Related papers: A core genetic module : the Mixed Feedback Loop
Recommender systems need to optimize various types of user feedback, e.g., clicks, likes, and shares. A typical recommender system handling multiple types of feedback has two components: a multi-task learning (MTL) module, predicting…
A qualitative model is presented, suggesting gravitational information is transduced into biological systems primarily by its effect on spatially organised membrane and cytoplasmic flows. Continuous low affinity interactions between…
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive feedback loops,…
We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of…
Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…
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…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
Given a multi-input, nonlinear, time-invariant, control-affine system and a controlled invariant, closed, embedded submanifold $\mathsf{N}$, the local transverse feedback linearization (TFL) problem seeks a coordinate and feedback…
Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…
Rhythmic and sequential subdivision of the elongating vertebrate embryonic body axis into morphological somites is controlled by an oscillating multicellular genetic network termed the segmentation clock. This clock operates in the…
A Federated Learning (FL) system typically consists of two core processing entities: the federation controller and the learners. The controller is responsible for managing the execution of FL workflows across learners and the learners for…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
A repressilator consists of a loop made up of three repressively interacting genes. We construct a hexagonal lattice with repressilators on each triangle, and use this as a model system for multiple interacting feedback loops. Using…
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…
The dynamic behaviors of microRNA and mRNA under external stress are studied with biological experiments and mathematics models. In this study, we developed a mathematic model to describe the biological phenomenon and for the first time…
Molecular communication (MC) enables cooperation of spatially dispersed molecular robots through the feedback control mediated by diffusing signal molecules. However, conventional analysis frameworks for the MC channels mostly consider the…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many…