Related papers: Transcription fluctuation effects on biochemical o…
Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise…
The influence of dissipation on the fluctuation statistics of the total energy is investigated through both a phenomenological and a stochastic model for dissipative energy-transfer through a cascade of states. In equilibrium the states…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
Gene transcriptional regulatory is an inherently noisy process. In this paper, the study of fluctuations in a gene transcriptional regulatory system is extended to the case of L\'evy noise, a kind of non-Gaussian noises which can describe…
We study quantum measurements of temporal equilibrium fluctuations in macroscopic quantum systems. It is shown that the fluctuation-dissipation theorem, as a relation between observed quantities, is partially violated in quantum systems,…
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…
When a quantum many-particle system exists on a randomly diluted lattice, its intrinsic thermal and quantum fluctuations coexist with geometric fluctuations due to percolation. In this paper, we explore how the interplay of these…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
The influence of the initial fluctuations on the onset of scaling in the quench to zero temperature of a two dimensional system with conserved order parameter, is analyzed in detail with and without topological defects. We find that the…
Understanding the dynamics of equilibration processes in quantum systems as well as their interplay with dissipation and fluctuation is a major challenge in quantum many-body theory. The timescales of such processes are investigated in…
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…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
We develop the statistical mechanics of the Hopfield model in a transverse field to investigate how quantum fluctuations affect the macroscopic behavior of neural networks. When the number of embedded patterns is finite, the Trotter…
In this paper we study the asymptotic behavior of mesoscopic fluctuations for the thinned Circular Unitary Ensemble. The effect of thinning is that the eigenvalues start to decorrelate. The decorrelation is stronger on the larger scales…
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…
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in…
We review the physical phenomena that arise when quantum mechanical energy levels are modulated in time. The dynamics resulting from changes in the transition frequency is a problem studied since the early days of quantum mechanics. It has…
Slow fluctuations of a qubit frequency are one of the major problems faced by quantum computers. To understand their origin it is necessary to go beyond the analysis of their spectra. We show that characteristic features of the fluctuations…