Related papers: Bifurcation in cellular evolution
Recently, plenty research has been done on discovering the role of energy dissipation in biological networks, most of which focus on the relationship of dissipation and functionality. However, the development of networks science urged us to…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
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…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Percolation and synchronization are two phase transitions that have been extensively studied since already long ago. A classic result is that, in the vast majority of cases, these transitions are of the second-order type, i.e. continuous…
We introduce a model for dynamic networks, where the links or the strengths of the links change over time. We solve the model by mapping dynamic networks to the problem of directed percolation, where the direction corresponds to the…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Percolation in complex networks is viewed as both: a process that mimics network degradation and a tool that reveals peculiarities of the underlying network structure. During the course of percolation, networks undergo non-trivial…
The analysis of network dynamics is oftentimes restricted to networks with one-dimensional internal dynamics. Here, we show how symmetry explains the relation between behavior of systems with one-dimensional internal dynamics and with…
Partial differential equations are a convenient way to describe reaction- advection-diffusion processes of signalling models. If only one cell type is present, and tissue dynamics can be neglected, the equations can be solved directly.…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
We disclose the generality of the intrinsic mechanisms underlying multistability in reciprocally inhibitory 3-cell circuits composed of simplified, low-dimensional models of oscillatory neurons, as opposed to those of a detailed Hodgkin-…
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Feedback circuits in biochemical networks which underly cellular signaling pathways are important elements in creating complex behavior. A specific aspect thereof is how stability of equilibrium points depends on model parameters. For…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…