Related papers: On three genetic repressilator topologies
We propose a simple model of network co-evolution in a game-dynamical system of interacting agents that play repeated games with their neighbors, and adapt their behaviors and network links based on the outcome of those games. The…
We establish a 3-manifold invariant for each finite-dimensional, involutory Hopf algebra. If the Hopf algebra is the group algebra of a group $G$, the invariant counts homomorphisms from the fundamental group of the manifold to $G$. The…
State-of-the-art methods for data-driven modelling of non-linear dynamical systems typically involve interactions with an expert user. In order to partially automate the process of modelling physical systems from data, many EA-based…
In this paper, dynamical systems theory and bifurcation theory are applied to investi- gate the rich dynamical behaviours observed in three simple disease models. The 2- and 3-dimensional models we investigate have arisen in previous…
Almost all current approaches for engineering modular logic components in synthetic biology use first-order regulators, including most CRISPR/CAS, TAL, zinc finger, and RNA interference systems. Many practitioners understand intuitively…
In this paper we describe the right-sided combinatorial Hopf structure of three Hopf algebras appearing in the context of renormalization in quantum field theory: the non-commutative version of the Fa\`a di Bruno Hopf algebra, the…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
A system of replicators with Hebbian random couplings is studied using dynamical methods. The self-reproducing species are here characterized by a set of binary traits and interact based on complementarity. In the case of an extensive…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Genes are connected in regulatory networks, often modelled by ordinary differential equations. Changes in expression of a gene propagate to other genes along paths in the network. At a stable state, the system's Jacobian matrix confers…
In science, we are interested not only in forecasting but also in understanding how predictions are made, specifically what the interpretable underlying model looks like. Data-driven machine learning technology can significantly streamline…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
This paper proposes a simple model to capture the complexity of multi-layer systems where their constituent layers affect, are affected by, each other. The physical layer is a circuit composed by a power source and resistors in parallel.…
Tensor decomposition is an important technique for capturing the high-order interactions among multiway data. Multi-linear tensor composition methods, such as the Tucker decomposition and the CANDECOMP/PARAFAC (CP), assume that the complex…
Transcriptional networks represent one of the most extensively studied types of systems in synthetic biology. Although the completeness of transcriptional networks for digital logic is well-established, *analog* computation plays a crucial…
Stochastic point processes with refractoriness appear frequently in the quantitative analysis of physical and biological systems, such as the generation of action potentials by nerve cells, the release and reuptake of vesicles at a synapse,…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcripion factors should explain the different…