Related papers: A core genetic module : the Mixed Feedback Loop

Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…

Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…

Glassy dynamics in active biological cells remain a subject of debate, as cellular activity rarely slows enough for true glassy features to emerge. In this study, we address this paradox of glassy dynamics in epithelial cells by integrating…

Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from…

Federated machine learning is a versatile and flexible tool to utilize distributed data from different sources, especially when communication technology develops rapidly and an unprecedented amount of data could be collected on mobile…

This note analyzes incoherent feedforward loops in signal processing and control. It studies the response properties of IFFL's to exponentially growing inputs, both for a standard version of the IFFL and for a variation in which the output…

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…

The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…

Multiple interlinked positive feedback loops shape the stimulus responses of various biochemical systems, such as the cell cycle or intracellular calcium release. Recent studies with simplified models have identified two advantages of…

We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…

Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…

G-protein-coupled receptors (GPCRs) are central to cellular information processing, yet the physical principles governing their switching behavior remain incompletely understood. We present a first principles theoretical framework, grounded…

We present a hybrid model of a biological filter, a genetic circuit which removes fast fluctuations in the cell's internal representation of the extra cellular environment. The model takes the classic feed-forward loop (FFL) motif and…

MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…

A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…

Multimodal Federated Learning (MFL) with mixed modalities enables unimodal and multimodal clients to collaboratively train models while ensuring clients' privacy. As a representative sample of local data, prototypes offer an approach with…

This paper presents an extensive framework focused on the control design, along with stability and performance analysis, of Grid-Following Inverters (GFL). It aims to ensure their effective operation under both stiff and weak grid…

Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…

Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…