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We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase…
Understanding complex systems which exhibit desynchronization as an emergent property should have important implications, particularly in treating neurological disorders and designing efficient communication networks. Here were demonstrate…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
Various rod-shaped bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant,…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
We have modeled the metabolic process running in aerobic cells as open nonlinear dissipative systems. The map of metabolic paths and the general scheme of a dissipative system participating in the transformation of steroids are constructed.…
Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen limiting conditions, in filaments of the genus Anabaena, some cells…
How do phase separated cellular structures set their size? To elucidate this, we study the dynamics and steady states of a phase separating nucleator that is advected by the self-straining cytoskeletal network which it nucleates. We find…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…
Pancreatic $\beta-$cells regulate insulin secretion through complex oscillations, which are vital for glucose control and diabetes research. In this paper, an existing mathematical model of $\beta-$cell dynamics is analyzed using a…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…