Related papers: Functional characteristics of a double positive fe…
This paper considers adiabatic reduction in both discrete and continuous models of stochastic gene expression. In gene expression models, the concept of bursting is a production of several molecules simultaneously and is generally…
Many cellular functions are based on the rhythmic organization of biological processes into self-repeating cascades of events. Some of these periodic processes, such as the cell cycles of several species, exhibit conspicuous irregularities…
Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of…
We conduct numerical analysis of the 2-dimensional discrete-time gene expression model originally introduced by Andrecut and Kauffman (Phys. Lett. A 367: 281-287, 2007). In contrast to the previous studies, we analyze the dynamics with…
Biological oscillators coordinate individual cellular components so that they function coherently and collectively. They are typically composed of multiple feedback loops, and period mismatch is unavoidable in biological implementations. We…
We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…
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…
The coding properties of cells with different types of receptive fields have been studied for decades. ON-type neurons fire in response to positive fluctuations of the time-dependent stimulus, whereas OFF cells are driven by negative…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation…
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive feedback loops,…
The implementation of a combination of continuous weak measurement and classical feedback provides a powerful tool for controlling the evolution of quantum systems. In this work, we investigate the potential of this approach from three…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…
Growth in confined spaces can drive cellular populations through a jamming transition from a fluid-like state to a solid-like state. Experiments have found that jammed budding yeast populations can build up extreme compressive pressures…
We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe the regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely…
The lac operon in Escherichia coli has been studied extensively and is one of the earliest gene systems found to undergo both positive and negative control. The lac operon is known to exhibit bistability, in the sense that the operon is…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…