Related papers: A Dynamic P53-MDM2 Model with Time Delay
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Periodic patterns in dynamical behaviours of biological models described by simple form differential delay equations are studied. Mathematical models are given by a class of scalar delay differential equations with a multiplicative time…
Systems with time delay play an important role in modeling of many physical and biological processes. In this paper we describe generic properties of systems with time delay, which are related to the appearance and stability of periodic…
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation,…
The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological…
Delays and stochasticity have both served as crucially valuable ingredients in mathematical descriptions of control, physical, and biological systems. In this work, we investigate how explicitly dynamical stochasticity in delays modulates…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Transcription is regulated through interplay between transcription factors, an RNA polymerase(RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at the initial binding of RNAP, its…
Objective: The reservoir of human immunodeficiency virus (HIV) latently infected cells is the major obstacle for eradication of acquired immunodeficiency syndrome (AIDS). Due to the noisy environment and multiple influencing factors in the…
The finite duration of collisions appear as time-nonlocality in the kinetic equation. Analyzing the corresponding quantum kinetic equation for dense interacting Fermi systems a delay differential equation is obtained which combines time…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
We study the periodic forced response of a system of two limit cycle oscillators that interact with each other via a time delayed coupling. Detailed bifurcation diagrams in the parameter space of the forcing amplitude and forcing frequency…
The transcription factor p53 is an important regulator of cell fate. Mutations in p53 gene are associated with many cancers. In response to signals such as DNA damage, p53 controls the transcription of a series of genes that cause cell…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…