Related papers: Boolean versus continuous dynamics on simple two-g…
A two-mode boson model, widely used for the physics of fast rotating nuclei and Bose-Einstein condensates, is studied in the context of entanglement control. We derive an analytical expression for the entanglement between the fields in this…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…
There are many different models--both continuous and discrete--used to describe gene mutation fixation. In particular, the Moran process, the Kimura equation and the replicator dynamics are all well known models, that might lead to…
Estimating the influence that individual nodes have on one another in a Boolean network is essential to predict and control the system's dynamical behavior, for example, detecting key therapeutic targets to control pathways in models of…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
We present initial results regarding the existence, stability and interaction of linear and nonlinear vibrational modes in a system of two coupled, one dimensional lattices with unequal numbers of masses. The effects on these nonlinear…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
We consider two minimal models of active fluid droplets that exhibit complex dynamics including steady motion, deformation, rotation and oscillating motion. First we consider a droplet with a concentration of active contractile matter…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Different Boolean networks may reveal similar dynamics although their definition differs, then preventing their distinction from the observations. This raises the question about the sufficiency of a particular Boolean network for properly…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…