities include the generation of squeezing in the…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
We solve exactly the non-Markovian dynamics of a cavity mode in the presence of a feedback loop based on homodyne measurements, in the case of a non-zero feedback delay time. With an appropriate choice of the feedback parameters, this…
Undesired acoustic feedback is a known issue in communication systems, such as speech in-car communication, public address systems, or hearing aids. Without additional precautions, there is a high risk that the adaptive filter - intended to…
Transport in a one-dimensional symmetric device can be activated by the combination of thermal noise and a bi-harmonic drive. For the study case of an overdamped Brownian particle diffusing on a periodic one-dimensional substrate, we…
Multiple time correlation functions are found in the dynamical description of different phenomena. They encode and describe the fluctuations of the dynamical variables of a system. In this paper we formulate a theory of non-Markovian…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The influence of optical feedback on semiconductor lasers has been a widely studied field of research due to fundamental interests as well as the optimization of optical data transmission and computing. Recent publications have shown that…
A new method is introduced for analysis of interactions between time-dependent coupled oscillators, based on the signals they generate. It distinguishes unsynchronized dynamics from noise-induced phase slips, and enables the evolution of…
Observations that rates of molecular evolution vary widely within and among lineages have cast doubts upon the existence of a single molecular clock. Differences in the timing of evolutionary events estimated from genetic and fossil…
We investigate the synchronization dynamics of two coupled noise-driven FitzHugh-Nagumo systems, representing two neural populations. For certain choices of the noise intensities and coupling strength, we find cooperative stochastic…
A feedback mechanism that involves the proteins p53 and mdm2, induces cell death as a controled response to severe DNA damage. A minimal model for this mechanism demonstrates that the respone may be dynamic and connected with the time…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
This paper is the second in a series devoted to the study of Langevin systems subjected to a continuous time-delayed feedback control. The goal of our previous paper [Phys. Rev. E 91, 042114 (2015)] was to derive second-law-like…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
Temporal coherence of driven-dissipative condensates is limited by phase noise. We show that mirror-mediated time-delayed self-feedback enables control of coherence in a trapped exciton-polariton condensate. Reinjecting a small fraction of…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
A genuine feature of projective quantum measurements is that they inevitably alter the mean energy of the observed system if the measured quantity does not commute with the Hamiltonian. Compared to the classical case, Jacobs proved that…