Related papers: Promoter methylation in a mixed feedback loop circ…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
Time-delayed quantum feedback is a fast and efficient method to control and stabilize few and many-body quantum systems. However, a proper understanding of such systems stays opaque due to the non-Markovian nature of the feedback protocol.…
DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of…
We describe an efficient approach to modelling cavity quantum electrodynamics (QED) with a time-delayed coherent feedback using quantum trajectory simulations. An analytical set of equations is derived to exploit the advantages of…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
The Hamiltonian mean-field (HMF) model is a system of fully coupled rotators which exhibits a second-order phase transition at some critical energy in its canonical ensemble. We investigate the case where the interaction between the rotors…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
Many biological processes display oscillatory behavior based on an approximately 24 hour internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic…
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many…
We study the effect of time-delayed feedback control and Gaussian white noise on the spatio-temporal charge dynamics in a semiconductor superlattice. The system is prepared in a regime where the deterministic dynamics is close to a global…
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…
A novel perturbative treatment of the time evolution operator of a quantum system is applied to the model describing a Raman-driven trapped ion in order to obtain a suitable 'effective model'. It is shown that the associated effective…
An exactly soluble non-linear interaction Hamiltonian is proposed to study fundamental properties of the entanglement dynamics for a coupled non-linear oscillators. The time-evolved state is obtained analytically for initial products of two…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
Feedback delay has been identified as a key ingredient in the quorum sensing synchronization of synthetic gene oscillators. While this influence has been evidenced at the theoretical level in a simplified system of degrade-and-fire…
We propose an exactly soluble W*-dynamical system generated by repeated harmonic perturbations of the one-mode quantum oscillator. In the present paper we deal with the case of isolated system. Although dynamics is Hamiltonian and…
We investigate feedback control of the cooperative dynamics of two coupled neural oscillators that is induced merely by external noise. The interacting neurons are modelled as FitzHugh-Nagumo systems with parameter values at which no…
We study how stronger noise can enhance the entanglement in inhomogeneously monitored quantum systems. We consider a free fermions model composed of two coupled chains - a system chain and an ancilla chain, each subject to its own different…