Related papers: Pseudo-Random Fluctuations, Stochastic Cooperativi…
In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
We study a stochastic system of interacting neurons and its metastable properties. The system consists of $N$ neurons, each spiking randomly with rate depending on its membrane potential. At its spiking time, the neuron potential is reset…
Exceptional points, a remarkable phenomenon in physical systems, have been exploited for sensing applications. It has been demonstrated recently that it can also utilize as sensory threshold in which the interplay between exceptional-point…
Many real-world systems are characterized by stochastic dynamical rules where a complex network of interactions among individual elements probabilistically determines their state. Even with full knowledge of the network structure and of the…
Using a generalized random recurrent neural network model, and by extending our recently developed mean-field approach [J. Aljadeff, M. Stern, T. Sharpee, Phys. Rev. Lett. 114, 088101 (2015)], we study the relationship between the network…
In this work we investigate time varying networks with complex dynamics at the nodes. We consider two scenarios of network change in an interval of time: first, we have the case where each link can change with probability pt, i.e. the…
Randomness is an unavoidable feature of the intracellular environment due to chemical reactants being present in low copy number. That phenomenon, predicted by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic…
This paper considers the behavior of discrete and continuous mathematical models for gene expression in the presence of transcriptional/translational bursting. We treat this problem in generality with respect to the distribution of the…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Machine learning has made tremendous progress in recent years, with models matching or even surpassing humans on a series of specialized tasks. One key element behind the progress of machine learning in recent years has been the ability to…
Stochasticity in gene expression can result in fluctuations in gene product levels. Recent experiments indicated that feedback regulation plays an important role in controlling the noise in gene expression. A quantitative understanding of…
Oscillatory dynamics are ubiquitous in biological networks. Possible sources of oscillations are well understood in low-dimensional systems, but have not been fully explored in high-dimensional networks. Here we study large networks…
Recently, a first step was made by the authors towards a systematic investigation of the effect of reaction-step-size noise - uncertainty in the step size of the reaction - on the dynamics of stochastic populations. This was done by…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
Understanding of short-term synaptic depression (STSD) and other forms of synaptic plasticity is a topical problem in neuroscience. Here we study the role of STSD in the formation of complex patterns of brain rhythms. We use a cortical…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…