Related papers: Transcription fluctuation effects on biochemical o…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
Phase-transitionlike behavior is found to occur in globally coupled systems of finite number of elements, and its theoretical explanation is provided. The system studied is a population of globally pulse-coupled integrate-and-fire cells…
Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood…
Nonlinear damping, the change in damping rate with the amplitude of oscillations plays an important role in many electrical, mechanical and even biological oscillators. In novel technologies such as carbon nanotubes, graphene membranes or…
How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations,…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Classic and recent results for gauge effects on the properties of the normal-to-superconducting phase transition in bulk and thin film superconductors are reviewed. Similar problems in the description of other natural systems (liquid…
In spatially distributed cellular systems, it is often convenient to represent complicated auxiliary pathways and spatial transport by time-delayed reaction rates. Furthermore, many of the reactants appear in low numbers necessitating a…
The dynamic behaviors of microRNA and mRNA under external stress are studied with biological experiments and mathematics models. In this study, we developed a mathematic model to describe the biological phenomenon and for the first time…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Fluctuations are a key property of both classical and quantum systems. While the fluctuations are well understood for many quantum systems at zero temperature, the case of an interacting quantum system at finite temperature still poses…
Biochemical oscillations are ubiquitous in living organisms. In an autonomous system, not influenced by an external signal, they can only occur out of equilibrium. We show that they emerge through a generic nonequilibrium phase transition,…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
In some instances, e.g. near phase transitions, thermodynamic fluctuations become macroscopically relevant, and relative amplitudes grow far above the standard $N^{-1/2}$ scale, with $N$ the number of particles. Such large fluctuations are…
Fluctuations of thermodynamic quantities become non-negligible and play an important role when the system size is small. We develop finite-time thermodynamics of fluctuations in microscopic heat engines whose environmental temperature and…
We study the dynamics of a nonlinear oscillator near the critical point where period-two vibrations are first excited with the increasing amplitude of parametric driving. Above the threshold, quantum fluctuations induce transitions between…
Quantum systems are typically characterized by the inherent fluctuation of their physical observables. Despite this fundamental importance, the investigation of the fluctuations in interacting quantum systems at finite temperature continues…
We study the effects of intrinsic noise on chemical reaction systems, which in the deterministic limit approach a limit cycle in an oscillatory manner. Previous studies of systems with an oscillatory approach to a fixed point have shown…
We study the effects of random fluctuations on quantum phase transitions by the energy gap analysis. For the infinite-ranged spin-glass models with a transverse field, we find that a strong sample-to-sample fluctuation effect leads to broad…