Related papers: Positive feedback and noise activate the stringent…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…
The phenomenon of cell sorting/segregation, by which cells organise spatially into clusters of specific cell type or function, is essential for tissue morphogenesis. This self-organization process involves an interplay between mechanical,…
A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate…
We study complex systems arising, in particular, in population dynamics, developmental biology, and bacterial metabolic processes, in which each individual element obeys a relatively simple hysteresis law (a non-ideal relay). Assuming that…
A reaction network consists of a finite number of species, which interact through predefined reaction channels. Traditionally such networks were modeled deterministically, but it is now well-established that when reactant copy numbers are…
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems…
Normal life activities between cells rely crucially on the homeostasis of the cellular microenvironment, but aging and cancer will upset this balance. In this paper, we introduce the microenvironmental feedback mechanism to the growth…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation…
The reaction dynamics for the H + HeH$^+$ $\rightarrow$ He + H$_2^+$ reaction in its electronic ground state is investigated using two different representations of the potential energy surface (PES). The first uses a combined kernel and…
Proliferating cells properly divide into their daughter cells through a process that is mediated by kinetochores, protein-complexes that assemble at the centromere of each sister chromatid. Each kinetochore has to establish a tight bipolar…
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as in…
In physics of living systems, a search for relationships of a few macroscopic variables that emerge from many microscopic elements is a central issue. We evolved gene regulatory networks so that the expression of target genes (partial…
In Escherichia coli the response to DNA damage shows strong cell-to-cell-heterogenity. This results in a random delay in cell division and asymmetrical binary fission of single cells, which can compromise the size homeostasis of the…
It has been known for many years that small fractions of persister cells resist killing in many bacterial colony-antimicrobial confrontations. These persisters are not believed to be mutants. Rather it has been hypothesized that they are…
Magombedze and Mulder in 2013 studied the gene regulatory system of Mycobacterium Tuberculosis (Mtb) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each subsystem, in the…
Cochlear outer hair cells (OHCs) have two mechanosensitive elements: the hair bundle with mechanotrasducer channels and the piezoelectric lateral wall of the cell body. The present report examines how these elements interact with each other…
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…