Related papers: Genetic Toggle Switch Without Cooperative Binding
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
We study long-range interacting systems driven by external stochastic forces that act collectively on all the particles constituting the system. Such a scenario is frequently encountered in the context of plasmas, self-gravitating systems,…
We solve a conjecture on multiple nondegenerate steady states, and prove bistability for sequestration networks. More specifically, we prove that for any odd number of species, and for any production factor, the fully open extension of a…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
The current paper is concerned with the asymptotic dynamics of two species competition systems with/without chemotaxis in heterogeneous media. In the previous work \cite{ITBWS17a}, we find conditions on the parameters in such systems for…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…
The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
We study the existence of stable matchings when agents have choice correspondences instead of preference relations. We extend the framework of \cite{chambers2017choice} by weakening the path independence assumption. For many-to-many…
Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…
Multisite phosphorylation plays an important role in intracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when the phosphorylation/dephosphorylation mechanism is distributive, that is,…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Topological theory predicts the necessary conditions for robust dimensional reduction in a host of quantum and classical systems. Models have recently been proposed for stochastic systems which describe many biological and chemical…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis,…
This paper investigates structural herdability in a special class of temporally switching networks with fixed topology. We show that when the underlying digraph remains unchanged across all snapshots, the network attains complete SS…