Related papers: A core genetic module : the Mixed Feedback Loop
Learning from multimodal datasets can leverage complementary information and improve performance in prediction tasks. A commonly used strategy to account for feature correlations in high-dimensional datasets is the latent variable approach.…
Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various crosslinking and other associated proteins largely determine the (visco)elastic response of cells. In this letter we…
Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially…
The mammalian circadian system comprises a network of cell-autonomous oscillators, spanning from the central clock in the brain to peripheral clocks in other organs. These clocks are tightly coordinated to orchestrate rhythmic physiological…
Often in bacterial regulatory networks, small noncoding RNAs (sRNA) interact with several mRNA species. The competition among mRNAs for binding to the same pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the…
Small inhibitory neuronal circuits have long been identified as key neuronal motifs to generate and modulate the coexisting rhythms of various motor functions. Our paper highlights the role of a cellular switching mechanism to orchestrate…
A number of biological rhythms originate from networks comprised of multiple cellular oscillators. But analytical results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has…
In this work we address the question of how oscillations are arrested in the mouse somitogenesis clock when the determination front reaches presomitic cells. Based upon available experimental evidence we hypothesize that the mechanism…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
In a purely inverter-based microgrid, both grid-forming (GFM) and grid-following (GFL) inverters will have a crucial role to play in frequency/voltage regulation and maintaining power sharing through their grid support capabilities.…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions,…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
In recent years, imitation learning using neural networks has enabled robots to perform flexible tasks. However, since neural networks operate in a feedforward structure, they do not possess a mechanism to compensate for output errors. To…
The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora of cellular processes, including cell…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We present a simple low-cost electronic circuit that is able to show two different dynamical regimens with oscillations of voltages and with constant values of them. This device is designed as a negative feedback three-node network inspired…