Related papers: Intracellular delay limits cyclic changes in gene …
In this paper, we consider two stochastic models of gene expression in prokaryotic cells. In the first model, sixteen biochemical reactions involved in transcription, translation and transcriptional regulation in the presence of inducer…
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…
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…
Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: the finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we provide a…
We present a detailed study of a scalar differential equation with threshold state-dependent delayed feedback. This equation arises as a simplification of a gene regulatory model. There are two monotone nonlinearities in the model: one…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
It is known that an identical delay in all transmission lines can destabilize macroscopic stationarity of a neural network, causing oscillation or chaos. We analyze the collective dynamics of a network whose intra-transmission delays are…
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…
Mathematical models of living cells have been successively refined with advancements in experimental techniques. A main concern is striking a balance between modelling power and the tractability of the associated mathematical analysis. In…
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 study a mathematical model describing the dynamics of a pluripotent stem cell population involved in the blood production process in the bone marrow. This model is a differential equation with a time delay. The delay describes the cell…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein.…
Time lags are ubiquitous in biophysiological processes and more generally in real-world complex networks. It has been recently proposed to use information-theoretic tools such as transfer entropy to detect and estimate a possible delay in…
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signaling molecules - morphogens - guide this process. The continuous positional information…
The epigenetic pathway of a cell as it differentiates from a stem cell state to a mature lineage-committed one has been historically understood in terms of Waddington's landscape, consisting of hills and valleys. The smooth top and…