Related papers: Cell State Transitions Beyond the Small-Noise Limi…
Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…
We study a simple chemical reaction system and effects of the internal noise. The chemical reaction system causes the same transition phenomenon discussed by Togashi and Kaneko [Phys. Rev. Lett. 86 (2001) 2459; J. Phys. Soc. Jpn. 72 (2003)…
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with…
Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…
Noise caused by fluctuations at the molecular level is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it…
Segregation of different cell types is a crucial process for the pattern formation in tissues, in particular during embryogenesis. Since the involved cell interactions are complex and difficult to measure individually in experiments,…
Recent single molecule experiments probing the passage process of a short single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to measure the passage time distribution. Building on a recent modelling approach (D. K.…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
The origin of nonlinear responses in cells has been suggested to be crucial for various cell functions including the propagation of the nervous impulse. In physics nonlinear behavior often originates from phase transitions. Evidence for…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
Noise in the local transition function is compared to fluctuations in the updating times of the cells. Obtained results are shown to be quite different in both cases. In this extended abstract we briefly explain the problem and present…
In neural circuits, statistical connectivity rules strongly depend on neuronal type. Here we study dynamics of neural networks with cell-type specific connectivity by extending the dynamic mean field method, and find that these networks…
Motility is characteristic of life, but a common basis for movement has remained to be identified. Diverse systems in motion shift between two states depending on interactions that turnover at the rate of an applied cycle of force. Although…
Thermal noise in a cellular automaton refers to a random perturbation to its function which eventually leads this automaton to an equilibrium state controlled by a temperature parameter. We study the 1-dimensional majority-3 cellular…
Exploring quantum phenomena beyond predictions of any classical model has fundamental importance to understand the boundary of classical and quantum descriptions of nature. As a typical property that a quantum system behaves distinctively…
We identify a new universality class of phase transitions that emerges in non-normal systems, extending the classical framework beyond eigenvalue instabilities. Unlike traditional critical phenomena, where transitions occur when eigenvalues…
Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
Dynamic encircling of exceptional points has attracted significant interest in recent years, as it can facilitate chiral transmission selectivity due to a nontrivial eigenstate evolution. Recently, multi-state systems have been explored,…
We study the effects of noise on the dynamics of a system of coupled self-propelling particles in the case where the coupling is time-delayed, and the delays are discrete and randomly generated. Previous work has demonstrated that the…